Journal articles on the topic 'CB-DOCK'
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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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Avezov, Hasan Tilloyevich, Baxtiyor Shukurulloevich Ganiyev, Gulyayra Qo`ldoshevna Xoliqova, Furqat G'ayrat o'g`li Salimov, and Ferangiz Sadilloevna Aslonova. "SIANUR KISLOTANING MOCHEVINA ALMASHINGAN HOSILALARINING ONLINE MOLEKULYAR DOKINGI VA PASS ANALIZI." Журнал химии товаров и народной медицины 1, no. 3 (July 26, 2022): 82–94. http://dx.doi.org/10.55475/jcgtm/vol1.iss3.2022.53.
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Ushbu maqolada CB-Dock va PASS onlayn prognozli dasturiy ta'minotidan foydalangan holda sianur kislotaning mochevina almashingan hosilalari molekulyar doking natijalari, shuningdek, biologik faollik nuqtai nazaridan ularni qo’llashning mumkin bo’lgan sohalari haqida ma’lumotlar keltirilgan.
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Liu, Yang, Maximilian Grimm, Wen-tao Dai, Mu-chun Hou, Zhi-Xiong Xiao, and Yang Cao. "CB-Dock: a web server for cavity detection-guided protein–ligand blind docking." Acta Pharmacologica Sinica 41, no. 1 (July 1, 2019): 138–44. http://dx.doi.org/10.1038/s41401-019-0228-6.
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De Zotti, R., V. Patussi, A. Fiorito, and F. Larese. "Sensitization to green coffee bean (GCB) and castor bean (CB) allergens among dock workers." International Archives of Occupational and Environmental Health 61, no. 1-2 (October 1988): 7–12. http://dx.doi.org/10.1007/bf00381601.
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Balansa, Walter, Lis C. Lukas, Frets J. Rieuwpassa, and Aprelia M. Tomasoa. "Aktivitas Antibakteri Sponge Agelas Nakamurai Terhadap Bakteri Gram Negative: Study In Vitro dan In Silico." Samakia : Jurnal Ilmu Perikanan 14, no. 1 (May 6, 2023): 76–84. http://dx.doi.org/10.35316/jsapi.v14i1.3012.
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Bakteri gram negatif tetap menjadi ancaman serius bagi akuakultur, ekonomi, dan kesehatan manusia. Ironisnya, sementara antibiotik yang efektif belum ditemukan, resistensi bakteri ini terhadap berbagai antibiotik meningkat dengan kecepatan yang mengkhawatirkan. Hal ini menunjukkan urgensi penemuan antibiotik baru, terutama antibiotik yang dapat menghambat replikasi enzim seperti DNA gyrase atau topoisomerase IV, yang saat ini menjadi target baru penemuan antibiotik. Tujuan dari penelitian ini adalah untuk mengetahui potensi antibakteri Agelas nakamurai terhadap A. hydrophila, A. salmonicida dan E. tarda menggunakan ekstrak spons (1, 10, dan 100) mg/mL dan tetrasiklin (1 mg/mL) sebagai kontrol positif dan memprediksi potensi antibakteri dari agelasine A-F (1-6) dan agelasidine A (7) dari A. nakamurai dari Kepulauan Sangihe terhadap protein topoisomerase IV melalui docking molekuler. Uji in vitro dilakukan dengan menggunakan metode Kirby Bauer dengan sedikit modifikasi dan studi in silico menggunakan CB-dock 2 dan Protein Ligand Interaction Profiler. Meskipun ekstrak menunjukkan aktivitas antibakteri yang lebih lemah terhadap A. hydrophila, A. salmonicida dan E. tarda dibandingkan tetrasiklin, molekul docking dengan CB-dock 2 menunjukkan bahwa agelasine A-F (1-6) dan agelasidin A (7) memiliki afinitas pengikatan yang lebih kuat (-7.1). hingga -8,6 kJ/mol) daripada tetrasiklin (10), ciprofloksasin (11) atau levofloksasin (12) (-6,6 hingga -8,3 kJ/mol). Docking molekuler pada agelasidin C (9) dan D (10) juga menunjukkan afinitas pengikatan yang kuat (-8,3 dan -8,8 kJ/mol) ke protein target 1S16 terutama akibat ikatan hidrogen dan interaksi hidrofobik. Secara kolektif, hasil ini menunjukkan potensi agelasidin A, C dan D sebagai modulator dari target antibiotik baru, enzim topoisomerase IV.
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Aung, Thet Htwe. "Proximicin A-C as prospective HER2-positive and negative breast cancer drugs: Molecular docking and in silico ADME modeling." IPS Journal of Molecular Docking Simulations 1, no. 1 (May 18, 2022): 1–11. http://dx.doi.org/10.54117/ijmds.v1i1.9.
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Breast cancer is the second leading cause of cancer-related death among women worldwide. Proximicin A-C are bioactive chemicals produced by the marine Verrucosispora strain, which have been shown to have potent cytostatic effect against human breast cancer [MCF 7]. HER2 (Human epidermal growth factor receptor 2) is a gene that has been linked to breast cancer development. The study’s goals are to (1) forecast the intensity of binding affinity and interactions between HER2 and proximicin A-C, and (2) analyze ADME characteristics of proximicin A-C (Absorption, Distribution, Metabolism, and Excretion). The CB-Dock web service was used to dock proximicin A-C and commonly used breast cancer medicines Neratinib (Nerlynx) and Talazoparib against HER2, and protein-ligand interaction findings were collected via the protein-ligand interaction profiler (PLP) web server. The SwissADME web server was used to investigate ADME properties of the substances. In terms of docking, proximicin A has a vina score of -8.6, proximicin B and C has a score of -10, Talazoparib has a vina score of -8.5, and Neratinib (Nerlynx) has a vina score of -10.2 on CB-Dock. This means that proximicin B and C bind to HER2 more strongly than proximicin A and Talazoparib. Furthermore, their high binding affinity is nearly equivalent to Neratinibs (Nerlynx). Talazoparib has a lower binding affinity for HER2 than proximicin A. With HER2, all three chemicals have a strong hydrogen bond and hydrophobic contact. SwissADME estimated that all three substances follow the Lipinski rule (RO5) and have a bioavailability score of 0.55. They don’t have any structural issue in medicinal chemistry (no alerts in PAINS and Brenk forecasts), and their synthetic accessibility scales range from 3 to 3.5. Only proximicin A, on the other hand, has the leadlikeness feature. All three drugs failed to cross the blood-brain barrier (BBB) in terms of pharmacokinetics. Proximicin A has a high absorption rate in the GI tract, whereas proximicin B-C has a low absorption rate in the GI tract (GI). Similarly, proximicin A is neither a P-gp substrate nor a CYP1A2, CYP2C19, CYP2C9, CYP2D6, or CYP3A4 inhibitor. Proximicin B-C, on the other hand, are P-gp substrates, and proximicin C is an inhibitor of all provided CYP enzymes, whilst proximicin B inhibits only three. Overall, proximicin A-C could be used as a possible breast cancer therapeutic candidate. Proximicin B-C will outperform proximicin A in terms of therapeutic efficacy. Proximicin A, on the other hand, will have better ADME qualities than Proximicin B-C. This study will provide the lead information for developing a new breast cancer medication with a good pharmacological profile.
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Sharma, Arun Dev, and Inderjeet Kaur. "Chemical Profile and in-silico Docking Studies on Bioactives from Essential Oil of Cymbopogan pendulus Targeting Penicillin Binding Proteins (PBPs) in Bacteria." Biology, Medicine, & Natural Product Chemistry 12, no. 1 (February 17, 2023): 225–32. http://dx.doi.org/10.14421/biomedich.2023.121.225-232.
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Antibiotic resistance in bacteria is the major concern worldwide. PBP (Penicillin binding proteins) have been cited as an appropriate target for therapeutic drug design. In the present study molecular docking followed by wet lab validation was designed to estimate the effect of potent bioactive molecules from Cymbopogan pendulus essential oil against PBP5 protein. GC-FID (gas chromatography with flame-ionization detection) based composition profile, and in-silico docking study was conducted by using CB-dock 2 analysis followed by 2D and 3D interactions. GC-FID revealed Limonene, Neral, Geranial, Linalool, Myrcene as major and minor compounds in Cymbopogan pendulus essential oil. The docking score indicated effective binding of ligands to PBP5. Interactions results indicated that, PBP5/ligand complexes form hydrogen and hydrophobic interactions. Wet lab study validated the anti-bacterial potential of oil against gram-positive and gram-negative bacteria. Therefore, essential oil from Cymbopogan pendulus essential oil may represent potential herbal treatment to mitigate bacterial infections.
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Dilshad, Erum, Muhammad Maaz, Suliman, and Naeem Mehmood Ashraf. "Identification of Anti-inflammatory Metabolites from Trigonella foenum-greacum using Computational Approaches." Current Trends in OMICS 2, no. 1 (June 28, 2022): 55–88. http://dx.doi.org/10.32350/cto.21.04.
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Human disease prevalence has increased as a result of modern lifestyles, stress, and toxic waste. Worldwide, researchers aim to discover therapeutic compounds which may cure and prevent the onset of diseases. So, this study was planned to discover potential anti-inflammatory metabolites from Trigonella foenum-graecum. It is an annual plant within the family Fabaceae. This plant is used as a spice throughout the world and has many beneficial medicinal effects. It is commonly grown in Pakistan, India, and some Middle Eastern countries. Ten bioactive compounds representative of all classes, namely alkaloid, flavonoid, phytic acid, 4-hydroxy isoleucine, sapogenin, quercetin, trigonelline, tricin, naringenin, and flavonol were selected. Molecular docking of these ligands was carried out against drug targets namely cyclooxygenase-2, Human Neutrophil Elastase (HNE), microsomal PGES-2, and tyrosinase by using CB Dock and AMDock software. Further refining by screening filters produced sapogenin as the lead compound. All the visualization analysis and interaction studies were performed using PyMol molecular visualization tool and Ligplot+. Celebrex was used as the standard for comparison. The comparison between sapogenin and Celebrex showed that the former is much more active than the standard drug. This is a novel finding. So, it might be explored further as a drug candidate to treat chronic inflammatory diseases in the future.
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Alavi, Mehran, M. R. Mozafari, Saba Ghaemi, Morahem Ashengroph, Fatemeh Hasanzadeh Davarani, and Mohammadreza Mohammadabadi. "Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study." Biomedicines 10, no. 12 (November 29, 2022): 3074. http://dx.doi.org/10.3390/biomedicines10123074.
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Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of −9.9 and −8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
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Ashraf, Huma, Erum Dilshad, Tayyaba Afsar, Ali Almajwal, Huma Shafique, and Suhail Razak. "Molecular Screening of Bioactive Compounds of Garlic for Therapeutic Effects against COVID-19." Biomedicines 11, no. 2 (February 20, 2023): 643. http://dx.doi.org/10.3390/biomedicines11020643.
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An outbreak of pneumonia occurred on December 2019 in Wuhan, China, which caused a serious public health emergency by spreading around the globe. Globally, natural products are being focused on more than synthetic ones. So, keeping that in view, the current study was conducted to discover potential antiviral compounds from Allium sativum. Twenty-five phytocompounds of this plant were selected from the literature and databases including 3-(Allylsulphinyl)-L-alanine, Allicin, Diallyl sulfide, Diallyl disulfide, Diallyl trisulfide, Glutathione, L-Cysteine, S-allyl-mercapto-glutathione, Quercetin, Myricetin, Thiocysteine, Gamma-glutamyl-Lcysteine, Gamma-glutamylallyl-cysteine, Fructan, Lauricacid, Linoleicacid, Allixin, Ajoene, Diazinon Kaempferol, Levamisole, Caffeicacid, Ethyl linoleate, Scutellarein, and S-allylcysteine methyl-ester. Virtual screening of these selected ligands was carried out against drug target 3CL protease by CB-dock. Pharmacokinetic and pharmacodynamic properties defined the final destiny of compounds as drug or non-drug molecules. The best five compounds screened were Allicin, Diallyl Sulfide, Diallyl Disulfide, Diallyl Trisulfide, Ajoene, and Levamisole, which showed themselves as hit compounds. Further refining by screening filters represented Levamisole as a lead compound. All the interaction visualization analysis studies were performed using the PyMol molecular visualization tool and LigPlot+. Conclusively, Levamisole was screened as a likely antiviral compound which might be a drug candidate to treat SARS-CoV-2 in the future. Nevertheless, further research needs to be carried out to study their potential medicinal use.
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Baig, Zunaira Ali, Amir Rashid, Ambreen Gul, Imran Raza, and Asifa Majeed. "Apoptosis in Human Papillomavirus-Induced Cervical Cancer Cells By Higher Doses of Ascorbic Acid." Pakistan Armed Forces Medical Journal 72, no. 4 (September 7, 2022): 1428–32. http://dx.doi.org/10.51253/pafmj.v72i4.8417.
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Objective: To assess the anti-cancer role of ascorbic acid using high doses against the cervical cancer cell line and to establish a cell culture facility in the laboratory.
Study Design: In Vitro Study.
Place and Duration of Study: Department of Biochemistry and Molecular Biology, Army Medical College, Rawalpindi Pakistan, from Aug 2014 to Jul 2015.
Methodology: HeLa cells were grown in Dulbecco’s modified eagle medium, and upon reaching confluency, cells were challenged with different doses of ascorbic acid. The MTT assay was employed to study the cytotoxic effects of increased doses of ascorbic acid on HeLa cells.
Results: An increasing dose of ascorbic acid was found to be cytotoxic toward HeLa cells, and its EC50 was found to be between 5-6µM. A high dose of ascorbic acid is selectively cytotoxic to HeLa cell lines of cervical cancer, which may imply the treatment of cervical cancer patients. NF- kB inducing kinase is a salient protein in TNFα-induced NF-kB activation. Ascorbate has been reported to inhibit that activation which has anti-apoptotic roles in tumour progression. CB-Dock was employed to propose the binding sites for NIK-Ascorbate interaction, which might be a therapeutic target for cancer cells.
Conclusion: The study concludes that high dose ascorbic acid is cytotoxic to cervical cancer cells HeLa and may have important implications in treating cervical cancer patients. Therapeutic intervention of this vitamin may contribute to suppressing cancer development.
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Lu, Shu-ting, Lu-lu Tang, Ling-han Zhou, Ying-tao Lai, Lan-xing Liu, and Yifan Duan. "Study on the Multitarget Mechanism and Active Compounds of Essential Oil from Artemisia argyi Treating Pressure Injuries Based on Network Pharmacology." Evidence-Based Complementary and Alternative Medicine 2022 (January 19, 2022): 1–15. http://dx.doi.org/10.1155/2022/1019289.
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In order to comprehensively explore multitarget mechanism and key active compounds of Artemisia argyi essential oil (AAEO) in the treatment of pressure injuries (PIs), we analyzed the biological functions and pathways involved in the intersection targets of AAEO and PIs based on network pharmacology, and the affinity of AAEO active compounds and core targets was verified by molecular docking finally. In our study, we first screened 54 effective components according to the relative content and biological activity. In total, 103 targets related to active compounds of AAEO and 2760 targets associated with PIs were obtained, respectively, and 50 key targets were overlapped by Venny 2.1.0. The construction of key targets-compounds network was achieved by the STRING database and Cytoscape 3.7.2 software. GO analysis from Matespace shows that GO results are mainly enriched in biological processes, including adrenergic receptor activity, neurotransmitter clearance, and neurotransmitter metabolic process. KEGG analysis by the David and Kobas website shows that the key targets can achieve the treatment on PIs through a pathway in cancer, PI3K-Akt signaling pathway, human immunodeficiency virus 1 infection, MAPK signaling pathway, Wnt signaling pathway, etc. In addition, molecular docking results from the CB-Dock server indicated that active compounds of AAEO had good activity docking with the first 10 key targets. In conclusion, the potential targets and regulatory molecular mechanisms of AAEO in the treatment of PIs were analyzed by network pharmacology and molecular docking. AAEO can cure PIs through the synergistic effect of multicomponent, multitarget, and multipathway, providing a theoretical basis and new direction for further study.
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Kumari, Uma, and Sudhanva Devaprasad Dixit. "NGS and Drug Development Pipeline for Alzheimers Disease." International Journal for Research in Applied Science and Engineering Technology 11, no. 7 (July 31, 2023): 2090–99. http://dx.doi.org/10.22214/ijraset.2023.55081.
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Abstract: Alzheimer's disease is a form of dementia characterized by the gradual and irreversible loss of cognitive abilities, primarily affecting memory, thinking, and behaviour.Globally, there are more than 50 million people that suffer from Alzheimer's.Alzheimer's disease, a complex and devastating neurodegenerative disorder, represents a profound challenge to modern neuroscience and medicine. Defined by the accumulation of abnormal protein aggregates, such as beta-amyloid plaques and tau tangles, within the brain, it inexorably disrupts essential neuronal connections and communication. This relentless deterioration leads to a gradual deterioration of cognitive functions, memory loss, and ultimately, a profound loss of independence for afflicted individuals. Unravelling the intricate molecular and cellular mechanisms underlying Alzheimer's remains an urgent scientific endeavour, offering hope for novel treatments and preventive strategies to confront this formidable adversary of the human brain. In this study, the variability of the human γ-secretase, 5FN5protein sequence was compared and evaluated with the reference sequence using MMDB, BLAST, and COBALT. RasMol was utilized to identify the domain and function of the human γ secretase for the analysis of structural properties. Molecular docking was performed to study the interaction of 5FN5 molecule and the associated ligandusing PyMOL. In the computer-aided drug designing approach, molecular docking was performed for 5FN5 protein, and CB-Dock was used to find optimized conformations between 5FN5 protein and E2012 drug, resulting in the minimum energy that bound to a particular protein. E2012 was found to be the accurate drug ligand for the binding site of gamma secretase with docking score of –9, acting as a modulator for 5FN5 protein.
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Naufal, Achmad Hanif, Regina Putri Virgirinia, and Fatchiyah Fatchiyah. "Molecular interaction of lavender (Lavandula angustifolia Mill) essential oil compounds as potential anxiolytic against α2δ subunit voltage gated calcium channel." Berkala Penelitian Hayati 29, no. 1 (December 19, 2022): 1–11. http://dx.doi.org/10.23869/bphjbr.29.1.20231.
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The effect of brain area connectivity caused by an imbalance of the glutamate neurotransmitter in the brains patients experiencing anxiety is determined by α2δ subunit calcium channel activity. Lavender (Lavandula angustifolia) has been investigated to have anxiolytic effects on in vitro studies by its modulation through GABA, NMDA, and serotonin receptors, especially in the amygdala and hippocampus. However, the molecular mechanism of Lavender small molecules to reduce anxiety through calcium channels remains unclear. This study aims to evaluate lavender essential oil compounds which are potentially anxiolytic through the in-silico approach as an inhibitor of the α2δ subunit VGCC. Compound tabulations were obtained from earlier studies and collected from Pubchem database, while the three-dimensional structure of α2δ the subunit was retrieved from RCSB PDB. The physicochemical properties of the compounds were analyzed by using SwissADME and pkCSM. Binding affinity screening and molecular interaction analysis were conducted through CB-Dock web server. From 32 compounds demonstrated for docking against α2δ VGCC, four of them including geranyl formate, neryl alcohol, and phellandral have most binding site similarities compared to pregabalin by pointing at Arg217. This residue was known to exerts the pharmacological action of pregabalin to reduce anxiety and pain. The binding affinity of the geranyl formate (-6,6 kcal/mol), neryl alcohol (-6,4 kcal/mol), and phellandral (-6,2 kcal/mol) were comparable to pregabalin (-6,8 kcal/mol). Molecular dynamic was indicated to predict conformational change of α2δ subunit after superimposed. Thus, current study was indicated that geranyl formate, neryl alcohol, and phellandral as lavender essential oil small molecules has potent beneficial function as anxiolytic potential candidate.
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Lv, Hao, Jiuxiang Wang, Yujun Zhu, and Ting Jiang. "Study on the Mechanism of Compound Kidney-Invigorating Granule for Osteoporosis based on Network Pharmacology and Experimental Verification." Evidence-Based Complementary and Alternative Medicine 2022 (January 4, 2022): 1–20. http://dx.doi.org/10.1155/2022/6453501.
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Background. This study used a combination of network pharmacology and experimental confirmation to clarify the mechanism of the compound kidney-invigorating granule (CKG) in treating osteoporosis (OP). Methods. The main bioactive compounds and corresponding targets of CKG were collected and screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Yet another Traditional Chinese Medicine (YaTCM), and UniProt databases. Disease targets of OP were summarized in GeneCards and the Comparative Toxicogenomics Database (CTD). Targets of CKG for OP were obtained by Venn diagram. The protein-protein interaction (PPI) network was constructed by the STRING database and then screened for hub genes through Cytoscape 3.7.2 software. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed and visualized by R software. Then, CB-Dock was used for molecular docking verification. Finally, we confirmed the antiosteoporosis effect of CKG through animal and cell experiments. Results. A total of 250 putative targets were obtained from 65 bioactive compounds in CKG. Among them, 140 targets were related to OP. Topological analysis of the PPI network yielded 23 hub genes. Enrichment analysis showed the targets of CKG in treating OP might concentrate on the MAPK signaling pathway, the TNF signaling pathway, the PI3K-Akt signaling pathway, etc. The results of molecular docking showed the bioactive components in CKG had good binding ability with the key targets. The experimental results showed that CKG-medicated serum had a promoting effect on proliferating hBMSCs, increasing the expression of AKT, PI3K, ERK1, and IkB in cells and decreasing the expression of IKK in cells. Conclusion. CKG has a complex of multicomponent, multitarget, and multipathway. This study lays the theoretical foundation for further in vitro and in vivo experimental studies and further expands the clinical applications of CKG.
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Tao, Yan-gu, Xiu-Fang Huang, Jun-yan Wang, Meng-ru Kang, Ling-jun Wang, and Shao-xiang Xian. "Exploring Molecular Mechanism of Huangqi in Treating Heart Failure Using Network Pharmacology." Evidence-Based Complementary and Alternative Medicine 2020 (April 23, 2020): 1–17. http://dx.doi.org/10.1155/2020/6473745.
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Heart failure (HF), a clinical syndrome with a high incidence due to various reasons, is the advanced stage of most cardiovascular diseases. Huangqi is an effective treatment for cardiovascular disease, which has multitarget, multipathway functions. Therefore, we used network pharmacology to explore the molecular mechanism of Huangqi in treating HF. In this study, 21 compounds of Huangqi, which involved 407 targets, were obtained and reconfirmed using TCMSP and PubChem databases. Moreover, we used Cytoscape 3.7.1 to construct compound-target network and screened the top 10 compounds. 378 targets related to HF were obtained from CTD and GeneCards databases and HF-target network was constructed by Cytoscape 3.7.1. The 46 overlapping targets of HF and Huangqi were gotten by Draw Venn Diagram. STRING database was used to set up a protein-protein interaction network, and MCODE module and the top 5 targets with the highest degree for overlapping targets were obtained. GO analysis performed by Metascape indicated that the overlapping targets were mainly enriched in blood vessel development, reactive oxygen species metabolic process, response to wounding, blood circulation, and so on. KEGG analysis analyzed by ClueGO revealed that overlapping targets were mainly enriched in AGE-RAGE signaling pathway in diabetic complications, IL-17 signaling pathway, HIF-1 signaling pathway, c-type lectin receptor signaling pathway, relaxin signaling pathway, and so on. Finally, molecular docking showed that top 10 compounds of Huangqi also had good binding activities to important targets compared with digoxin, which was carried out in CB-Dock molecular docking server. In conclusion, Huangqi has potential effect on regulating overlapping targets and GE-RAGE signaling pathway in diabetic complications, IL-17 signaling pathway, HIF-1 signaling pathway, and so on to be a latent multitarget, multipathway treatment for HF.
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Bai, Yunpeng, Guangwen Wang, Jinhua Lan, Ping Wu, Guowu Liang, Jinhui Huang, Zheng Wu, Yirong Wang, and Chunbo Chen. "Mass Spectrometric Behavior and Molecular Mechanisms of Fermented Deoxyanthocyanidins to Alleviate Ulcerative Colitis Based on Network Pharmacology." International Journal of Analytical Chemistry 2022 (March 21, 2022): 1–12. http://dx.doi.org/10.1155/2022/9293208.
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Aims. Ulcerative colitis (UC) is a type of chronic idiopathic inflammatory bowel disease with a multifactorial pathogenesis and limited treatment options. The aim of the present study is to investigate the hydrogen deuterium exchange mass spectrometry (HDX-MS) behaviors of fermented deoxyanthocyanidins and their molecular mechanisms to alleviate UC by using quantum chemistry and network pharmacology. Methods. Tandem MS indicated at least two fragmentation pathways through which deuterated vinylphenol-deoxyanthocyanidins could generate different product ions. Quantum calculations were conducted to determine the transition states of the relevant molecules and analyze their optimized configuration, vibrational characteristics, intrinsic reaction coordinates, and corresponding energies. The potential targets of deoxyanthocyanidins in UC were screened from a public database. The R package was used for Gene Ontology (GO) and KEGG pathway analyses, and the protein–protein interactions (PPIs) of the targets were assessed using Search Tool for the Retrieval of Interacting Genes (STRING). Finally, molecular docking was implemented to analyze the binding energies and action modes of the target compounds through the online tool CB-Dock. Results. Quantum calculations indicated two potential fragmentation pathways involving the six-membered ring and dihydrogen cooperative transfer reactions of the vinylphenol-deoxyanthocyanidins. A total of 146 and 57 intersecting targets of natural and fermented deoxyanthocyanidins were separately screened out from the UC database and significant overlaps in GO terms and KEGG pathways were noted. Three shared hub targets (i.e., PTGS2, ESR1, and EGFR) were selected from the two PPI networks by STRING. Molecular docking results showed that all deoxyanthocyanidins have a good binding potential with the hub target proteins and that fermented deoxyanthocyanidins have lower binding energies and more stable conformations compared with natural ones. Conclusions. Deoxyanthocyanidins may provide anti-inflammatory, antioxidative, and immune system regulatory effects to suppress UC progression. It is proposed for the first time that fermentation of deoxyanthocyanidins can help adjust the structure of the intestinal microbiota and increase the biological activity of the natural compounds against UC. Furthermore, HDX-MS is a helpful strategy to analyze deoxyanthocyanidin metabolites with unknown structures.
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Zhuang, Yanping, Xuan Zhang, Simin Luo, Fangzhi Wei, Yitian Song, Guiling Lin, Minghui Yao, and Aimin Gong. "Exploring the Molecular Mechanism of Zhi Bai Di Huang Wan in the Treatment of Systemic Lupus Erythematosus Based on Network Pharmacology and Molecular Docking Techniques." Processes 10, no. 10 (September 21, 2022): 1914. http://dx.doi.org/10.3390/pr10101914.
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Objective: To investigate the molecular mechanism and simulated validation of Zhi Bai Di Huang Pill (ZBDHP) for the treatment of systemic lupus erythematosus (SLE) using network pharmacology and molecular docking techniques. Methods: The active ingredients of ZBDHP were obtained through the TCMSP database and the Canonical SMILES of the active ingredients were queried through Pubchem. The targets of the active ingredients were predicted in the SwissTarget database based on the SMILES. The SLE-related disease targets were obtained through the GeneCards, OMIM and DisGenets databases, and the intersection targets of ZBDHP and SLE were obtained using the Venny 2.1.0 online platform. Intersection targets build a visual protein interaction network (PPI) through the STRING database, and the core targets were identified by network topology analysis. GO analysis and KEGG pathway enrichment analysis of the intersecting targets were performed using the DAVID database. Finally, the molecular docking of the first four active ingredients and the first four core target genes were verified by Pubchem, the PDB database and CB-Dock online molecular docking technology. Results: ZBDHP screened 91 potential active ingredients and 816 potential targets. Among them, 141 genes were intersected by ZBDHP and SLE. The network topology analysis showed that the main active ingredients were Hydroxygenkwanin, Alisol B, asperglaucide, Cerevisterol, etc., and the key target genes were TNF, AKT1, EGFR, STAT3, etc. GO and KEGG enrichment analysis showed that common targets interfere with biological processes or molecular functions such as signal transduction protein phosphorylation, inflammatory response, transmembrane receptor protein tyrosine kinase activity, etc., through multiple signaling pathways, such as pathways in cancer, Kaposi sarcoma-associated herpesvirus infection, the PI3K-Akt signaling pathway, lipid and atherosclerosis, hepatitis B, etc. Molecular docking results showed that the active components of ZBDHP have good binding activity to the core targets of SLE. Conclusions: This study reveals that the ZBDHP treatment of SLE is a complex mechanistic process with multi-components, multi-targets and multi-pathways, and it may play a therapeutic role in SLE by inhibiting the production, proliferation and apoptosis of inflammatory factors. In conclusion, the present study provides a theoretical basis for further research on ZBDHP.
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Wang, Xuan, Qiong Liu, Sisi Wu, Nana Xu, Hua Li, and Aihua Feng. "Identifying the Effect of Celastrol Against Ovarian Cancer With Network Pharmacology and In Vitro Experiments." Frontiers in Pharmacology 13 (March 18, 2022). http://dx.doi.org/10.3389/fphar.2022.739478.
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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.
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"Blind docking of 4-Amino-7-Chloroquinoline analogs as potential dengue virus protease inhibitor using CB Dock a web server." Indian Journal of Biochemistry and Biophysics, 2023. http://dx.doi.org/10.56042/ijbb.v60i1.64604.
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Rahmon, Kanmodi, Habeeb Bankole, Oddiri Regina, Arowosegbe Michael, Alabi Ridwan, Ahmodu Oladejo, AbdulRasheed Bilal, Muritala Rauf, and Rahmon Saheed. "Repurposing Antipsychotic Agents Against Targets Of Angiogenesis Pathways For Cancer Therapy: An In-Silico Approach." Current Drug Discovery Technologies 20 (June 6, 2023). http://dx.doi.org/10.2174/1570163820666230606113158.
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Background: Antipsychotics interfere with virtually all hallmarks of cancer, including angiogenesis. Vascular endothelial growth factor receptors (VEGFRs) and platelet-derived growth receptors (PDGFRs) play crucial roles in angiogenesis and represent targets of many anti-cancer agents. We assessed and compared the binding effects of antipsychotics and receptor tyrosine kinase inhibitors (RTKIs) on VEGFR2 and PDGFRα. Methods: FDA-approved antipsychotics and RTKIs were retrieved from DrugBank. VEGFR2 and PDGFRα structures were obtained from Protein Data Bank and loaded on Biovia Discovery Studio software to remove nonstandard molecules. Molecular docking was carried out using PyRx and CB-Dock to determine the binding affinities of protein-ligand complexes. Results: Risperidone exerted the highest binding effect on PDGFRα (-11.0 Kcal/mol) as compared to other antipsychotic drugs and RTKIs. Risperidone also demonstrated a stronger binding effect on VEGFR2 (-9.6 Kcal/mol) than the RTKIs, pazopanib (-8.7 Kcal/mol), axitinib (-9.3 Kcal/mol), vandetanib (-8.3 Kcal/mol), lenvatinib ( -7.6 Kcal/mol) and sunitinib (-8.3 Kcal/mol). Sorafenib (an RTKI), however, exhibited the highest VEGFR2 binding affinity of 11.7 Kcal/mol. Conclusion: Risperidone's superior binding affinity with PDGFRα when compared to all reference RTKIs and antipsychotic drugs, as well as its stronger binding effect on VEGFR2 over the RTKIs, sunitinib, pazopanib, axitinib, vandetanib, and lenvatinib, imply that it could be repurposed to inhibit angiogenic pathways and subjected to pre-clinical and clinical trials for cancer therapy.
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Oflaz, Ofcan, Hatice Mergen, and Tülin Demir. "Researching of resistance to etravirine in some HIV-1 low-level viremia strains by in-silico methods." Turkish Journal of Biochemistry, August 25, 2023. http://dx.doi.org/10.1515/tjb-2023-0166.
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Abstract Objectives Human immunodeficiency virus (HIV) is a significant infection that attacks immune system cells and integrates its genetic material into host cells. Left untreated, it leads to acquired immunodeficiency syndrome (AIDS). Antiretroviral therapy (ART) is used to control HIV infection. Etravirine (ETR) is an important non-nucleoside reverse transcriptase inhibitor (NNRTI) utilized in the treatment of HIV. Low-level viremia (LLW) is a serious clinical condition, and the underlying mechanisms remain incompletely understood. The aim of our study is to analyze and elucidate the resistance status of Lys104Gln, Lys102Gln, Lys101Arg-Lys104Arg, Ser191Phe, Ile94Leu-Lys104Arg, Lys104Glu-His235Leu, Ala98Ser and Val179Ile mutations using in-silico methods, which are identified as low-level viremic strains, because their resistance status to ETR is unknown. Methods Homology modeling was performed using the Swiss Model program. Molecular docking of ETR with the reverse transcriptase (RT) enzyme was conducted using the CB-Dock program developed by AutoDock Vina. Protein-ligand interaction analysis was carried out using the protein-ligand interaction profiler (PLIP). Results A98S and V179I mutations altered the physicochemical properties of the region, resulting in changes to the conformational structure of the NNRTI hydrophobic pocket compared to the wild-type and consequently decreased docking scores. Conclusions Based on the evaluation of literature data and in-silico analyses, it is believed that A98S and V179I mutations may alter the conformational structure of the hydrophobic pocket where ETR binds, potentially resulting in low-level resistance against ETR.
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Das, Via, Destiny Pinto, Tejasvi Hariharan, Tanusree Banerjee, Riya Ubale, Avi Uppalapati, and Gayathri Renganathan. "A Comprehensive Modeling of Bioenhancers Docked to Transport Proteins to Enhance Bioavailability." Journal of Student Research 11, no. 4 (November 30, 2022). http://dx.doi.org/10.47611/jsrhs.v11i4.3727.
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With pharmaceutical availability being a pertinent issue in modern medicine, the ability of bioenhancers to increase the bioavailability of a drug, thereby reducing the required dosage, can be critical for reducing treatment costs. Flavonoids, one form of bioenhancers, are metabolites that increase the availability through inhibition of key proteins in gut epithelial cells and transport proteins. Bioenhancers have the potential to inhibit proteins that limit absorption, thus increasing the amount of a target drug that can enter systemic circulation, increasing bioavailability. P-glycoprotein (P-gp) is one of the membrane transport proteins whose function is to transport drugs in and out of the cell. Human serum albumin (HSA), the most abundant protein in the human plasma, is a protein that serves to transport several signals and other compounds throughout the circulatory system. This study assessed the binding of various bioenhancers (piperine, quercetin, capsaicin, naringin, genistein, lysergol, sinomenine, tangeretin) to various forms of P-gp, HSA and ABC transporters to improve drug bioavailability. We hypothesized that the bioenhancers would bind to these transport proteins, thereby inhibiting them and increasing bioavailability.An examination of the geometric shape complementarity scores in PatchDock and the binding affinities (ΔG kcal/mol) from three other web servers (Webina, DockThor, CB-Dock) showed that naringin produces the most optimal binding scores overall. Given the promising optimal binding scores, the data provides critical insight into administering bioenhancers with drugs to improve bioavailability, as well as suggesting that naringin may be a valuable compound to conduct further tests in vitro and in vivo.
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Yan, Zijun, Liangjing Xia, Xingmeng Xu, Bingsuo Ma, Xiaoyan Yuan, Kun Yang, Kexin Li, Xianwen Ye, Liangming Zhang, and Tong Chen. "Exploring calcium channel blocker as a candidate drug for Pseudomonas aeruginosa through network pharmacology and experimental validation." Chemical Biology & Drug Design, August 20, 2023. http://dx.doi.org/10.1111/cbdd.14322.
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AbstractCalcium channel blocker (CCB) is known to possess antibacterial effects. We aimed to apply network pharmacology (docking and protein–protein interaction [PPI] analyses) to predict the potential targets and mechanisms of CCB against Pseudomonas aeruginosa (PA) as well as to verify the effect of these drugs. The chemical structures of three CCBs were obtained through the Drug Bank platform. The potential channel proteins, efflux pump proteins and ion channel proteins of CCB against bacteria were derived from the literature. These proteins were collected through the PDB and Uniprot platform. The binding mode of the docking complexes was simulated by the CB‐Dock platform and Discovery Studio 2019 Client software. The PPI network was constructed by the String platform and Cytoscape 3.8.2 platform. GO was explained by the PANTHER platform. The pathway diagram was drawn with the Pathway Builder Tool 2.0 software. The inhibitory effect of CCB on PA was verified through antibacterial experiments. Finally, 76 proteins were obtained: the iron channel protein of PA demonstrated a good docking relationship with all three CCBs, and the optimum binding energy was approximately −9.0 kcal/mol. GO analysis (biological process [BP], cellular component [CC], and molecular function [MF]) of protein genes showed a good docking relationship (optimum binding energy <−8.0 kcal/mol). The MF annotation results indicated that the target of CCB may be present on the PA membrane protein. The ion channel protein PPI enrichment p‐value was 6.65e‐08, and PfeA showed the strongest correlation. The experimental results suggested that CCB could inhibit the growth of PA. CCB might be an effective and interesting antimicrobial treatment strategy as CCB can potentially inhibit the growth of PA.
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Hasan, Tarique N., Syed S. Naqvi, Mati Ur Rehman, Rooh Ullah, Muhammad Ammad, Narmeen Arshad, Qurat Ul Ain, Shabana Perween, and Arif Hussain. "Ginger ring compounds as an inhibitor of spike binding protein of alpha, beta, gamma and delta variants of SARS-CoV-2: An in-silico study." Narra J 3, no. 1 (February 13, 2023). http://dx.doi.org/10.52225/narra.v3i1.98.
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The available drugs against coronavirus disease 2019 (COVOD-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are limited. This study aimed to identify ginger-derived compounds that might neutralize SARS-CoV-2 and prevent its entry into host cells. Ring compounds of ginger were screened against spike (S) protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The S protein FASTA sequence was retrieved from Global Initiative on Sharing Avian Influenza Data(GISAID) and converted into “.pdb” format using Open Babel tool. A total of 306 compounds were identified from ginger through food and phyto-databases. Out of those, 38 ring compounds were subjected to docking analysis using CB Dock online program which implies AutoDock Vina for docking. The Vina score was recorded, which reflects the affinity between ligands and receptors. Further, the Protein Ligand Interaction Profiler (PLIP) program for detecting the type of interaction between ligand-receptor was used. SwissADME was used to compute druglikeness parameters and pharmacokinetics characteristics. Furthermore, energy minimization was performed by using Swiss PDB Viewer (SPDBV) and energy after minimization was recorded. Molecular dynamic simulation was performed to find the stability of protein-ligand complex and root-mean-square deviation (RMSD) as well as root-mean-square fluctuation (RMSF) were calculated and recorded by using myPresto v5.0. Our study suggested that 17 out of 38 ring compounds of ginger were very likely to bind the S protein of SARS-CoV-2. Seventeen out of 38 ring compounds showed high affinity of binding with S protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The RMSD showed the stability of the complex was parallel to the S protein monomer. These computer-aided predictions give an insight into the possibility of ginger ring compounds as potential anti-SARS-CoV-2 worthy of in vitro investigations.
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TEJASWINI, ACHYUTUNI VENKATA NAGA, and RAMESH MALOTHU. "EVALUATION OF STRUCTURAL, MOLECULAR INTERACTION AND SIMULATION STUDY OF L-ASPARAGINASE OF Streptomyces koyangensis." Journal of Biochemistry International, March 14, 2022, 1–13. http://dx.doi.org/10.56557/jobi/2022/v9i27482.
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A vital step in drug discovery is structural and interaction assessment. L-asparaginase is a highly used compound in various treatment regimens which includes combinational therapies. The application is not only limited to treating Acute lymphoblastic leukemia, where it is also found effective for myeloid leukemia and canine lymphoma. The study details about L-asparaginase of Streptomyces koyangensis (WP_203215894). Structural insights are obtained by evaluation with GalaxyTBM. The constructed 3D-model is based on L-asparaginase models belonging to Escherichia coli, Wolinella succinogenes and Helicobacter pylori. The Ramachandran assessment corresponds to 91.4% of residues in the favourable region while ProSA infers to -8.9 Z-score. Further, QMEAN4 score of -0.46, 92.903 ERRAT score as well as 100% of residues in agreement with Verify3D theory describe the quality of the protein to be good and acceptable. The protein is identified to be secreted in the cytoplasm as per subsequent CELLO version2.5. Docking studies involving L-asparaginase (WP_203215894) molecule with L-asparagine resulted in the lowest energy of -4.5 kcal/mol along with prominent active sites recognized by PyRx. Similar prediction in addition to -4.6 and -4.8 kcal/mol is also resulted by CB-Dock. Further, the binding conformation referring to affinity of -4.5 kcal/mol is also supported by the interpretation of GalaxySite with identification of the same residues involved in ligand interaction. High values of affinity correspond to the analysis by SwissDock referring to -9.42 kcal/mol. The RMSF plot generated as part of protein flexibility analysis by CABS flex 2.0 depicted varied fluctuations however, the crucial residues interacting with the ligand are computed to have RMSF value < 2 represents rigidity. The therapeutic effectiveness of the enzyme has created interest in terms of tracing prospective sources and conducting computational analysis. The anticipated structure of WP_203215894 and derived assumptions are helpful and contribute valuable information for future in-vitro findings on L-asparaginase.
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Dharmasiri B.D.H.N., Senanayake G., Perera P., Halmillawewa A., and Attanayake R.N. "Evaluation of Lignin Degrading Ability and In-silico Analysis and Molecular Docking of Laccase of Schizophyllum commune with Lignin." Proceedings of International Forestry and Environment Symposium 26 (June 7, 2022). http://dx.doi.org/10.31357/fesympo.v26.5750.
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White-rot fungi have a unique and strong ability to degrade lignin, the most abundant and the strongest natural polymer on earth. The ligninolytic enzymes of these fungi comprise of three groups of oxidative extracellular enzymes mainly, lignin peroxidase (LiP), manganese dependent peroxidase (MnP) and laccase. Fungal laccases are considered to be directly involved with the degradation of lignin. Due to the broad substrate specificity and unique ability of biodegradation, fungal laccases have a great value in industrial and biotechnological applications like bioremediation, detoxification of industrial dyes and treatment of other pollutants. The objectives of this study was to evaluate the lignin degradation ability and laccase producing ability of selected fungal isolates originated from decaying hardwoods of Dimbulagala forest reserve, Sri Lanka and to predict the three-dimensional (3D) structure of laccase from Schizophyllum commune and its binding to lignin using in silicohomology modeling and molecular docking. Ten fungal isolates originated from decaying hardwoods were screened for the lignin degradation ability by using lignin amended malt extract plate assay and laccase producing ability by using guaiacol amended PDA plates. Seven isolates showed lignin degradation ability and five of them were laccase producers. Since S. commune could produce laccase, degrade lignin and laccase protein sequence is available, it was subjected to homology modeling. Homologous templates were identified using BLASTP across Protein Data Bank from NCBI. Laccase from Cerrena sp. was selected as the template for 3D model building of laccase from S. commune using Modeller 10.1. The quality of resulted 3D model of the protein was verified by its energy and stereochemical properties. The unstable regions were selected and remodeled by loop modelling using ModLoop web server. The results of evaluation of the remodeled structure by stereochemical quality and energy was found to be improved and showed that predicted model was of good quality due to the presence of maximum residues in the favored region. Later CB-Dock server was used to perform molecular docking studies using lignin model compounds. The amino acid residues of modeled laccase of S. commune in contact with the lignin based model compounds were identified. These findings help uncovering the lignin degradation mechanisms by S. communelaccases and are useful in biofuel production and bioremediation.
Keywords: Laccase, Homology modeling, Molecular docking, LigninAcknowledgement: Authors acknowledge the TWAS research grant (18-020 RG/BIO/AS_I), ICGEB research grant (CRP/LKA18-03) and NSF Sri Lanka (RG/2019/BT/03)