Journal articles on the topic 'SWISS DOCK'

Objective: The 2, 4-thiazolidinedione containing compounds could lead to most promising scaffolds with higher efficiency toward the targets recognized for its antidiabetic activity when combined with azaglycine moiety. The objective of the present work was to merge functionalized aza glycines with 2, 4-thiazolidinediones, perform in silico evaluation by molecular properties prediction and undertake the molecular docking studies with targets relevant to diabetes, bacterial and viral infections using Swiss Dock programme for unraveling the target identification which can be used for further designing.Methods: (i) In silico studies were performed using Molinspiration online tool, Swiss ADME website and Swiss Target Prediction websites to compute the physicochemical descriptors, oral bioavailability and brain penetration. (ii) Molecular docking studies were performed using Swiss Dock web service for enumeration of binding affinities and assess their biological potentiality.Results: The results predicted good drug likeness, solubility, permeability and oral bioavailability for the compounds. All the compounds showed good docking scores as compared to the reference drugs. The N-oleoyl functionalized aza glycine derivative demonstrated superior binding properties towards all the studied target reference proteins, suggesting its significance in pharmacological actions.Conclusion: The binding interactions observed in the molecular docking studies suggest good binding affinity of the oleoyl functionalized aza glycine derivative, indicating that this derivative would be a promising lead for further investigations of anti-viral, anti-inflammatory and anti-diabetic activities.

Jab1 (c-Jun activation domain-binding protein-1) overexpression has been extensively linked to cancer development (or metastasis) in various malignancies by positively regulating cancer cell proliferation or inactivating several tumor suppressors. Recent research has focused on utilizing plant products to target crucial elements of dysregulated signaling pathways to elucidate a potent cancer therapeutic approach. Terpenoids have shown significant anti-inflammatory and anti-cancerous properties in a broader range of carcinomas by inducing apoptosis. Through an extensive literature search, we have selected only those terpenoids (from the NPACT database) that have not been explored against Jab1 (CSN5, COP9 signalosome subunit 5) in breast cancer for our research study. We have used two docking servers, PATCH DOCK, and CB DOCK, to find the binding interaction between selected terpenoids and Jab1. Further, we have also used SWISS ADME to investigate the pharmacokinetics of selected ligands. Amongst all selected ligands, lutein (belongs to the xanthophylls class) has displayed maximum binding energy in both CB Dock and Patch Dock analysis. Hence, our preliminary in silico results have shown lutein as the potent lead candidate for developing a better drug against breast cancer. However, more in silico and in vitro studies are still needed to validate the inhibitory potential of lutein terpenoid against Jab1 in breast cancer.

Epigenetic changes and glycation play a significant role in the progression of life-threatening diseases like diabetes, cancer, cardiovascular diseases (CVDs), neurodegenarative diseases (ND) and others. Exploring natural sources for overall therapeutic effect can be a beneficial approach for treating these life threatening diseases. The phytocemicals apigenin, aegeline, marmelosin, kaempferol, pyrrolemarumine 4”-O-alpha-L-rhamnopyranoside and garcinol from Durva, Bael, Custard apple, Moringa and Kokum were evaluated for their therapeutic value using in silico techniques. These phytochemicals and target structures (molecules from diseases pathologies from KEGG database), were obtained from PubChem and PDB, respectively. The docking studies, pharmaceutical parameters and toxicity studies were done using Swiss Dock, Swiss ADME for and Pro Tox II. The above phytochemicals have shown optimal lipophilicity, insaturation, flexibility and solubility. Molecular weight was less than 500 Da and LD50 values for each of these was above 400 mg kg-1. Amongst all phytochemicals, garcinol was found to be ideal for dermal drugs.

Hydrogen peroxide, 1,1-Diphenyl-2-picryl-hydrazyl (DPPH) and Phosphomolybdenum in-vitro assay was employed to determine the antioxidant potency of glycopeptides RN Mannose, RK starch, RNRN Mannose and RHRCR Starch using ascorbic acid as the standard drug. The percentage scavenging activity of the glycopeptides were determined at different concentrations and the IC50 value of the test compounds were subsequently compared with that of ascorbic acid. RN Mannose was found to be most potent antioxidant compound. Also, Swiss dock study was performed with three glycopeptides, viz., RHRCR Mannose, RN Mannose and RNRN Mannose.Among these, RHRCR Mannose was found to have the best affinity for the receptor with stearic energy -0.2306kcal/mol.

Background & Objective: Comparative molecular field analysis (CoMFA) of 27 analogues of 2-((pyridin-3-yloxy)methyl)piperazine derivatives was carried out using software Tripos SYBYL X. Optimal r2 (0.854) and q2 (0.541) values were obtained for the developed 3D-QSAR model. The contour plots obtained from CoMFA analysis have shown 13.84% steric contribution and 66.14% electrostatic contribution towards an anti-inflammatory activity. Methods: The homology model of the receptor protein, α7 nicotinic acetylcholine, was generated in SWISS MODELLER using auto template mode and was analysed for the quality using Procheck, QMEAN Z-score, Anolea and GROMOS plots. The QMEAN score for the model was observed to be - 3.862. The generated model of alpha 7 nicotinic acetylcholine receptor was used for docking study of 27 piperazine analogues using Auto-Dock 4.2.5.1. Results: The dock score obtained from docking analysis was then correlated with experimental pIC50 values for in-silico validation of the developed CoMFA model and a good correlation was obtained with correlation coefficient (r2) value of -0.7378. Conclusion: The present investigation suggests an optimal 3D-QSAR with CoMFA model for further evaluating new chemical entities based on piperazine skeleton.

Cis-Z-alpha-bisabolene epoxide (bisabolene) compound is extracted from Cassia fistula plant bark, which is a medicinal tree that contains many useful drug substances, the compound can act as a drug predictably similar to vitamin E, with the same function as an antioxidant which can act on pregnane X receptor on the body cells. The gas chromatography-mass spectrometry (GC-MS) analysis was used to identify the constituents of the n-hexane extract. Drug Bank was used to find similar compounds. The ID of the pregnane x receptor (PXR) was retrieved from the PDB database. Then the bisabolene ligand was used for docking with the receptor using Swiss Dock. Finally, the Swiss ADME was used to study and predict the pharmacological parameters. It was found that bisabolene can act as an antioxidant and alternative to vitamin E in the pregnane x receptor and with good pharmacological predicted results. When bisabolene is used as an effective ligand with pregnane X receptor alternative to vitamin E, care must be taken because the compound can penetrate the blood-brain barrier (BBB) with a specific amount.

Docking is one of the most widely utilized technique used method in structure -based drug design because of its capability to predict the binding conformation of ligands to appropriate target. Ability of binding/ affinity towards the target i.e., bioactive peptides or specific receptor provides strong evidence of binding conformation pattern and affinity for further investigation. Aim- The present study was conducted for evaluation of current API’s potential used in COVID-19. Methods: In-silico molecular docking was performed using softwares such as SWISS ADME, MOLSOFT, MOLINSPIRATION, PYMOL, AUTO-DOCK VINA AND BIOVIA DS VISUALIZER. Results: The current research comprehend the drug likeliness character of selected API’s and their binding affinity with various targets selected by SWISS TARGET PREDICTION. Conclusion: The present investigation suggests that all the targets follow Lipinski rule of five except Remdesivir and Anakinra besides which it possesses enhanced binding affinity toward targets, the binding energy of the protein ligand interaction additionally confirms that the ligand fits into the dynamite pockets which proves to be evident for further in- vivo and in-vitro evaluations.

Diabetes is the becoming one of the most common problem all over the world. About 1 in 10 persons are suffering from diabetes and most from type 2 diabetes. It occurs due to problem in pancreas which further results defect in the insulin secretion, as insulin maintains blood glucose level. The effect of Alpha-Amyrin Acetate, Myrcene and Vasicine compounds against Islet Amyloid polypeptide (IAPP) protein was seen through molecular docking studies. IAPP acts as complementary to insulin in regulating the sugar level for the treatment of diabetes disease by virtual screening. Different tools and software used in this research were Uniprot, Pubchem, Swiss ADMS, PyRx, Auto dock Vina/MGL tool and PyMOL.

Cancer continues to be a global health burden, necessitating the exploration of innovative anti-cancer therapeutics. This study leverages computational biology tools such as molecular docking, ligand-based virtual screening, and ADMET to evaluate quercetin flavonoids as potential PI3K inhibitors for cancer treatment. Using Swiss Similarity and CB-Dock tools, 51 compounds were identified that showed promising interactions with PI3K. DB01645 exhibited the highest binding affinity among these, with a Vina score of -8.6. ADMET analysis revealed that this compound has favorable physicochemical properties, moderate lipophilicity, and good water solubility. The study adds to the growing evidence that Quercetin flavonoids have significant potential as next-generation anti-cancer agents targeting the PI3K pathway.

Acute kidney injury (AKI) is a syndrome characterised by the rapid loss of the kidney’s excretory function and is typically diagnosed by the accumulation of end products of nitrogen metabolism (urea and creatinine) or decreased urine output, or both. It is the clinical manifestation of several disorders that affect the kidney acutely. No specific therapies have yet emerged that can attenuate AKI or expedite recovery; thus, the only treatment is supportive therapies and intensive care. The present study was aimed to provide an insight into the importance of a metalloproteinase involved in the pathological conditions of AKI and potentially is a unique target for therapeutic intervention during the disease; Meprin. The data obtained using literature search from PubMed and interaction networks analysis software STRING strongly support the concept that meprin acts as a major matrix degrading enzyme in the kidney, and thus creating an environment that leads to impairment in cellular function rather than cellular stability in response to AKI. The present study discerns the structure of meprin alpha subunit usingin silicotools SWISS-MODE, Phyre2 web server and identify the active site and critical amino acid residues in the active site using AADS (IIT Delhi), 3DLigandSite and DoGSiteScorer. Further it is documented that actinonin, a naturally occurring antibacterial agent as a pharmacologically active intervention for the metalloproteinase’s α subunit by blocking its active sites from the environment which was validated using molecular docking algorithms of SWISS-DOCK and FlexX.

Acute kidney injury (AKI) is a syndrome characterised by the rapid loss of the kidney’s excretory function and is typically diagnosed by the accumulation of end products of nitrogen metabolism (urea and creatinine) or decreased urine output, or both. It is the clinical manifestation of several disorders that affect the kidney acutely. No specific therapies have yet emerged that can attenuate AKI or expedite recovery; thus, the only treatment is supportive therapies and intensive care. The present study was aimed to provide an insight into the importance of a metalloproteinase involved in the pathological conditions of AKI and potentially is a unique target for therapeutic intervention during the disease; Meprin. The data obtained using literature search from PubMed and interaction networks analysis software STRING strongly support the concept that meprin acts as a major matrix degrading enzyme in the kidney, and thus creating an environment that leads to impairment in cellular function rather than cellular stability in response to AKI. The present study discerns the structure of meprin alpha subunit using in silico tools SWISS-MODE, Phyre2 web server and identify the active site and critical amino acid residues in the active site using AADS (IIT Delhi), 3DLigandSite and DoGSiteScorer. Further it is documented that actinonin, a naturally occurring antibacterial agent as a pharmacologically active intervention for the metalloproteinase’s α subunit by blocking its active sites from the environment which was validated using molecular docking algorithms of SWISS-DOCK and FlexX.

Epilepsy is a severe neurological illness that affects millions of people the globally and is characterized by unpredicted and intermittent seizures.This research aimed to investigate the antiepileptic and antioxidant properties of papaverine derivatives using in-silico, in-vitro, and in-vivo methods.Epileptic seizure was induced in Swiss albino mice of either gender by administering PTZ (pentylenetetrazol). The antioxidant potential of test compounds was computed using previously published DPPH assay methods with minor modifications, while In-silico experiments were conducted using Auto-dock Vina (1.5.6) software and post dock analysis was completed using Discovery Studio Visualizer. The results showed that both compounds have strong antioxidant potential, with a noticeable change in color when compared to ascorbic acid as a control, and very low mortality when anti-epileptic potential was observed. The development of seizures was greatly delayed at first, but after 30 minutes of PTZ, they were completely gone. Both synthesized derivatives also comply the andquot;Lipinskiand#39;s rule of 5andquot;, which states that after structural alterations, extensive investigations, and trials, the chemical products would be evaluated for epilepsy management in the future In-silico investigations demonstrated that ligands with sufficient hydrogen bonds, pi-pi bonds, and Vander-Waals forces have a suitable propensity to engage with the binding pocket of selected protein targets. The current investigation of papaverine derivatives and their binding affinities against gamma aminobutyric acid (GABA) protein may have a vital function in epilepsy aetiology, according to the results of the studies. H1 and H2 were further verified in vivo for their anticonvulsant and antioxidant therapeutic potential. This could lead to more research into neurological problems.

Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as—Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (−21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis.

A class of innovative benzimidazole-1,3,4-Oxadiazole derivatives is a significant heterocyclic molecule for therapeutic development. In heterocyclic chemistry, the novel 1,3,4-Oxadiazole nucleus has a wide range of uses, including antibacterial, treatment. Molecular docking is frequently employed in contemporary drug design to comprehend drug-receptor interaction. Swiss dock, PyRx, and discovery studio visualizer (DSV) tools were used to predict in-silico ADME properties. In the current investigation, substituted benzimidazole-1,3,4-Oxadiazole derivatives were taken for docking studies against 6AYB an Naegleria fowleri CYP51-ketoconazole complex. The main objective of the study is to perform docking of the selected benzimidazole-1,3,4-oxadiazole derivatives on the protein and compare the docking score with standard ketoconazole. The molecular docking study was conducted using PyRx and the discovery studio visualizer (DSV) program, Naegleria fowleri CYP51-ketoconazole complex (6AYB) was obtained from the protein data bank (PDB) site. It was found that the docking score of all sixteen 1,3,4-Oxadiazole compounds ranged from -8.1 to -8.9 Kcal/mol. The novel benzimidazole with 1,3,4-Oxadiazole derivatives has been found to possess antibacterial properties, many substituted 1,3,4-Oxadiazole derivatives have been reported for the activity

The reuse of medicines is a practical and rapid response when early solutions are required for sudden-onset health problems such as SARS-CoV-2, the causative agent of the COVID-19 pandemic during the years 2020 - 2021. In this study we set out to determine by in silico assays with bioinformatics tools using the Swiss Dock online server and in vitro by enzyme-linked immunosorbent assays whether azole derivatives (such as fluconazole, secnidazole, clotrimazole) and ivermectin, can inhibit the interaction between human ACE2 and the RBD domain of SARS-CoV-2 S protein. The result of the docking of azoles and ivermectin showed a significant inhibitory action against RBD of SARS-CoV- 2 S protein and the binding energy. Since the results obtained in the in vitro assays showed a significant inhibition absorbance (OD value < 0.611) of the binding of hACE2 and the SARS-CoV-2 RBD, our results suggest that these azole derivatives can be considered as potential therapeutic candidates. This may suggest that the drugs studied can be used individually or in therapeutic combinations in trials to evaluate effectiveness in patients suffering from COVID-19 both early in the infection and in late stages. Secnidazole and fluconazole are commercially available and affordable drugs.

Background. Shu Gan Jie Yu (SGJY) capsule has a good effect on relieving depressive symptoms in China. However, the mechanism of action is still unclear. Therefore, systemic pharmacology and molecular docking approaches were used to clarify its corresponding antidepressant mechanisms. Methods. Traditional Chinese Medicine Database and Analysis Platform (TCMSP), the Encyclopedia of Traditional Chinese Medicine (ETCM), and Swiss Target Prediction servers were used to screen and predict the bioactive components of the SGJY capsule and their antidepressive targets. Mild to moderate depression (MMD) related genes were obtained from GeneCards and DisGeNET databases. A network of bioactive components-therapeutic targets of the SGJY capsule was established by STRING 11.5 and Cytoscape 3.9.0 software. Gene function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by utilizing Database for Annotation, Visualization, and Integrated Discovery (DAVID) platform. Active components were taken to dock with the hypothetical proteins by iGEMDOCK and SwissDock, and the docking details were visually displayed by UCSF Chimera software. Then, the related research literature of the SGJY capsule was reviewed, summarized, sorted, and analyzed, including experimental evidence and clinical experience. Results. Seven active components and 45 intersection targets were included in the study. PPI network had genuinely uncovered the potential therapeutic targets, such as AKT1, HSP90AA1, ESR1, EGFR, and PTGS2. KEGG pathway analysis showed that the mechanism of the SGJY capsule on MMD was mainly involved in the PI3K-Akt signaling pathway. Conclusions. In this study, we have successfully predicted the biochemically active constituents, potential therapeutic targets, and comprehensively predicted the related drug-gene interaction of the SGJY capsule for treating MMD and provided a basis for subsequent experiments.

Adathodai kudineer (AK) a Classical Siddha formulation is used to treat various fevers which cause moderate to severe acute respiratory symptoms as is indicated in the text. GC-MS analysis was carried out to identify the presence of potent lead molecules in AK against novel corona virus. The aqueous extract has shown the following bioactive compounds such as Napthalene, Benzene Propanol, Benzene Acetic Acid, Furazan-3-amine, Pyrazol-4-Carboxylic acid, 2(3H) Furanone. The ethanolic extract of AK exhibited the molecular compounds such as Eucalyptol, Toluene, 2-Carene, Alpha-Copaene, 1,6-Cyclodecadiene, Aromadendrene, Gamma-murolene, Beta-copaene, Cubebol, Selina-3,7 (11) - Diene, 2-Butanone. Molecular docking is a powerful approach in current trends to identify the possibility of pharmacological effects of medicinal compounds which could be exerted over their Corresponding Protein targets which are relevant for causing disease. Using Auto dock Vina Software, the biomolecules of AK were analyzed through molecular docking against SARS-CoV-2 Spike Protein (PDB ID 6LU7) and SARS-CoV-2 Spike Protein – ACE 2 receptor complex (6LZG). ADME properties were also recorded for the aqueous and ethanolic extracts of AK compounds using online tool SWISS ADME. The binding energy observed were of the order: -10.9 Kcal/mol, -8.0 Kcal/mol, -7.8 Kcal/mol for the compounds Alpha-Copaene, Gamma-Murolene, Selina-3,7 (11)–Diene respectively towards the protein target 6LZG and -8.2 Kcal/mol, -6.6 Kcal/Mol, -6.5 Kcal/Mol, for the compounds Alpha-Copaene, Cubebol, Aromadendrene respectively towards for the target 6LU7. These findings confirm that the Siddha formulation Adathodai Kudineer has some potent activity against SARS-CoV-2 Virus COVID19 disease.

Abstract Malaria remains one of the most infectious life-threatening diseases in the world. The lingering effect of drug resistance by malarial parasites, especially Plasmodium falciparum, has made it essential for the continuous search for novel antimalarial drugs that can act on new protein targets and through new modes of action. Amidoxime functional groups have, in recent years, shown to be good incorporations in heterocyclic backbones due to their vast biological activities. Hence, the antimalarial activities of some amidoxime-containing heterocyclic compounds have been predicted using molecular docking studies to determine the binding affinities and the inhibition constants of the compounds. The amidoxime-containing compounds were downloaded from the ZINC database and docked, using Auto Dock vina, against the active sites of homology modelled Plasmodium falciparumadenylosuccinate lyase (PfADSL) as obtained from the SWISS-MoDeL. The grid box was constructed using 80, 80, and 80, pointing in x, y, and z directions, respectively, with a grid point spacing of 0.375 A. The post-docking analysis, which entails determining the hydrogen bond formed and the bond length between the compounds and the protein target, was carried out using AutoDockTools, LigPlot and PyMOLmolecular viewer. The docking studies showed that the compounds possess binding affinities ranging from -8.6 to- 5.7 kcal/mol, with ZINC2268942 having the lowest binding affinity. The presence of the amidoxime-functional group on the best hit contributed significantly to the hydrogen bonds formed between the compound and the binding sites of PfADSL,which were observed atThr 124D, Ser 125D, Thr 172C, His 173C, Gln 250D, and Ser 299A. The results obtained from the molecular docking studies will be helpful in the development of a potential antimalarial drug that can target PfADSL after careful experimental validation of the target, then in vitro and in vivo screening.

Pinus roxburghii, also known by the name “Himalayan chir pine,” belongs to the Pinaceae family. Rhipicephalus (Boophilus) microplus tick is one of the most significant bovine ectoparasites, making it a major vector of economically important tick-borne diseases. The researchers conducted adult immersion tests (AIT) and larval packet tests (LPT) to investigate the acaricidal effect of P. roxburghii plant extract on R. (B.) microplus and its potential modulatory function when used with cypermethrin. Eggs were also assessed for their weight, egg-laying index (IE), hatchability rate, and control rate. After exposure to essential extract concentrations ranging from 2.5 to 40 mg/mL for 48 h, adult female ticks’ oviposition inhibition and unfed R. (B.) microplus larvae’s mortality rates were analyzed. Engorged females exposed to P. roxburghii at 40 mg/mL had reduced biological activity (oviposition, IE) compared to positive and negative controls. A concentration of 40 mg/mL of P. roxburghii caused 90% mortality in R. (B.) microplus larvae, whereas cypermethrin (the positive control) caused 98.3% mortality in LPT. In AIT, cypermethrin inhibited 81% of oviposition, compared to the 40 mg/mL concentration of P. roxburghii, which inhibited 40% of the ticks’ oviposition. Moreover, this study assessed the binding capacity of selected phytocompounds with the targeted protein. Three servers (SWISS-MODEL, RoseTTAFold, and TrRosetta) recreated the target protein RmGABACl’s 3D structure. The modeled 3D structure was validated using the online servers PROCHECK, ERRAT, and Prosa. Molecular docking using Auto Dock VINA predicted the binding mechanisms of 20 drug-like compounds against the target protein. Catechin and myricetin showed significant interactions with active site residues of the target protein, with docking scores of −7.7 kcal/mol and −7.6 kcal/mol, respectively. In conclusion, this study demonstrated the acaricidal activity of P. roxburghii extract, suggesting its potential as an alternative natural acaricide for controlling R. (B.) microplus.

Background: Balaguluchyadi kashayam, a polyherbal Ayurvedic decoction prepared from Sidacordifolia L., Tinospora cordifolia (Willd.) Miers, and Cedrusdeodara (Roxb. ex D.Don) G.Don, is used in Ayurveda for the treatment of chronic inflammatory conditions. Although this herbal decoction has been used for a long period for treating chronic inflammatory conditions, the mechanism of action of the decoction in reducing inflammatory conditions associated with chronic inflammation has not been clearly understood. Mass spectroscopy-based identification of bioactive molecules present in the decoction and its interaction with enzymes/proteins involved in the pathogenesis of chronic inflammation has been carried and reported in this study. Introduction: Polyherbalism is one of the major principles of Ayurveda. Various phytoconstituents with different activities in the polyherbal decoction act on multi targets of a wide range of diseases. Balaguluchyadi kashayam is a polyherbal decoction prescribed for chronic inflammatory etiologies and the present study aims to evaluate the binding potential of the compounds, identified from Balaguluchyadi kashayam to enzymes/proteins involved in the development and progression of chronic inflammation. Methods: The bioactive compounds present in the Balaguluchyadi Kashayam fractions were extracted by preparative HPLC and identified using UPLC MS Q-TOF. The physicochemical characteristics and ADMET properties of the compounds were calculated using Mol soft, Swiss ADME and OSIRIS data warrior software. Then the binding interactions between the molecules and the proinflammatory mediators such as 5 Lipoxygenase, Cyclooxygenase 2, Tumor necrosis factoralpha convertase enzyme (TACE) and Caspase 1 were determined using molecular docking software Auto Dock 4.0 (http://autodock.scripps.edu/downloads). Results: The identified bioactive molecules in the decoction showed a good binding affinity towards the enzymes/proteins involved in the development and progression of chronic inflammation compared to the binding affinity of known inhibitors/drugs to the respective enzymes/proteins. Conclusion: The bioactive molecules identified in Balaguluchyadi Kashayam could be developed as potential therapeutic molecules against enzymes/proteins involved in the development and progression of chronic inflammation.

Objective: Hypoxia plays a significant role in governing many vital signalling molecules in the central nervous system (CNS). Hypoxic exposure has also been depicted as a stimulus for oxidative stress, increase in lipid peroxidation, DNA damage, blood-brain dysfunction, impaired calcium (Ca2+) homoeostasis and agglomeration of oxidized biomolecules in neurons, which act as a novel signature in diverse neurodegenerative and oncogenic processes. On the contrary, the presence of abnormally impaired expression of HIF-1α under hypoxic insult could serve as an indication of the existence of tumors and neuronal dysfunction as well. For instance, under hypoxic stress, amyloid-β protein precursor (AβPP) cleavage is triggered due to the higher expression of HIF-1α and thus leads to synaptic loss. The objective of this research is to perform comparative studies of biomolecules in regulating HIF-1α activity based on in silico approaches that could establish a potential therapeutic window for the treatment of different abnormalities associated with impaired HIF-1α.Methods: We employed various in silico methods such as drug-likeness parameters namely Lipinski filter analysis, Muscle tool, SWISS-MODEL, active site prediction, Auto Dock 4.2.1 and LigPlot1.4.5for molecular docking studies.Results: 3D structure of HIF-1α was generated and Ramachandran plot obtained for quality assessment. RAMPAGE displayed 99.5% of residues in the most favoured regions. 0% residues in additionally allowed and 0.5% disallowed regions of the HIF-1α protein. Further, initial screenings of the molecules were done based on Lipinski’s rule of five. Cast P server used to predict the ligand binding site suggests that this protein can be utilised as a potential drug target. Finally, we have found Naringenin to be most effective amongst three biomolecules in modulating HIF-1α based on minimum inhibition constant, Ki and highest negative free energy of binding with the maximum interacting surface area during docking studies.Conclusion: The present study outlines the novel potential of Biomolecules in regulating HIF-1α activity for the treatment of different abnormalities associated with impaired HIF-1α.

Background: Compound Xiao-ai-fei honey ointment (CXHO) is an anticancer preparation with a long history in Uyghur folk medicine in China and has been used for the treatment of gastric cancer (GC) in Xinjiang, China. Nevertheless, the mechanism of its anticancer effect remains to be investigated. Methods: Bioactive ingredients of CXHO were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. Target genes of ingredients were acquired via the PubChem and Swiss target prediction database. Gene expression profiling of GC was obtained from GSE54129 in the GEO database and analyzed using the limma package in R. The hub genes associated with CXHO in GC were validated using the TIMER2.0 database, GEPIA2 database and Auto Dock tools. The effect of CXHO on migration of GC cells was detected by Transwell chamber assay and Wound healing assay. The effect of CXHO on expression levels of MMP2/MMP9 and NF-κb, PI3K/AKT signaling pathway was detected by Western blot assay. Results: Forty-five bioactive ingredients and their 819 related genes were found. A total of 462 differentially expressed genes were identified between GC patients and healthy controls. Seventeen common target genes were identified as hub genes CXHO against GC. Among them, MMP2 and MMP9 were significantly associated with tumor immune infiltrates and had good binding affinity with effective ingredients. Moreover, we validated the mRNA and protein expression levels and prognostic value of MMP2 and MMP9 by different databases. In addition, Kyoto encyclopedia of genes and genomes and gene ontology analyses showed that the 17 common target genes were mainly involved in steroid hormone biosynthesis and cancer-related pathways. Experimental results showed that CXHO inhibited migration of GC cells and down regulated the expression levels of MMP2/MMP9, NF-κb. In addition, CXHO can inhibited PI3K/AKT signaling pathway. Conclusion: We identified and experimental validated 2 pivotal target genes of CXHO against GC and preliminarily analyzed the potential mechanisms by which CXHO inhibits the development of GC. All these findings support CXHO as a promising drug for the treatment of GC.

Aim. The incidence of ulcerative colitis (UC) is increasing steadily in developed countries, it is plaguing nearly 1 million people in the United States and European countries, while developing countries have had a rapidly increased incidence over the past decades. Curcuma is widely used in treating malaria, UC, Crohn’s disease, and colon cancer, which lead to diarrhea and bloody stool. However, the systemic mechanism of curcuma in treating UC is still unclear. Our work was supposed to expound how does curcuma alleviate UC in a comprehensive and systematic way by network pharmacology, molecular docking, and experiment verification. Methods. Traditional Chinese Medicine System Pharmacology Database (TCMSP), Shanghai Chemistry & Chemical Industry Data Platform (SGST), and papers published in Chinese Network Knowledge Infrastructure (CNKI) and PubMed were used to collect the chemical constituents of curcuma based on ADME (absorption, distribution, metabolism, and excretion). And effective targets were predicted by Swiss Target Prediction to establish the curcuma-related database. The disease targets of UC were screened by GeneCards and DrugBank databases, and Wayne (Venn) analysis was carried out with curcuma targets to determine the intersection targets. AutoDock software and TCMNPAS system were used to dock the core chemical components of curcuma with key UC targets. Protein interaction (PPI) network was constructed based on the STRING database and Cytoscape software. Gene function GO analysis and KEGG pathway enrichment analysis were carried out by using Metascape database. Finally, HE staining was performed to identify the inflammatory infiltration and expression difference in TNF-α and STAT3 before and after the treatment of curcuma which was verified by immunoblotting. Results. Twelve active components containing 148 target genes were selected from curcuma. Potential therapeutic targets of curcuma in the treatment of UC were acquired from 54 overlapped targets from UC and curcuma. Molecular docking was used to filter the exact 24 core proteins interacting with compounds whose docking energy is lower than −5.5 and stronger than that of 5-aminosalicylic acid (5-ASA). GO and KEGG analyses showed that these targets were highly correlated with EGFR tyrosine kinase inhibitor resistance, PI3K-Akt signaling pathway, JAK-STAT signaling pathway, MAPK signaling pathway, and inflammatory bowel disease (IBD). Experiments verified curcuma relieved pathological manifestation and decreased the expression of TNF-α and STAT3. Conclusion. Curcuma relieved the colon inflammation of ulcerative colitis via inactivating TNF pathway, inflammatory bowel disease pathway, and epithelial cell signaling in Helicobacter pylori infection pathway, probably by binding to STAT3 and TNF-α.

Eight novel Schiff bases derived from benzil dihydrazone (BDH) or benzil monohydrazone (BMH) and four fused-ring carbonyl compounds (3-formylindole, FI; 3-acetylindole, AI; 3-formyl-1-methylindole, MFI; 1-formylnaphthalene, FN) were synthesized and characterized by elemental analysis, ESI–QTOF–MS, 1H and 13C NMR spectroscopy, as well as single-crystal X-ray diffraction. They are (1Z,2Z)-1,2-bis{(E)-[(1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethane (BDHFI), C32H24N6, (1Z,2Z)-1,2-bis{(E)-[1-(1H-indol-3-yl)ethylidene]hydrazinylidene}-1,2-diphenylethane (BDHAI), C34H28N6, (1Z,2Z)-1,2-bis{(E)-[(1-methyl-1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethane (BMHMFI) acetonitrile hemisolvate, C34H28N6·0.5CH3CN, (1Z,2Z)-1,2-bis{(E)-[(naphthalen-1-yl)methylidene]hydrazinylidene}-1,2-diphenylethane (BDHFN), C36H26N4, (Z)-2-{(E)-[(1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethanone (BMHFI), C23H17N3O, (Z)-2-{(E)-[1-(1H-indol-3-yl)ethylidene]hydrazinylidene}-1,2-diphenylethanone (BMHAI), C24H19N3O, (Z)-2-{(E)-[(1-methyl-1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethanone (BMHMFI), C24H19N3O, and (Z)-2-{(E)-[(naphthalen-1-yl)methylidene]hydrazinylidene}-1,2-diphenylethanone (BMHFN) C25H18N2O. Moreover, the in vitro cytotoxicity of the eight title compounds was evaluated against two tumour cell lines (A549 human lung cancer and 4T1 mouse breast cancer) and two normal cell lines (MRC-5 normal lung cells and NIH 3T3 fibroblasts) by MTT assay. The results indicate that four (BDHMFI, BDHFN, BMHMFI and BMHFN) are inactive and the other four (BDHFI, BDHAI, BMHFI and BMHAI) show severe toxicities against human A549 and mouse 4T1 cells, similar to the standard cisplatin. All the compounds exhibited weaker cytotoxicity against normal cells than cancer cells. The Swiss Target Prediction web server was applied for the prediction of protein targets. After analyzing the differences in frequency hits between these active and inactive Schiff bases, 18 probable targets were selected for reverse docking with the Surflex-dock function in SYBYL-X 2.0 software. Three target proteins, i.e. human ether-á-go-go-related (hERG) potassium channel, the inhibitor of apoptosis protein 3 and serine/threonine-protein kinase PIM1, were chosen as the targets. Finally, the ligand-based structure–activity relationships were analyzed based on the putative protein target (hERG) docking results, which will be used to design and synthesize novel hERG ion channel inhibitors.

Die EU plant 100 Prozent Klimaneutralität bis 2050. Wie kann dies mit Blick auf Verpackung und Konsument:innen umgesetzt werden? Aktuell gibt es viele freiwillige Umweltlabels und dazu viel Information, doch das Durcheinander ist gross. PACKaktuell sprach mit Patrik Geisselhardt von Swiss Recycling über zielführende Kommunikation.

In this paper, we present the evolution of Swiss Media and Communication Studies over the last decade by summarizing the main results from a project funded by the Swiss University Conference (2008–2017). We give an overall picture of the growth in the field (in terms of student numbers, resources and activities), look at diversity in terms of topics (two clusters are identified and presented with respect to various indicators), present changes at the level of individual research units (where we find variance in terms of evolution), give insights into publication patterns (two different publication cultures are found) and describe mobility and career pathways in the field. We observe limited mobility within Switzerland, internal pathways at the level of doctoral students and post-docs, and international mobility, mainly within the same linguistic region, at the professorial level. We conclude that the field has reached a consolidation phase and achieved a rather stable situation, but faces new challenges, with digitalization and the pressure towards homogenization in publication output among the most important.

Peroxisome proliferator-activated receptor-alpha (PPAR-α) activation by fenofibrate reduces blood pressure and sodium retention during DOCA-salt hypertension. PPAR-αactivation reduces the expression of inflammatory cytokines, such as interleukin-6 (IL-6). Fenofibrate also induces cytochrome P450 4A (CYP4A) and increases 20-hydroxyeicosatetraenoic acid (20-HETE) production. This study tested whether the administration of fenofibrate would reduce blood pressure by attenuating plasma IL-6 and renal expression of cyclooxygenase-2 (COX-2), while increasing expression of renal CYP4A during 7 days of DOCA-salt hypertension. We performed uni-nephrectomy on 12–14 week old male Swiss Webster mice and implanted biotelemetry devices in control, DOCA-salt (1.5 mg/g) treated mice with or without fenofibrate (500 mg/kg/day in corn oil, intragastrically). Fenofibrate significantly decreased mean arterial pressure and plasma IL-6. In kidney homogenates, fenofibrate increased CYP4A and decreased COX-2 expression. There were no differences in renal cytochrome P450, family 2, subfamily c, polypeptide 23 (CYP2C23) and soluble expoxide hydrolase (sEH) expression between the groups. Our results suggest that the blood pressure lowering effect of PPAR-αactivation by fenofibrate involves the reduction of plasma IL-6 and COX-2, while increasing CYP4A expression during DOCA-salt hypertension. Our results may also suggest that PPAR-αactivation protects the kidney against renal injury via decreased COX-2 expression.

Riedi AK, Drögemüller C, Gurtner C et al. Bovine dilatative Kardiomyopathie: Altbekannt und dennoch gegenwärtig. SAT 2018; 160 (5): 289–293 Herzerkrankungen beim Rind sind medizinisch herausfordernd, sowohl diagnostisch als auch therapeutisch. Dass eine genaue Diagnostik trotzdem sinnvoll ist, zeigt die bovine dilatative Kardiomyopathie (BDCMP), die immer noch mit 2 % in der Schweizer Rinderpopulation vorkommt. Dieser Gendefekt kam besonders Ende der 1970er Jahre bei Kühen der Rasse Swiss Fleckvieh zur Ausprägung und lässt sich auf den 1946 geborenen Stier „Reflection Sovereign“ zurückführen. Durch zuchthygienische Maßnahmen konnte die Prävalenz deutlich gesenkt werden, doch immer wieder fallen Tiere mit Leistungseinbußen und Rechtsherzinsuffizienz auf, bei denen die Verdachtsdiagnose BDCMP gestellt werden kann. Im Folgenden werden drei Fallberichte besprochen.

Purpose The following article is a “Q&A interview” conducted by Joanne Pransky of Industrial Robot Journal as a method to impart the combined technological, business and personal experience of a prominent, robotic industry PhD and inventor regarding his pioneering efforts and the commercialization of bringing a technological invention to market. This paper aims to discuss these issues. Design/methodology/approach The interviewee is Dr Raffaello D’Andrea, a highly successful entrepreneur and proven business leader and one of the world’s foremost leaders in robotics and machine learning. D’Andrea is Founder, CEO and Chairman of the Board at Verity, the world’s leading autonomous indoor drone company, as well as a Professor of Dynamic Systems and Control at the Swiss Federal Institute of Technology (ETH) in Zurich. D’Andrea is also one of the co-founders and advisors of Robo-Global, an index and research company focused on investments in robotics, automation and artificial intelligence. In this interview, D’Andrea shares some of his business and personal experiences of working in industry and academia and his criteria for turning his ideas into successful working systems. Findings Raffaello D’Andrea’s entire career is built on his ability to bridge theory and practice. D’Andrea combined his love for science with his need to create and received a BS degree in engineering science at the University of Toronto, where he was awarded the Wilson Medal as the top graduating student in 1991. He obtained both his MS and PhD degrees in electrical engineering at Caltech, and then he joined the Cornell faculty as an assistant professor. While on leave from Cornell, from 2003 to 2007, he co-founded the disruptive warehouse automation company Kiva Systems, where he led the systems architecture, robot design, robot navigation and coordination, and control algorithms efforts. In 2014, D’Andrea took robotics technology into the air and founded Verity, the world’s first company to deliver a fully integrated autonomous, indoor drone-based system solution. Originality/value Raffaello D’Andrea combines academia, business and the arts to reinvent autonomous systems. D’Andrea was a founding member of the Systems Engineering Program at Cornell, where he established robot soccer as the flagship, multidisciplinary team project. In addition to pioneering the use of semi-definite programming for the design of distributed control systems, he went on to lead the Cornell Robot Soccer Team to win four world international RoboCup championships. Kiva Systems, co-founded by D’Andrea and acquired by Amazon in 2012, helped the re-branded Amazon Robotics to disrupt the entire warehousing and logistics systems industry. Additionally, D’Andrea is an internationally-exhibited new media artist, best known for the Robotic Chair (Ars Electronica, ARCO, London Art Fair, National Gallery of Canada) and Flight Assembled Architecture (FRAC Centre). With his team at Verity, he created the drone design and choreography for Cirque Du Soleil’s Paramour on Broadway, Metallica’s WorldWired Tour and Céline Dion’s Courage Tour. Other D’Andrea creations include the Flying Machine Arena, where flying robots perform aerial acrobatics, juggle balls, balance poles and cooperate to build structures; the Distributed Flight Array, a flying platform consisting of multiple autonomous single propeller vehicles that are able to drive, dock with their peers and fly in a coordinated fashion; the Balancing Cube, a dynamic sculpture that can balance on any of its edges or corners and its little brother Cubli, a small cube that can jump up, balance and walk; Blind Juggling Machines that can juggle balls without seeing them, and without catching them. D’Andrea is also collaborating with scientists, engineers, and wingsuit pilots to create an actively controlled suit that will allow humans to take off and land at will, to gain altitude, even to perch, while preserving the intimacy of wingsuit flight. D’Andrea has received the IEEE Robotics and Automation Award, the Engelberger Robotics Award, the IEEE/IFR Invention and Entrepreneurship Award in Robotics and Automation and the Presidential Early Career Award for Scientists and Engineers. In 2020, he was inducted in the National Inventors Hall of Fame and elected to the National Academy of Engineering.

Regierungen und Verwaltungen richten ihr Handeln vermehrt auf Nachhaltigkeit aus. Doch wie erfolgreich sind sie dabei? Wir stellen ein Instrument zur Messung nachhaltigkeitsbezogener interner Governance-Kapazität vor. Die Anwendung auf Schweizer Kantone offenbart deutliche Kapazitätsunterschiede und zeigt Möglichkeiten zur Stärkung staatlicher Governance-Kapazität auf.Sustainability has become an important guiding principle that has not only found its way into numerous policies, but also into the “engine rooms” of governance. Governments and administrations have established diverse governance arrangements orienting state actions towards sustainability. How does this integration of sustainability into governmental and administrative activity succeed? This paper proposes an instrument for the measurement and comparison of sustainability-oriented internal governance capacity and operationalizes it in the context of Swiss cantons. The application of the measurement tool documents the diversity of governance arrangements and their different capacities. It shows where, and how, the sustainability governance of governments and administrations can be further strengthened.

"Der Text vergleicht zwei fetischistische Puppenexperimente des 20. Jahrhunderts. Auf der einen Seite steht der vielbeachtete Versuch Oskar Kokoschkas, die verlorene Alma Mahler durch eine lebensechte Puppe zu ersetzen. Auf der anderen Seite geht es um die verborgen gehaltenen Bücher des Schweizer Einsiedlers Armand Schulthess, bevölkert von Hunderten von erotischen Collage-Frauen, die kunstvoll zusammengeklebt, vernäht und ineinander gefaltet sind. So unterschiedlich das zugrundeliegende fetischistische Ritual auch ausfällt, so zeigt sich in beiden Anordnungen doch eine grundlegende Übereinstimmung: In beiden Fällen nimmt das Inkarnieren die Form einer Operationskette an, die das Bild ins Register einer mimetischen Transformationsontologie überstellt. The paper compares two fetishistic experiments with puppets of the 20th century. On the one hand, there is Oskar Kokoschka’s much discussed attempt to replace the lost Alma Mahler with a life-size doll. On the other hand, the paper treats the secret books of Swiss hermit Armand Schulthess, populated by hundreds of erotic women, which are artfully glued, sewn and folded together. However different the underlying fetishistic ritual may be, the two groups show a fundamental agreement: In both cases, the process of incarnating becomes a chain of operations, translating the image into the register of a mimetic ontology of transformation. "

Heat shock proteins 70 (Hsp70) are chaperones consisting of a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD), the latter of which binds protein clients. After ATP binds to the NBD, the SBD α/β subdomains’ shared interface opens, and the open SBD docks to the NBD. Such allosteric effects are stabilized by the newly formed NBD-SBD interdomain contacts. In this paper, we examined how such an opening and formation of subdomain interfaces is affected during the evolution of Hsp70. In particular, insertion and deletion events (indels) can be highly disruptive for the mechanical events since such changes introduce a collective shift in the pairing interactions at communicating interfaces. Based on a multiple sequence alignment analysis of data collected from Swiss-Prot/UniProt database, we find several indel-free regions (IFR) in Hsp70. The two largest IFRs are located in interdomain regions that participate in allosteric structural changes. We speculate that the reason why the indels have a lower likelihood of occurrence in these regions is that indel events in these regions cause dysfunction in the protein due to perturbations of the mechanical balance. Thus, the development of functional allosteric machines requires including in the rational design a concept of the balance between structural elements.

Introduction Methods Resuts Discussion Conclusions Acknowledgments Authors' contributions Competing interests Ethical approval References Effect of Methotrexate and Omega-3 Combination on Cytogenetic Changes of Bone Marrow and Some Enzymatic Antioxidants: An Experimental Study Inaam N. Ali1, Muthana M. Awad2, Alaa S. Mahmood2,* 1 Water and Environment Directorate, Ministry of Sciences and Technology, Baghdad, Iraq 2 Department of Biology, College of Science, University of Anbar, Anbar, Iraq * Corresponding author: A. S. Mahmood (alaashm91@gmail.com) Abstract: Objective: To assess the effect of methotrexate and omega-3 combination on cytogenetic changes of bone marrow and activities of some enzymatic antioxidants. Methods: Fifty-six mature male Wistar rats were divided into two experimental groups and a control group. The first experimental group was sub-divided into three sub-groups depending on the concentration of methotrexate (MTX): X1 (0.05 mg/kg MTX), X2 (0.125 mg/kg MTX) and X3 (0.250 mg/kg MTX), which were given intraperitoneally on a weekly basis for eight weeks. The second experimental group (MTX and omega-3 group) was also sub-divided into three sub-groups (Y1, Y2 and Y3), which were injected intraperitoneally with 0.05, 0.125 and 0.25 mg/kg MTX, respectively, weekly for eight weeks accompanied by the oral administration of 300 mg/kg omega-3. The rats of the control group were given distilled water. The enzymatic activity of catalase (CAT), superoxide dismutase (SOD) and glutathione reductase (GR) were measured in the sera of rats. In addition, the mitotic index (MI) and chromosomal aberrations of bone marrow were also studied. Results: MTX resulted in a significant decrease in the activities of CAT, SOD and GR compared to the controls. It also increased the MI and chromosomal aberrations of rat bone marrows. On the other hand, omega-3 significantly increased the activities of the investigated enzymatic antioxidants and reduced the MI and chromosomal aberrations in treated mice when given in combination with MTX. Conclusions: MTX has a genotoxic effect on the bone marrow by increasing the MI and all types of chromosomal aberrations and decreasing the enzymatic activity of CAT, SOD and GR. The addition of omega-3 can lead to a protective effect by reducing the toxic and mutagenic effects of MTX. Keywords: Methotrexate, Omega-3, Antioxidant, Wistar rat, Chromosomal aberration, Mitotic index 1. Introduction Methotrexate (MTX) is a folic acid antagonist because of their chemical similarity [1]. Vezmar et al. [2] showed that MTX affects the synthesis of nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) by interfering with the biosynthesis of thymine and purines. It also directly affects the rapidly dividing and intact cells, especially those in the mucous membranes of the mouth, intestine and bone marrow [3]. Omega-3 is a type of unsaturated fats, which are classified as essential fatty acids that cannot be manufactured by the body and should be taken with food [4]. Sources of omega-3 include fish oils, such as salmon, sardines and tuna, as well as soybeans, walnuts, raisins and linseed, almonds and olive oils [5]. Omega-3 is used in the prevention of a number of diseases such as rheumatoid arthritis, ulcerative colitis, asthma, atherosclerosis, cancer, and cardiovascular diseases [6]. A large amount of evidence indicates that omega-3 fatty acids have significant health benefits, including anti-inflammatory and antioxidant properties besides their effect on blood cholesterol levels [7]. Antioxidants retard the oxidation process by different mechanisms such as the removal of free radicals [8]. Enzymatic antioxidants include catalase (CAT), which is the first line of defense in the cell that removes hydrogen peroxide formed during biological processes by converting it into an aldehyde, and superoxide dismutase (SOD). There are three major families of SOD enzymes: manganese SOD (Mn-SOD) in the mitochondria and peroxisomes, iron SOD (Fe-SOD) in prokaryote cells and copper/zinc SOD (Cu-Zn SOD) in the cytoplasm of eukaryote cells [9]. Therefore, changes in the metal co-factors (manganese, iron, copper and zinc) can alter the effectiveness of SOD and may lead to diseases as a result of oxidative stress [10]. Glutathione reductase (GR) is also an enzymatic antioxidant that converts the oxidized glutathione to the reduced glutathione in the presence of NADPH, which is oxidized to NADP [11]. Therefore, the aim of the present study was to assess the effects of MTX and omega-3 on the cytogenetic changes of bone marrow as well as the activities of CAT, SOD and GR enzymatic antioxidants in male rats. 2. Method 2.1. Laboratory animals and experimental design Fifty-six mature male Wistar rats (Rattus norvegicus), aged 10–12 weeks old and weighing 250–300 gm, were used in the present study. The rats were kept in separate cages, with natural 13- hour light and 11-hour dark periods in a contamination-free environment with a controlled temperature (28.0 ± 1.0°C). In addition, rats were maintained on a standard diet and tap water ad libitum. The rats were randomly allocated to two experimental groups and a control group. The first experimental group (MTX group) included 24 rats injected intraperitoneally with different MTX dilutions with distilled water [12]. It was sub-divided into three sub-groups (eight rats per sub-group) according to MTX concentration as follows: X1 (0.05 mg/kg MTX), X2 (0.125mg/kg MTX) and X3 (0.25 mg/kg MTX). All rats were given a single dose of the specified MTX concentration weekly for eight weeks. The second experimental group (MTX and omega-3 group) included 24 rats allocated to three sub-groups (Y1, Y2 and Y3), which were injected intraperitoneally with 0.05, 0.125 and 0.25 mg/kg MTX, respectively, weekly for eight weeks accompanied by the oral administration of 300 mg/kg omega-3. The control group included eight rats that were intraperitoneally injected with distilled water and given a single dose of distilled water orally weekly for eight weeks. 2.2. Blood collection and processing After the end of the dosing period, 5 ml of blood were withdrawn from the heart (by cardiac puncture) using a 5 cc disposable syringe. The collected blood was immediately poured into a clean sterile screw-capped tube (plain tube) and left for coagulation in a water bath at 37°C for 15 minutes. After coagulation of blood, the plain tube was centrifuged for 5 minutes at 1500 rpm. Then the samples were stored at -20°C for subsequent analysis. 2.3. Measurement of the activity of antioxidant enzymes The antioxidant activities of CAT, SOD and GR were measured using enzyme-linked immunosorbent assay kits purchased from Kamiya Biomedical Company (Seattle, WA, US), according to the manufacturer's instructions. 2.4. Cytogenetic study of bone marrow Rats were killed by cervical dislocation, and their hip bones were cleaned from surrounding muscles and then dissected by cutting both ends of the bone. Five milliliters of physiological buffered saline were injected inside the bone to withdraw bone marrow into a test tube. Tubes were centrifuged at 2000 rpm/10 minutes. The supernatant was then removed, and 10 ml of KCL solution (0.075 M) were added to the sediment. The mixture was then incubated at 37 °C in a water bath for 30 minutes, with shaking from time to time. The tubes were then centrifuged at 2000rpm/10 minutes to remove the supernatant. However, 5 ml of a freshly prepared fixative solution (methanol: glacial acetic acid 1:3) were added gradually in the form of droplets into the inner wall of the tube with constant mixing. After that, the tubes were placed at 4 °C for half an hour to fix the cells. This process was repeated for three times, and the cells were then suspended in 2 ml of the fixative solution. The tubes were centrifuged at 2000 rpm for 5 minutes, and the supernatant was then removed while the cells were re-suspended in 1-2 ml of cold fixative solution. After shaking the tubes, 4–5 drops were then taken from each tube onto a clean slide from a height of about three feet to provide an opportunity for the cells and nuclei to spread well. The slides were stained with acridine orange solution (0.01%) for 4–5 minutes, incubated in Sorensen’s buffer (0.06M, pH 6.5) for a minute. and then examined using a fluorescence microscope Olympus BX 51 America at a wavelength of 450–500 nm [13, 14]. A total of 1000 cells were examined, and both dividing and non-dividing cells were calculated [13]. Mitotic index (MI) was calculated according to the following formula [13]: MI= No. of dividing cells / 1000 × 100 2.5. Analysis of chromosomal aberrations of bone marrow cells A total of 1000 dividing cells were examined on the stained slides under a fluorescence microscope at a wavelength of 45–500 nm. The examined cells were at the first metaphase of the mitotic division, where chromosomal aberrations are clear and can be easily seen [13]. 2.6. Statistical analysis Data were analyzed using the Statistical Analysis System (SAS®) software, version 9.1 (Cary, NC, USA) [15]. Effects were expressed as mean ± standard error (SE) and statistically compared using a completely randomized design analysis of variance and least significant differences. Differences at P values <5 were considered statistically significant. 3. Results 3.1. Effects of MTX and MTX-omega-3 combination on antioxidant enzymatic activities Table (1) shows significantly lower SOD activities among rats treated with MTX or MTX-omega-3 compared to controls. Moreover, sera of rats receiving relatively high doses of MTX (sub-groups X2 and X3) showed the lowest enzymatic activities of 4.29 ± 0.01 IU and 3.93 ± 0.11 IU, respectively. On the other hand, CAT activity differed significantly between treated and control rats as well as among treated rats themselves, In this respect, the controls showed the highest activity of 39.38 ±0.02 IU, while those receiving the highest MTX concentration, either alone or in combination with omega-3 (sub-groups X3 and Y3), showed the lowest activities of 30.97 ± 0.03 IU and 32.12± 0.06 IU, respectively. Regarding GR activity, control rats showed a higher activity of 53.09± 0.05 IU compared to treated ones; however, the differences in GR activities in rats given low doses of MTX, either alone or in combination with omega-3 (sub-groups X1 and Y1), were not statistically significant. On the other hand, rats in sub-groups X3 and Y3 showed the lowest GR activities of 34.59 ± 0.63 IU and 37.15 ±0.01, respectively, with statistically significant differences from other sub-groups. 3.2. Effects of MTX and MTX-omega-3 combination on mitotic index of bone marrow cells Figure (1) shows a significant decrease in the MI in all treated groups compared to control. In addition, there was a reverse association between MTX concentration and MI, where rats treated with the highest dose of MTX (sub-group X3) showed a significant decrease in MI compared to all other treated rat sub-groups. In addition, rats in sub-groups treated with MTX and omega-3 (sub-groups Y1, Y2 and Y3) showed a significant increase in MI compared to their counterpart rats receiving MTX only. Table 1. Activity of antioxidant enzymes in rats treated with MTX and MTX-omega-3 Group Enzymatic activity (mean± SE) SOD (IU) CAT (IU) GR (µmol) Control 6.41±0.02 a 39.38±0.02 a 53.09±0.05 a X1 (0.05 mg MTX/ kg) 5.33±0.01 b 37.81±0.01 c 51.12±0.06 a Y1 (0.05 mg MTX + 300 mg omega-3/ kg) 6.08±0.04 a 38.40±0.02 b 51.97±0.03 a X2 (0.125 mg MTX/ kg) 4.29±0.01 cd 33.13±0.01 e 42.34±0.03 b Y2 (0.125 mg MTX + 300 mg omega-3/ kg) 4.99±0.40 b 36.68±0.02 d 43.02±3.04 b X3 (0.25 mg MTX/ kg) 3.93±0.11 d 30.97±0.03 g 34.59±0.63 c Y3 (0.25 mg MTX + 300 mg omega-3/ kg) 4.47±0.02 c 32.12±0.06 f 37.15±0.01 c SE, Standard error; IU, international unit; SOD, superoxide dismutase; CAT, catalase; GR, glutathione reductase; *statistically significant at P < 0.05; **statistically significant at P < 0.01. Means with different letters within the same column showed a statistically significant difference. 3.3. Effects of MTX and MTX-omega-3 combination on chromosomal aberrations of bone marrow cells Rats receiving higher concentrations of MTX (sub-group X3) showed a significant increase in all types of chromosomal aberrations, i.e., chromatid gaps, chromosome gaps, chromatid breaks, chromosome breaks, deletions and simple fragments (Figure 2 and Table 2) than those of the control group or other treated sub-groups. All rats treated with MTX-omega-3 combination showed a significant decrease in almost all types of chromosomal aberrations compared to their counterpart rats receiving MTX alone (Table 2). Figure 1. Effect of MTX and MTX-omega-3 on the MI of bone marrow cells of treated rats compared to the controls. The groups X1 (0.05 MTX), X2 (0.125 MTX) and X3 (0.250 MTX) were compared to the control group, while the groups Y1 (0.05 MTX+ omega-3), Y2 (0.125 MTX+ omega-3) and Y3 (0.25 MTX+ omega-3) were compared to X1, X2 and X3, respectively. Figure 2. Effect of MTX and MTX-omega-3 on chromosomal aberration as seen under fluorescence microscope after staining with acridine orange: (1) a simple fragment; (2) a chromatid gap; (3) a chromosomal gap (A) and a chromosomal break (B). 4. Discussion The present experiment reveals that the addition of omega-3 to MTX alleviates its effects on the activities of the antioxidant enzymes CAT, SOD and GR, and decreases the MI as well as all types of chromosomal aberrations in the bone marrow cells. Daham et al. [16] showed that the decline in antioxidants associated with chemotherapy is attributed to the increase in lipid peroxidation caused by these kinds of drugs, which increase the level of free radicals. In addition, Weijl et al. [17] showed that some chemotherapeutic drugs have a negative effect on the antioxidant levels such as GR, whose activity decreases as a result of its involvement in many cellular processes such as cell defenses against the toxicity of some compounds. Al-Dalawy et al. [18] found that the decrease in the level of SOD is an evidence of its increased activity due to the increased release of free radicals. MTX causes an increase in the release of free radicals, including the OH radical that causes direct damage to DNA [16]. Al-Helaly [19] showed that the amount of food taken has an effect on antioxidants, where nutritional deficiency decreases the antioxidant levels, thus increasing free radicals that cause damage to DNA. Table 2. Chromosomal aberrations of bone marrow cells in rats treated with MTX and MTX-omega-3 Group Type of chromosomal aberration(mean ± SE) Chromatid gap Chromosome Gap Chromatid breaks Chromosome breaks Deletion Simple Fragments Chromosomal aberration (%) Control 1.33±0.33 e 0.00±0.00 e 1.67±0.33 c 0.33±0.15 c 0.00±0.00 0.67±0.33 cd 0.04±0.005 f X1 2.75±0.47 cd 1.50±0.28 cd 2.50±0.64 bc 1.00±0.41 bc 0.50±0.28 bc 0.75±0.25 bcd 0.09±0.02 de Y1 1.75±0.47 de 0.75±0.25 de 1.50±0.28 c 1.00±0.00 bc 0.75±0.25 abc 0.75±0.25 abc 0.065±0.005 ef X2 4.67±0.33 b 2.67±0.33 ab 2.67±0.33 bc 1.67±0.33 ab 0.67±0.33 abc 1.67±0.33 ab 0.14±0.006 bc Y2 3.00±0.00 c 2.00±0.00 bc 3.00±0.057 bc 1.33±0.33 b 0.67±0.33 abc 0.33±0.15 d 0.106±0.003 cd X3 6.80±0.37 a 3.00±0.31 a 4.60±0.74 a 2.40±0.24 a 1.40±0.24 a 1.80±0.37 a 0.20±0.017 a Y3 5.60±0.40 ab 2.40±0.24 ab 3.60±0.24 ab 1.80±0.20 ab 1.20±0.20 ab 1.40±0.24 abc 0.16±0.003 b LSD 1.231** 0.814** 0.602** 0.841** 0.774* 0.941** 3.499* SE, Standard error; * statistically significant at P < 0.05; ** statistically significant at P < 0.01. Means with different letters within the same column showed a statistically significant difference. X1 (0.05 mg MTX/ kg); X2 (0.125 mg MTX/ kg); X3 (0.25 mg MTX/ kg); Y1 (0.05 mg MTX + 300 mg omega-3/ kg); Y2 (0.125 mg MTX + 300 mg omega-3/ kg); Y3 (0.25 mg MTX + 300 mg omega-3/ kg). In the present study, the intraperitoneal administration of MTX to rats also caused a decrease in the MI of bone marrow and a significant increase in the rate of abnormal chromosomal aberration compared to the control rats. This finding is consistent with those reported previously [20], [21]. The effect of MTX can be attributed to its ability to interfere with the genetic material, leading to the appearance of toxic and mutagenic consequences. Rushworth et al. [22] reported that MTX leads to a lack of dihydrofolate reductase, which is the key to the growth and cell division processes. This, in turn, leads to a reduction of the nucleotides involved in the building of DNA and, therefore, to a stop or obstruction of the repair mechanisms of the damaged DNA. In addition, Wong and Choi [23] concluded that MTX inhibits the action of enzymes controlling the purine metabolism, which leads to the accumulation of adenosine in addition to the damage of the molecule itself and to the occurrence of chromosomal aberrations. Jafer et al. [24] reported the ability of MTX to induce chromosomal aberration in humans or animals by preventing the repair of DNA and affecting the proteins found in chromosomes. These findings were also confirmed by Hussain et al. [25], who found that MTX causes an increase in chromosomal aberrations. In the present study, the MI showed a significant increase in rat sub-groups treated with MTX-omega-3 combination, but there was a decrease in the rate of chromosomal aberration, which confirms the role of omega-3 unsaturated fatty acids in protecting the cell from the impact of free radicals [26], [27]. Attia and Nasr [28] reported the antioxidant effect of omega-3, which was attributed to the reduction in lipid peroxidation and the increase in SOD and CAT or the stimulation of GR. It is noteworthy that GR leads to the synthesis of reduced glutathione, which is important in the defense of the cell against toxic substances and the prevention of the occurrence of mutations [29]. 5. Conclusions MTX significantly decreases the activity of enzymatic antioxidants, reduce the MI and increase the chromosomal aberrations of all types in bone marrow. This gives further evidence on the genotoxic effects of MTX on the bone marrow. On the other hand, omega-3 shows a protective effect by reducing the toxic and mutagenic effects of MTX. Acknowledgments The authors thank the staff of the Water and Environment Directorate, Ministry of Science and Technology, Baghdad, Iraq for their cooperation. They also thank Dr. Jasim Al-Niami for his technical and scientific guidance. Authors' contributions INA, MMA and ASM contributed to the study design and analyzed data. All authors contributed to the manuscript drafting and revising and approved the final submission. Competing interests The authors declare that they have no competing interests associated with this article. Ethical approval The ethical clearance of this study was obtained from the Ethics Committee of the College of Science, University of Anbar (Reference No. A. D. 51 in 30/8/2015). References Yuen CW, Winter ME. Methotrexate (MTX). In: Basic clinical pharmacokinetics, Winter ME, editor. Philadelphia, USA: Lippincott Williams & Wilkins; 2010. p.p. 304–25. 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Introduction Methods Resuts Discussion Conclusions Acknowledgments Authors' contributions Competing interests Ethical approval References Effect of Methotrexate and Omega-3 Combination on Cytogenetic Changes of Bone Marrow and Some Enzymatic Antioxidants: An Experimental Study Inaam N. Ali1, Muthana M. Awad2, Alaa S. Mahmood2,* 1 Water and Environment Directorate, Ministry of Sciences and Technology, Baghdad, Iraq 2 Department of Biology, College of Science, University of Anbar, Anbar, Iraq * Corresponding author: A. S. Mahmood (alaashm91@gmail.com) Abstract: Objective: To assess the effect of methotrexate and omega-3 combination on cytogenetic changes of bone marrow and activities of some enzymatic antioxidants. Methods: Fifty-six mature male Wistar rats were divided into two experimental groups and a control group. The first experimental group was sub-divided into three sub-groups depending on the concentration of methotrexate (MTX): X1 (0.05 mg/kg MTX), X2 (0.125 mg/kg MTX) and X3 (0.250 mg/kg MTX), which were given intraperitoneally on a weekly basis for eight weeks. The second experimental group (MTX and omega-3 group) was also sub-divided into three sub-groups (Y1, Y2 and Y3), which were injected intraperitoneally with 0.05, 0.125 and 0.25 mg/kg MTX, respectively, weekly for eight weeks accompanied by the oral administration of 300 mg/kg omega-3. The rats of the control group were given distilled water. The enzymatic activity of catalase (CAT), superoxide dismutase (SOD) and glutathione reductase (GR) were measured in the sera of rats. In addition, the mitotic index (MI) and chromosomal aberrations of bone marrow were also studied. Results: MTX resulted in a significant decrease in the activities of CAT, SOD and GR compared to the controls. It also increased the MI and chromosomal aberrations of rat bone marrows. On the other hand, omega-3 significantly increased the activities of the investigated enzymatic antioxidants and reduced the MI and chromosomal aberrations in treated mice when given in combination with MTX. Conclusions: MTX has a genotoxic effect on the bone marrow by increasing the MI and all types of chromosomal aberrations and decreasing the enzymatic activity of CAT, SOD and GR. The addition of omega-3 can lead to a protective effect by reducing the toxic and mutagenic effects of MTX. Keywords: Methotrexate, Omega-3, Antioxidant, Wistar rat, Chromosomal aberration, Mitotic index 1. Introduction Methotrexate (MTX) is a folic acid antagonist because of their chemical similarity [1]. Vezmar et al. [2] showed that MTX affects the synthesis of nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) by interfering with the biosynthesis of thymine and purines. It also directly affects the rapidly dividing and intact cells, especially those in the mucous membranes of the mouth, intestine and bone marrow [3]. Omega-3 is a type of unsaturated fats, which are classified as essential fatty acids that cannot be manufactured by the body and should be taken with food [4]. Sources of omega-3 include fish oils, such as salmon, sardines and tuna, as well as soybeans, walnuts, raisins and linseed, almonds and olive oils [5]. Omega-3 is used in the prevention of a number of diseases such as rheumatoid arthritis, ulcerative colitis, asthma, atherosclerosis, cancer, and cardiovascular diseases [6]. A large amount of evidence indicates that omega-3 fatty acids have significant health benefits, including anti-inflammatory and antioxidant properties besides their effect on blood cholesterol levels [7]. Antioxidants retard the oxidation process by different mechanisms such as the removal of free radicals [8]. Enzymatic antioxidants include catalase (CAT), which is the first line of defense in the cell that removes hydrogen peroxide formed during biological processes by converting it into an aldehyde, and superoxide dismutase (SOD). There are three major families of SOD enzymes: manganese SOD (Mn-SOD) in the mitochondria and peroxisomes, iron SOD (Fe-SOD) in prokaryote cells and copper/zinc SOD (Cu-Zn SOD) in the cytoplasm of eukaryote cells [9]. Therefore, changes in the metal co-factors (manganese, iron, copper and zinc) can alter the effectiveness of SOD and may lead to diseases as a result of oxidative stress [10]. Glutathione reductase (GR) is also an enzymatic antioxidant that converts the oxidized glutathione to the reduced glutathione in the presence of NADPH, which is oxidized to NADP [11]. Therefore, the aim of the present study was to assess the effects of MTX and omega-3 on the cytogenetic changes of bone marrow as well as the activities of CAT, SOD and GR enzymatic antioxidants in male rats. 2. Method 2.1. Laboratory animals and experimental design Fifty-six mature male Wistar rats (Rattus norvegicus), aged 10–12 weeks old and weighing 250–300 gm, were used in the present study. The rats were kept in separate cages, with natural 13- hour light and 11-hour dark periods in a contamination-free environment with a controlled temperature (28.0 ± 1.0°C). In addition, rats were maintained on a standard diet and tap water ad libitum. The rats were randomly allocated to two experimental groups and a control group. The first experimental group (MTX group) included 24 rats injected intraperitoneally with different MTX dilutions with distilled water [12]. It was sub-divided into three sub-groups (eight rats per sub-group) according to MTX concentration as follows: X1 (0.05 mg/kg MTX), X2 (0.125mg/kg MTX) and X3 (0.25 mg/kg MTX). All rats were given a single dose of the specified MTX concentration weekly for eight weeks. The second experimental group (MTX and omega-3 group) included 24 rats allocated to three sub-groups (Y1, Y2 and Y3), which were injected intraperitoneally with 0.05, 0.125 and 0.25 mg/kg MTX, respectively, weekly for eight weeks accompanied by the oral administration of 300 mg/kg omega-3. The control group included eight rats that were intraperitoneally injected with distilled water and given a single dose of distilled water orally weekly for eight weeks. 2.2. Blood collection and processing After the end of the dosing period, 5 ml of blood were withdrawn from the heart (by cardiac puncture) using a 5 cc disposable syringe. The collected blood was immediately poured into a clean sterile screw-capped tube (plain tube) and left for coagulation in a water bath at 37°C for 15 minutes. After coagulation of blood, the plain tube was centrifuged for 5 minutes at 1500 rpm. Then the samples were stored at -20°C for subsequent analysis. 2.3. Measurement of the activity of antioxidant enzymes The antioxidant activities of CAT, SOD and GR were measured using enzyme-linked immunosorbent assay kits purchased from Kamiya Biomedical Company (Seattle, WA, US), according to the manufacturer's instructions. 2.4. Cytogenetic study of bone marrow Rats were killed by cervical dislocation, and their hip bones were cleaned from surrounding muscles and then dissected by cutting both ends of the bone. Five milliliters of physiological buffered saline were injected inside the bone to withdraw bone marrow into a test tube. Tubes were centrifuged at 2000 rpm/10 minutes. The supernatant was then removed, and 10 ml of KCL solution (0.075 M) were added to the sediment. The mixture was then incubated at 37 °C in a water bath for 30 minutes, with shaking from time to time. The tubes were then centrifuged at 2000rpm/10 minutes to remove the supernatant. However, 5 ml of a freshly prepared fixative solution (methanol: glacial acetic acid 1:3) were added gradually in the form of droplets into the inner wall of the tube with constant mixing. After that, the tubes were placed at 4 °C for half an hour to fix the cells. This process was repeated for three times, and the cells were then suspended in 2 ml of the fixative solution. The tubes were centrifuged at 2000 rpm for 5 minutes, and the supernatant was then removed while the cells were re-suspended in 1-2 ml of cold fixative solution. After shaking the tubes, 4–5 drops were then taken from each tube onto a clean slide from a height of about three feet to provide an opportunity for the cells and nuclei to spread well. The slides were stained with acridine orange solution (0.01%) for 4–5 minutes, incubated in Sorensen’s buffer (0.06M, pH 6.5) for a minute. and then examined using a fluorescence microscope Olympus BX 51 America at a wavelength of 450–500 nm [13, 14]. A total of 1000 cells were examined, and both dividing and non-dividing cells were calculated [13]. Mitotic index (MI) was calculated according to the following formula [13]: MI= No. of dividing cells / 1000 × 100 2.5. Analysis of chromosomal aberrations of bone marrow cells A total of 1000 dividing cells were examined on the stained slides under a fluorescence microscope at a wavelength of 45–500 nm. The examined cells were at the first metaphase of the mitotic division, where chromosomal aberrations are clear and can be easily seen [13]. 2.6. Statistical analysis Data were analyzed using the Statistical Analysis System (SAS®) software, version 9.1 (Cary, NC, USA) [15]. Effects were expressed as mean ± standard error (SE) and statistically compared using a completely randomized design analysis of variance and least significant differences. Differences at P values <5 were considered statistically significant. 3. Results 3.1. Effects of MTX and MTX-omega-3 combination on antioxidant enzymatic activities Table (1) shows significantly lower SOD activities among rats treated with MTX or MTX-omega-3 compared to controls. Moreover, sera of rats receiving relatively high doses of MTX (sub-groups X2 and X3) showed the lowest enzymatic activities of 4.29 ± 0.01 IU and 3.93 ± 0.11 IU, respectively. On the other hand, CAT activity differed significantly between treated and control rats as well as among treated rats themselves, In this respect, the controls showed the highest activity of 39.38 ±0.02 IU, while those receiving the highest MTX concentration, either alone or in combination with omega-3 (sub-groups X3 and Y3), showed the lowest activities of 30.97 ± 0.03 IU and 32.12± 0.06 IU, respectively. Regarding GR activity, control rats showed a higher activity of 53.09± 0.05 IU compared to treated ones; however, the differences in GR activities in rats given low doses of MTX, either alone or in combination with omega-3 (sub-groups X1 and Y1), were not statistically significant. On the other hand, rats in sub-groups X3 and Y3 showed the lowest GR activities of 34.59 ± 0.63 IU and 37.15 ±0.01, respectively, with statistically significant differences from other sub-groups. 3.2. Effects of MTX and MTX-omega-3 combination on mitotic index of bone marrow cells Figure (1) shows a significant decrease in the MI in all treated groups compared to control. In addition, there was a reverse association between MTX concentration and MI, where rats treated with the highest dose of MTX (sub-group X3) showed a significant decrease in MI compared to all other treated rat sub-groups. In addition, rats in sub-groups treated with MTX and omega-3 (sub-groups Y1, Y2 and Y3) showed a significant increase in MI compared to their counterpart rats receiving MTX only. Table 1. Activity of antioxidant enzymes in rats treated with MTX and MTX-omega-3 Group Enzymatic activity (mean± SE) SOD (IU) CAT (IU) GR (µmol) Control 6.41±0.02 a 39.38±0.02 a 53.09±0.05 a X1 (0.05 mg MTX/ kg) 5.33±0.01 b 37.81±0.01 c 51.12±0.06 a Y1 (0.05 mg MTX + 300 mg omega-3/ kg) 6.08±0.04 a 38.40±0.02 b 51.97±0.03 a X2 (0.125 mg MTX/ kg) 4.29±0.01 cd 33.13±0.01 e 42.34±0.03 b Y2 (0.125 mg MTX + 300 mg omega-3/ kg) 4.99±0.40 b 36.68±0.02 d 43.02±3.04 b X3 (0.25 mg MTX/ kg) 3.93±0.11 d 30.97±0.03 g 34.59±0.63 c Y3 (0.25 mg MTX + 300 mg omega-3/ kg) 4.47±0.02 c 32.12±0.06 f 37.15±0.01 c SE, Standard error; IU, international unit; SOD, superoxide dismutase; CAT, catalase; GR, glutathione reductase; *statistically significant at P < 0.05; **statistically significant at P < 0.01. Means with different letters within the same column showed a statistically significant difference. 3.3. Effects of MTX and MTX-omega-3 combination on chromosomal aberrations of bone marrow cells Rats receiving higher concentrations of MTX (sub-group X3) showed a significant increase in all types of chromosomal aberrations, i.e., chromatid gaps, chromosome gaps, chromatid breaks, chromosome breaks, deletions and simple fragments (Figure 2 and Table 2) than those of the control group or other treated sub-groups. All rats treated with MTX-omega-3 combination showed a significant decrease in almost all types of chromosomal aberrations compared to their counterpart rats receiving MTX alone (Table 2). Figure 1. Effect of MTX and MTX-omega-3 on the MI of bone marrow cells of treated rats compared to the controls. The groups X1 (0.05 MTX), X2 (0.125 MTX) and X3 (0.250 MTX) were compared to the control group, while the groups Y1 (0.05 MTX+ omega-3), Y2 (0.125 MTX+ omega-3) and Y3 (0.25 MTX+ omega-3) were compared to X1, X2 and X3, respectively. Figure 2. Effect of MTX and MTX-omega-3 on chromosomal aberration as seen under fluorescence microscope after staining with acridine orange: (1) a simple fragment; (2) a chromatid gap; (3) a chromosomal gap (A) and a chromosomal break (B). 4. Discussion The present experiment reveals that the addition of omega-3 to MTX alleviates its effects on the activities of the antioxidant enzymes CAT, SOD and GR, and decreases the MI as well as all types of chromosomal aberrations in the bone marrow cells. Daham et al. [16] showed that the decline in antioxidants associated with chemotherapy is attributed to the increase in lipid peroxidation caused by these kinds of drugs, which increase the level of free radicals. In addition, Weijl et al. [17] showed that some chemotherapeutic drugs have a negative effect on the antioxidant levels such as GR, whose activity decreases as a result of its involvement in many cellular processes such as cell defenses against the toxicity of some compounds. Al-Dalawy et al. [18] found that the decrease in the level of SOD is an evidence of its increased activity due to the increased release of free radicals. MTX causes an increase in the release of free radicals, including the OH radical that causes direct damage to DNA [16]. Al-Helaly [19] showed that the amount of food taken has an effect on antioxidants, where nutritional deficiency decreases the antioxidant levels, thus increasing free radicals that cause damage to DNA. Table 2. Chromosomal aberrations of bone marrow cells in rats treated with MTX and MTX-omega-3 Group Type of chromosomal aberration(mean ± SE) Chromatid gap Chromosome Gap Chromatid breaks Chromosome breaks Deletion Simple Fragments Chromosomal aberration (%) Control 1.33±0.33 e 0.00±0.00 e 1.67±0.33 c 0.33±0.15 c 0.00±0.00 0.67±0.33 cd 0.04±0.005 f X1 2.75±0.47 cd 1.50±0.28 cd 2.50±0.64 bc 1.00±0.41 bc 0.50±0.28 bc 0.75±0.25 bcd 0.09±0.02 de Y1 1.75±0.47 de 0.75±0.25 de 1.50±0.28 c 1.00±0.00 bc 0.75±0.25 abc 0.75±0.25 abc 0.065±0.005 ef X2 4.67±0.33 b 2.67±0.33 ab 2.67±0.33 bc 1.67±0.33 ab 0.67±0.33 abc 1.67±0.33 ab 0.14±0.006 bc Y2 3.00±0.00 c 2.00±0.00 bc 3.00±0.057 bc 1.33±0.33 b 0.67±0.33 abc 0.33±0.15 d 0.106±0.003 cd X3 6.80±0.37 a 3.00±0.31 a 4.60±0.74 a 2.40±0.24 a 1.40±0.24 a 1.80±0.37 a 0.20±0.017 a Y3 5.60±0.40 ab 2.40±0.24 ab 3.60±0.24 ab 1.80±0.20 ab 1.20±0.20 ab 1.40±0.24 abc 0.16±0.003 b LSD 1.231** 0.814** 0.602** 0.841** 0.774* 0.941** 3.499* SE, Standard error; * statistically significant at P < 0.05; ** statistically significant at P < 0.01. Means with different letters within the same column showed a statistically significant difference. X1 (0.05 mg MTX/ kg); X2 (0.125 mg MTX/ kg); X3 (0.25 mg MTX/ kg); Y1 (0.05 mg MTX + 300 mg omega-3/ kg); Y2 (0.125 mg MTX + 300 mg omega-3/ kg); Y3 (0.25 mg MTX + 300 mg omega-3/ kg). In the present study, the intraperitoneal administration of MTX to rats also caused a decrease in the MI of bone marrow and a significant increase in the rate of abnormal chromosomal aberration compared to the control rats. This finding is consistent with those reported previously [20], [21]. The effect of MTX can be attributed to its ability to interfere with the genetic material, leading to the appearance of toxic and mutagenic consequences. Rushworth et al. [22] reported that MTX leads to a lack of dihydrofolate reductase, which is the key to the growth and cell division processes. This, in turn, leads to a reduction of the nucleotides involved in the building of DNA and, therefore, to a stop or obstruction of the repair mechanisms of the damaged DNA. In addition, Wong and Choi [23] concluded that MTX inhibits the action of enzymes controlling the purine metabolism, which leads to the accumulation of adenosine in addition to the damage of the molecule itself and to the occurrence of chromosomal aberrations. Jafer et al. [24] reported the ability of MTX to induce chromosomal aberration in humans or animals by preventing the repair of DNA and affecting the proteins found in chromosomes. These findings were also confirmed by Hussain et al. [25], who found that MTX causes an increase in chromosomal aberrations. In the present study, the MI showed a significant increase in rat sub-groups treated with MTX-omega-3 combination, but there was a decrease in the rate of chromosomal aberration, which confirms the role of omega-3 unsaturated fatty acids in protecting the cell from the impact of free radicals [26], [27]. Attia and Nasr [28] reported the antioxidant effect of omega-3, which was attributed to the reduction in lipid peroxidation and the increase in SOD and CAT or the stimulation of GR. It is noteworthy that GR leads to the synthesis of reduced glutathione, which is important in the defense of the cell against toxic substances and the prevention of the occurrence of mutations [29]. 5. Conclusions MTX significantly decreases the activity of enzymatic antioxidants, reduce the MI and increase the chromosomal aberrations of all types in bone marrow. This gives further evidence on the genotoxic effects of MTX on the bone marrow. On the other hand, omega-3 shows a protective effect by reducing the toxic and mutagenic effects of MTX. Acknowledgments The authors thank the staff of the Water and Environment Directorate, Ministry of Science and Technology, Baghdad, Iraq for their cooperation. They also thank Dr. Jasim Al-Niami for his technical and scientific guidance. Authors' contributions INA, MMA and ASM contributed to the study design and analyzed data. All authors contributed to the manuscript drafting and revising and approved the final submission. Competing interests The authors declare that they have no competing interests associated with this article. Ethical approval The ethical clearance of this study was obtained from the Ethics Committee of the College of Science, University of Anbar (Reference No. A. D. 51 in 30/8/2015). References Yuen CW, Winter ME. Methotrexate (MTX). In: Basic clinical pharmacokinetics, Winter ME, editor. Philadelphia, USA: Lippincott Williams & Wilkins; 2010. p.p. 304–25. Google Scholar Vezmar S, Becker A, Bode U, Jaehde U. Biochemical and clinical aspects of methotrexate neurotoxicity. Chemotherapy 2003; 49: 92–104. DOI PubMed - Google Scholar Tian H, Cronstein BN. Understanding the mechanisms of action of methotrexate implications for the treatment of rheumatoid arthritis. Bull NYU Hosp Jt Dis 2007; 65: 168–73. PubMed - Google Scholar El-Khayat Z, Rasheed WI, Elias T, Hussein J, Oraby F, Badawi M, et al. Protective effect of either dietary or pharmaceutical n-3 fatty acids on bone loss in ovariectomized rats. Maced J Med Sci 2010; 3: 9–16. DOI - Google Scholar Kris-Etherton PM, Harris WS, Appel LJ; Nutrition Committee. Fish consumption, fish oil, omega-3 fatty acids and cardiovascular disease. Arterioscler Thromb Vasc Biol 2003; 23: e20–30. DOI - PubMed - Google Scholar Calder PC. Polyunsaturated fatty acids and inflammation. Prostaglandins Leukot Essent Fatty Acids 2006; 75: 197–202. 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Abstract Background Periodontitis is a multi-factorial infection with red complex bacteria playing a crucial role in the pathogenesis. As bacteria are tending to develop resistance against conventional antibiotics, new treatment modalities need to be developed. Antimicrobial peptides (AMPs) are potential tools for drug development and are gaining widespread interest. β-defensin 1 is an important AMP and forms the first-line host defense mechanism. The present study analyzed the structure and molecular docking of β-defensin 1 with the virulence factors of red complex bacteria of periodontitis. The physico-chemical properties of β-defensin 1 were determined by various online tools such as ProtParam, ProteinPredict, ToxinPred, and BioPep web servers. The structure of β-defensin 1was predicted by the SWISS-MODEL web server and the structure was evaluated by different web tools. The structure of lipopolysaccharide of Porphyromonas gingivalis was drawn using Chem3D ultra 11.0 software. The structure of important protein virulence factors of red complex bacteria of periodontitis was determined by the SWISS-MODEL web server. The interaction study between β-defensin 1 and virulence factors was carried out by molecular docking using Auto dock version 4.0 software and pyDock WEB server. Results Using online tools, β-defensin 1 was predicted to be stable and non-toxic. SWISS-MODEL web server predicted Ramachandran score as 94.12% and clash score 0.0 for β-defensin 1. Auto dock version 4.0 software and pyDock WEB server analyzed the interaction to have low binding energies and hydrogen bonds were formed between the peptide and virulence factors. Conclusion β-defensin 1 was found to have good binding interaction with the disease-causing factors of red complex bacteria of periodontitis and in turn could play a role in reducing the severity of infection. β-defensin 1 could be a potential candidate for drug development for periodontitis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. Since then, COVID-19, the disease caused by SARS-CoV-2, has become a rapidly spreading pandemic that has reached most countries in the world. So far, there are no vaccines or therapeutics to fight this virus. Here, I present an in silico analysis of the virus spike glycoprotein (recently determined at atomic resolution) and provide insights into how antibodies against the 2002 virus SARS-CoV might be modified to neutralize SARS-CoV-2. I ran docking experiments with Rosetta Dock to determine which substitutions in the 80R and m396 antibodies might improve the binding of these to SARS-CoV-2 and used molecular visualization and analysis software, including UCSF Chimera and Rosetta Dock, as well as other bioinformatics tools, including SWISS-MODEL. Supercomputers, including Bridges Large, Stampede and Frontera, were used for macromolecular assemblies and large scale analysis and visualization.

Abstract Background SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain (RBD). Methods Here, conserved RBD from 186-countries were compared with WUHAN-Hu-1 wild-type (CLUSTAL-X2/Pymol). The RBD of ACE2-bound nCOV2 crystal-structure 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the different locations of CUT4 (most-effective from total 4 proposed fragments; CUTs) were tested with Swiss-Model-Expacy. Results Blind-docking of mutated-CUTs in ACE2 completely rejected the nCOV2 binding to ACE2. Further, competitive-docking/binding-analyses (by PRODIGY) demonstrated few more bonding (LYS31-PHE490 and GLN42-GLN498) of CUT4 (than wild) and hindered TYR41-THR500 interaction with ACE2. Moreover, mutated-CUT4 even showed higher blocking effect against spike-ACE2 binding. Conclusion In summary, CUT4-mutant rejects whole glycosylated-nCoV2 in all pre-dock, post-dock and competitive-docking conditions. The present work strategy is relevant because it could be able to block at the first level entry of the virus to the host cells.

Background: Testis-specific protein on Y chromosome (TSPY) is the output of a tandem gene cluster. TSPY expression has been observed in gonadoblastoma and numerous distinct kinds of germ cell tumors, such as carcinoma in situ/intratubular germ cell neoplasia, seminoma, and extragonadal intracranial germ cell tumors (GCT). Myrtus communis extract rich in α-pinene showed high antioxidant and anticancer activity against a TSPY. Methods: The molecular weight and theoretical isoelectric of the TSPY proteins were calculated, using the ExPASSY ProtParam tools. Some software like mega 6, BioEdit, NEB cutter (New England Biolabs), and CAP3 were used to analyze clustering and find restriction enzymes on the TSPY sequence. To evaluate the nucleotide diversity of all sequences, the number of diverse situations and Tajima’s and Watterson’s estimators of theta were assessed. Nucleotide polymorphism can be measured by several parameters, such as haplotypes diversity, nucleotide diversity, Theta using Dnasp software. To find interaction networks of protein-protein search tool for the retrieval of interacting genes/proteins (STRING) tools and to predict 3D structure, SWISS-MODEL was used; however, for docking protein-peptide based on interaction, Swiss Dock, Galaxy web, and CABS-dock software were employed. Results: We report a high (0.91) dN/dS index, positive Tajima's D, Fu, and Li’s tests, and a non-significant D test suggesting the occurrence of old modifications or a decrease of newborn mutations in the TSPY gene family. Interestingly, several hub proteins produced a strong chain or an operative module within their protein groups, such as nucleosome assembly protein (1NAP1L), RBMXL2, TBL1Y, and AMELY, which are all associated with the same cellular appliance elements and/or genetic uses. The docking of the TSPY target with α-pinene using docking revealed that the computationally-prognosticated lowest energy networks of TSPY are established by intermolecular hydrogen bonds and stacking interactions. Conclusions: The results of this study demonstrated that α-pinene interacts with the TSPY protein target and could be developed as a promising candidate for the new anticancer agent.

Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance, and it is hitherto incurable. Among different therapeutic modalities, glucose co-transporter (SGLT) inhibitors have gained prominence. In the current study, we have screened natural compounds as potential SGLT inhibitor and compared with conventional gliflozin drugs. We have selected human SGLT 1 and 2 sequences modeled by homology modeling using SWISS-MODEL server, stability analysis was performed in silico. We used CDOCKER to dock the selected gliflozin drugs and natural compounds with SGLT 1 and 2. We further checked adsorption, distribution, metabolism, excretion, and toxicity using ADMETSAR tools and identified Sophoraflavonone G as a potential natural compound with good binding energy and drug-like characteristics. The molecular dynamic simulation revealed sophoraflavonone G binds with SGLT2 and forms a stable complex.

The SARS-CoV-2 corona virus disease 2019 (COVID-19) has rapidly spread around the world, presenting a serious pandemic danger. The present study seeks to investigate the biological activity of phytocompounds produced from various medicinal plants, notably Barleria prionitis Linn, Bougainvillea (Nyctaginaceae), and Fig (Angeer), against the SARS-COV-2 major protease (Mpro) protein utilizing a molecular docking approach. Since it is necessary for viral transcription and replication, the SARS-COV-2 major protease (Mpro) protein of the corona virus is an alluring therapeutic target for SARS-CoV-2. The protein target and ligands were interacted with using SWISS Dock and Open Babel. The major protease (Mpro) protein's binding energy was lowest with the barlerinoside from the Barleria plant (G = -9.78 kcal/mol. Numerous phytochemicals had low binding energies with the primary protease protein (Mpro), suggesting that they could be more potent against the COVID-19 virus.

Abstract Background Hepatocellular carcinoma (HCC) is the most common primary liver malignancy. Phloretin (PH) possesses anticancer, antitumor, and hepatoprotective effects, however, the effects and potential mechanisms of phloretin remain elusive. Methods Five HCC cells were tested in vitro for sensitivity to PH, Sorafenib (Sor) or both and the apoptosis, signal transduction and phosphatase activity were analyzed. To validate the role of SHP-1, we used PTP inhibitor III and SHP-1 siRNA. Further, we used purified SHP-1 proteins or HCC cells expressing deletion N-SH2 domain or D61A point mutants to study the PH efficacy on SHP-1. The `in vivo studies were conducted using HepG2 and SK-Hep1 and Sor resistant HepG2SR and Huh7SR xenografts. Molecular docking was done with Swiss dock and Auto Dock Vina. Results PH inhibited cell growth and induced apoptosis in all HCC cells by upregulating SHP-1 expression and downregulating STAT3 expression and further inhibited pAKT/pERK signaling. PH activated SHP-1 by disruption of autoinhibition of SHP-1, leading to reduced p-STAT3Tyr705 level. PH induced apoptosis in two Sor-resistant cell lines and overcome STAT3, AKT, MAPK and VEGFR2 dependent Sor resistance in HCCs. PH potently inhibited tumor growth in both Sor-sensitive and Sor-resistant xenografts in vivo by impairing angiogenesis, cell proliferation and inducing apoptosis via targeting the SHP-1/STAT3 signaling pathway. Conclusion Our data suggest that PH inhibits STAT3 activity in Sor-sensitive and -resistant HCCs via SHP-1–mediated inhibition of STAT3 and AKT/mTOR/JAK2/VEGFR2 pathway. Our results clearly indicate that PH may be a potent reagent for hepatocellular carcinoma and a noveltargeted therapy for further clinical investigations. Graphical abstract

Aim: We aimed to reveal the function of celastrol in the treatment of ovarian cancer using network pharmacology and molecular docking.Background: Ovarian cancer is a growth of cells that forms in the ovaries. Celastrol is a useful bioactive compound derived from the root of the thunder god vine.Method: Celastrol and ovarian cancer targets were determined by analyzing datasets. Protein–protein interaction (PPI) networks were obtained with network pharmacology. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Molecular docking using SWISS-MODEL, CB-Dock and Discovery Studio was conducted. A methylthiazolyltetrazolium bromide (MTT) assay was performed to evaluate cell proliferation. Cell apoptosis and cell cycle were measured with a fluorescence assay. Reverse transcription PCR (RT-PCR) and Western blot were performed to measure the expression of core targets.Result: Celastrol possessed 29 potential targets, while ovarian cancer possessed 471 potential targets. The core PPI network contained 163 nodes and 4,483 edges. The biological processes identified in the GO analysis indicated that the targets were related with the cellular response to DNA damage stimulus, DNA recombination, and cell proliferation, among other processes. The KEGG analysis indicated that the pathways were related with the cell cycle, viral carcinogenesis, and MAPK signaling pathway, among others. The three core targets shared between the core PPI network and celastrol targets were MYC, CDC37, and FN1. Celastrol directly combined with the targets according to the results from CB-Dock and Discovery Studio. Celastrol inhibited ovarian cancer cell proliferation and promoted ovarian cancer cell apoptosis in a dose-dependent manner. RT-PCR and Western blot analyses showed that celastrol inhibited core target expression. In addition, celastrol also influenced the related inflammatory signaling pathways in ovarian cancer cells.Conclusion: Celastrol exerts effective antitumor activity toward ovarian cancer. Celastrol regulated cell proliferation, DNA repair and replication, apoptotic processes, and inflammatory responses in ovarian cancer cells.

Aim: To check the effect of mutation on the binding affinity of Starch branching enzyme II with maltopentaose substrate. Place and Duration of Study: Department of Bioinformatics, Centre for Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, between May 2022 and July 2022. Methodology: The wild type rice SBEIIb and mutated rice SBEIIb protein were modelled using SWISS MODEL and subjected to PROCHECK for validation of the modelled protein. These protein structures were docked with ligand maltopentaose using Auto dock vina of PyRx software. The docked structures were visualized in BIOVIA Discovery studio. Results: There was a decrease in binding affinity after mutating the protein at 2 of the maltopentaose binding sites (Y178A & F234A). The binding energy of wild type rice SBEIIb protein was -7.5kcal mol-1 whereas after mutation it decreased to -5.8 kcal mol-1. The number of hydrogen bonds also decreased from 8 to 4 respectively. Conclusion: Double mutation of binding site residues resulted in binding affinity as well as interactions. In silico analysis prior to wet lab experiments lead to rational choice of mutations that may lead to the production of rice grains with reduced amylopectin content.

Significance of the study: The present study has attempted to assess Bcl2 the efficacy of combination of the Nigella sativa and Cuscuta reflexa to target BCL-2 for anticancer treatment through computer aided drug designing approach.Insilico analysis is frequently used in physicochemical characterisation, the discovery and improvement of novel compounds with affinity to a target, and the elucidation of absorption, distribution, metabolism, excretion, and toxicity features. Aim: The aim of this study is to assess the efficacy of Nigella sativa and Cuscuta reflexa in targeting Bcl2-antiapoptotic protein in Oral Squamous Cell Carcinoma through Insilico analysis. Materials and Methods: The present study was designed to formulate a drug against Oral Squamous cell carcinoma against the target protein Bcl-2. Protein Database (PDB) was used to select and analyse the protein. Based on the literature search, the original molecules selected were thymoquinone, tannin pyrogallol, Cuscutin, kaempferol, nigellicine and the ligand structures were obtained ZINC15 database. Target protein structure was recognised through Protein sequence from PB (Protein Data Bank). Swiss ADME was used for assessing the properties of the molecules. Twenty new molecules were identified from zinc pharmer and docking was done for all the 20 using Swiss dock. Binding energy was assessed and compared with the original molecules.ZINC73690300 and ZINC73690304 had better binding energy than that of original molecules. Both molecules can be potential candidates for Bcl2 inhibition to prevent OSCC. Results: ZINC73690300 and ZINC73690304 had better binding energy than that of the original molecules. Both molecules can be potential candidates for Bcl-2 inhibition to prevent OSCC. Conclusion: The present study evaluated the binding energy and bioavailability of the combined extract, thus attempting to predict the target ligand binding between the compounds in OSCC before attempting in vitro studies.-

Due to the rapid growth of the COVID-19 pandemic and its outcomes, developing a remedy to fight the predicament is critical. So far, it has infected more than 214,468,601 million people and caused the death of 4,470,969 million people according to the August 27, 2021, World Health Organization's (WHO) report. Several studies have been published on both computational and wet-lab approaches to develop antivirals for COVID-19, although there has been no success yet. However, the wet-lab approach is laborious, expensive, and time-consuming, and computational techniques have screened the activity of bioactive compounds from different sources with less effort and cost. For this investigation, we screened the binding affinity of fungi-derived bioactive molecules toward the SARS coronavirus papain-like protease (PLpro) by using computational approaches. Studies showed that protease inhibitors can be very effective in controlling virus-induced infections. Additionally, fungi represent a vast source of bioactive molecules, which could be potentially used for antiviral therapy. Fifty fungi-derived bioactive compounds were investigated concerning SARS-CoV-2 PLpro by using Auto Dock 4.2.1, Gromacs 2018. 2, ADMET, Swiss-ADME, FAF-Drugs 4.023, pKCSM, and UCLA-DOE server. From the list of the screened bioactive compounds, Dihydroaltersolanol C, Anthraquinone, Nigbeauvin A, and Catechin were selected with the Auto-Dock results of −8.68, −7.52, −10.46, and −10.58 Kcal/mol, respectively, based on their binding affinity compared to the reference drug. We presented the drug likeliness, toxicity, carcinogenicity, and mutagenicity of all compounds using ADMET analysis. They interacted with the amino acid residues, Gly163, Trp106, Ser111, Asp164, and Cys270, through hydrogen bonds. The root-mean-square deviation (RMSD), root-mean-square fluctuations (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg) values revealed a stable interaction. From the overall analyses, we can conclude that Dihydroaltersolanol C, Anthraquinone, Nigbeauvin A, and Catechin are classified as promising candidates for PLpro, thus potentially useful in developing a medicine for COVID-19.

Aim The present study aimed to identify the potent 123-triazole derivatives for synthesis and also assess their anti-bacterial activity.Methodology In silico design of novel analogues was carried out for ten derivatives using Auto Dock Vina and compared with standard drug Ciprofloxacin. Swiss ADME software was used to analyze lsquoLipinski Rule of Fiversquo and drug likeness properties. Three derivatives which obeyed rule of five having desired physicochemical properties and highest docking score were synthesized PDB code 2K35. The synthesis was carried out in two step process to determine their antibacterial activity. The synthesized compounds were structurally elucidated using Fourier-transform infrared spectroscopy FTIR Nuclear Magnetic Resonance 1H NMR and Mass spectroscopy .Results Antibacterial activity of different compounds was observed by disc diffusion method against two organisms E. coli and Streptococcus. Among the tested compounds 4A showed significant antibacterial activity. Compounds 6A and 8A also exhibited appreciable antibacterial activity against E. coli while compound 6A showed appreciable antibacterial activity against Streptococcus.Conclusion According to data obtained from the present study piperazine incorporated triazole derivatives were found to possess effective antibacterial activity. Further modifications of triazole based compounds at different positions to generate new molecules with potent anti-tumor activities will be described in future.

Background: Ginseng (Panax ginseng) is a herb of medicinal and nutritional importance. Ginseng has been used since ancient times for the treatment of numerous ailments as it has many therapeutic properties. Several phytoconstituents are present in Panax ginseng that possess a variety of beneficial pharmacological properties. Objective: To explore the potential of phytoconstituents of Panax ginseng in the treatment of depression, a molecular modeling technique was utilized targeting monoamine oxidase-A (MAOA). Methods: A total of sixty-one phytoconstituents of ginseng were drawn with the help of ChemBioDraw Ultra 12.0 software and PDBs for MAO-A enzyme were retrieved from the RCSB PDB database. The prepared ligands were screened for MAO-A properties using the software Molegro Virtual Docker (MVD 2010.4.1.0). All the prepared ligands were evaluated for drug-likeliness properties using Swiss ADME. Result: Among the docking studies of 60 Ginseng phytochemicals including one standard, 15 phytoconstituents with the highest dock score and better binding interactions were selected further for absorption, distribution, metabolism and excretion (ADME) studies. Stachyose (-227.287, 17 interactions), Raffinose (-222.157, 14 interactions), and Ginsenoside Rg1 (-216.593, 10 interactions) were found to possess better interactions as compared to Clorgyline taken as a standard drug. Conclusion: Stachyose was found to be the most potent inhibitor of MAO-A enzyme under investigation and can be a potential lead molecule for the development of newer phytochemical-based treatment of depression.

Background: Alzheimer’s disease (AD), an irreversible complex neurodegenerative disorder, is most common type of dementia, with progressive loss of cholinergic neurons. Based on the multi- factorial etiology of Alzheimer’s disease, novel ligands strategy appears as up-coming approach for the development of newer molecules against AD. This study is envisaged to investigate anti-Alzheimer’s potential of 10 synthesized compounds. The screening of compounds (1-10) was carried out using in silico techniques. Methods: For in silico screening of physicochemical properties of compounds molinspiration property engine v.2018.03, Swiss ADME online web-server and pkCSM ADME were used. For pharmacodynamic prediction PASS software while toxicity profile of compounds were analyzed through ProTox-II online software. Simultaneously, molecular docking analysis was performed on mouse AChE enzyme (PDB ID:2JGE, obtained from RSCB PDB) using Auto Dock Tools 1.5.6. Results: Based on in silico studies, compound 9 and 10 have been found to have better drug likeness, LD50 value, and better anti-Alzheimer’s, nootropic activities. However, these compounds had poor blood brain barrier (BBB) permeability. Compound 4 and 9 were predicted with better docking score for AChE enzyme. Conclusion: The outcome of in silico studies have suggested, out of various substitutions at different positions of pyridoxine-carbamate, compound 9 have shown promising drug likeness, with better safety and efficacy profile for anti-Alzheimer’s activity. However, BBB permeability appears as one the major limitation of all these compounds. Further studies are required to confirm its biological activities.

Background: Alzheimer's disease (AD) is major cause of morbidity in world, affecting about 5.8 million and 4 million people in India. Current anti-AD treatments are limited in their usage. Objective: Some natural promising herbal drugs that might be utilised as an alternative treatment for AD have been reported by several researchers for their neuroprotective action. Based on this, we chose these flavonoids Curcumin, Quercetin, Bilobalide, Ferulic acid, Reservetrol and donepezil (conventional Acetylcholine esterase inhibitor) as ligands for molecular docking studies. Methods: The Molecular docking interactions studied between these components with Acetylcholine esterase, Butyrylcholine esterase, and tau protein by Auto dock software. Prediction of ADME properties were performed by Swiss ADME. Binding interactions of the ligands at target protein binding sites were examined using Discovery studio visualizer 2021. Results: The binding energy for quercetin in the active site of enzymes was -9.5 , -7.8 , -8.2 kcal/mol which was much greater than other flavonoids and comparable to standard drug donepezil binding energy -10.3, -7.5,-7.9 kcal/mol. Quercetin in combination with standard AChEs inhibitor, could be alternative treatment for AD. Conclusion: This work focuses on recognizing structural features and comparing selected flavonoids and conventional Acetylcholine esterase (AChEs) inhibitor for molecular docking with three primary targets of AD namely AChEs, Butyrylcholine esterase, and tau protein. This in silico study concluded that quercetin had significant docking interactions and good pharmacokinetic features, making potentially therapeutic candidates for the treatment of AD indicating future studies will be needed.