Relevant bibliographies by topics / SWISS DOCK

Academic literature on the topic 'SWISS DOCK'

Author: Grafiati
Published: 26 October 2023

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Journal articles on the topic "SWISS DOCK"

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Begum, Arifa, Shaheen Begum, Prasad Kvsrg, and Bharathi K. "IN SILICO STUDIES ON FUNCTIONALIZED AZAGLYCINE DERIVATIVES CONTAINING 2, 4-THIAZOLIDINEDIONE SCAFFOLD ON MULTIPLE TARGETS." International Journal of Pharmacy and Pharmaceutical Sciences 9, no. 8 (August 1, 2017): 209. http://dx.doi.org/10.22159/ijpps.2017v9i8.19835.

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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.
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2

Pandey, Pratibha, Fahad Khan, Kiran Yadav, Kartikey Singh, Akhlakur Rehman, Avijit Mazumder, and Minhaj Ahmad Khan. "Screen natural terpenoids to identify potential Jab1 inhibitors for treating breast cancer." Trends in Immunotherapy 7, no. 1 (June 29, 2023): 2055. http://dx.doi.org/10.24294/ti.v7.i1.2055.

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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.
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Jamkhedkar, Suruchi, Anakha P. Nair, Kishori R. Hirode, Mayuri D. Chavan, Mili P. Jain, and Prachi P. Majumdar. "IN SILICO ANALYSIS OF PHYTOCHEMICALS FROM VARIOUS PLANT SOURCES AS DRUG CANDIDATES AGAINST LIFE-THREATENING DISEASES." Indian Drugs 60, no. 05 (May 28, 2023): 89–101. http://dx.doi.org/10.53879/id.60.05.13290.

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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.
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4

Nagarajan, Kandasamy, Parul Grover, Roma Ghai, Ayushi Teharia, Sanjeev Chauhan, and Jagannath Sahoo. "In vitro antioxidant potency of some smaller chain glycopeptides with the prediction of IC50 values." International Journal of Pharmacology and Toxicology 4, no. 2 (July 19, 2016): 127. http://dx.doi.org/10.14419/ijpt.v4i2.6298.

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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.
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Purohit, Deepika, Vandana Saini, Sanjiv Kumar, Ajit Kumar, and Balasubramanian Narasimhan. "Three-dimensional Quantitative Structure-activity Relationship (3DQSAR) and Molecular Docking Study of 2-((pyridin-3-yloxy)methyl) Piperazines as α7 Nicotinic Acetylcholine Receptor Modulators for the Treatment of Inflammatory Disorders." Mini-Reviews in Medicinal Chemistry 20, no. 11 (July 17, 2020): 1031–41. http://dx.doi.org/10.2174/1389557519666190904151227.

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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.
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Inas Osman Khojali and Mohammed Yousif Mohammed. "Bisabolene compound extracted from cassia fistula and docked as antioxidant and vitamin E alternative predicted drug design." GSC Advanced Research and Reviews 15, no. 1 (April 30, 2023): 069–75. http://dx.doi.org/10.30574/gscarr.2023.15.1.0111.

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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.
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7

Jadhav, Sagar Ashok, Payal Chavan, Supriya Suresh Shete, Dipti Shantisagar Patil, Saroj Dyandev Kolekar, Godfrey Rudolph Mathews, Dipak Babaso Bhingardev, and Pravin Kondiba Pawar. "In Silico ADMET and Docking Study of Selected Drug Used in Therapy of COVID-19." Journal of Pharmaceutical Technology, Research and Management 10, no. 1 (May 7, 2022): 47–73. http://dx.doi.org/10.15415/jptrm.2022.101006.

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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.
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8

Kumar, Tushar. "Molecular Docking Studies of Possible Treatment of Diabetes using Vasicine against Islet Amyloid Polypeptide." International Journal for Research in Applied Science and Engineering Technology 9, no. VI (June 30, 2021): 4202–9. http://dx.doi.org/10.22214/ijraset.2021.35984.

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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.
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Patil, Khushabu, Mahesh Nemade, Anjali Bedse, Piyush Bedse, Rakesh Ranjan, Harshal Tare, and Manish Bedse. "Virtual Screening, Molecular Docking, and ADMET Analysis of Flavonoids as a Potential Pi3k Inhibitor for Cancer Treatment." INTERNATIONAL JOURNAL OF DRUG DELIVERY TECHNOLOGY 13, no. 03 (September 25, 2023): 966–70. http://dx.doi.org/10.25258/ijddt.13.3.31.

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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.
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Chatterjee, Deepyan. "Understanding the Exacerbating Role of the Metalloproteinase Meprin during AKI, an In Silico Approach." International Letters of Natural Sciences 57 (August 2016): 18–25. http://dx.doi.org/10.18052/www.scipress.com/ilns.57.18.

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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.
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Dissertations / Theses on the topic "SWISS DOCK"

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GARG, YAMI. "REGULATION OF HYPOXIA INDUCIBLE FACTORS VIA HISTONE DEACETYLASE 3 INHIBITOR DRUGS AND A COMPARISON BETWEEN THEIR INTERACTIONS." Thesis, 2022. http://dspace.dtu.ac.in:8080/jspui/handle/repository/19033.

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Hypoxia is a condition of impaired oxygen levels in the body. This cellular response is mediated by Hypoxia-Inducible Factors (HIF), where the levels of HIF-1 are increased. This article is concerned with the cross-talk of Wnt signaling, HIF-1 α, Ubiquitin Proteasome System, and Histone Deacetylase 3 using bioinformatics softwares and databases that are an application of computer science and biology. PLMD, AutoDock, SwissDock, Swiss ADME, and Open Babel are various computational applications used under the study. It has been known that Wnt-signaling is regulated by HIF-1 in neuronal stem cells. Futhermore, high HIF-1α increases VEGF levels that lead to abnormal pathological angiogenesis, triggering the release of TGFs which leads to the accumulation of AβPP and secretion of neurotoxic peptides. This research refers to a study where valproic acid, an HDAC has been known to restore the functions of NEP and loss of the memory that had been caused by prenatal hypoxia in an adult human neuroblastoma cell line. Moreover, the other drugs,i.e. vorinostat, pracinostat, entinostat, and mocetinostat, are known to inhibit Histone deacetylase 3 activitieswere analysed using blind docking. These drugs are primarily involved in treating different types of advanced cancers like breast cancer, lymphoma, acute myelogenous leukemia, T-cell lymphoma etc. Therefore, under this study, the interaction between HIF-1α and HDAC 3 has been analyzed using PPI Network Analysis followed by molecular docking of HDAC 3 and the drugs under comparison. The results have shown Valproic acid is involved in treating neurological disorders previously but mocetinostat shows better inhibition against HDAC 3, and thus HIF-1α. Hence, these drugs under study can be used as a putative drug in the treatment of Alzheimer’s disease. The findings direct future prospects towards laboratory experiments between valproic acid, vorinostat, pracinostat, entinostat, and mocetinostat, and its inhibitory effect on HDAC 3 to prevent Alzheimer’s disease.
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Books on the topic "SWISS DOCK"

1

Schön ist doch das Leben. Biographie in Briefen. Aufbau-Verlag, 2001.

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Über Geld schreibt man doch!: Eine Anthologie. Zytglogge AG, 2011.

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