Consensus scoring-based virtual screening and molecular dynamics simulation of some TNF-alpha inhibitors

Informatics in Medicine Unlocked - Tập 28 - Trang 100833 - 2022
Ibrahim Damilare Boyenle1, Temitope Isaac Adelusi1, Abdeen Tunde Ogunlana1, Rofiat Adeyemi Oluwabusola2, Najahtulahi Opeyemi Ibrahim3, Ajao Tolulope1, Ogundepo Sunday Okikiola4, Bamigbade Lukman Adetunji5, Ibraheem Omotayo Abioye6, Abdul-Quddus Kehinde Oyedele1,2
1Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
2Nigerian Institute of Medical Research, Nigeria
3Federal Institute of Research, Oshodi, Nigeria
4Federal Medical Centre, Keffi, Nigeria
5Emirate College of Health Sciences and Technology, Kano, Nigeria
6Department of Anatomy, Ladoke Akintola University of Technology, Ogbomoso, Nigeria

Tài liệu tham khảo

Ndayisaba, 2019, TNFα inhibitors as targets for protective therapies in MSA: a viewpoint, J Neuroinflammation, 16, 80, 10.1186/s12974-019-1477-5 Lu, 2015, The TNFα converting enzyme (TACE) from ayu (Plecoglossus altivelis) exhibits TNFα shedding activity, Mol Immunol, 63, 497, 10.1016/j.molimm.2014.10.010 Zhao, 2001, Pulmonary hypoplasia in mice lacking tumor necrosis factor-alpha converting enzyme indicates an indispensable role for cell surface protein shedding during embryonic lung branching morphogenesis, Dev Biol, 232, 204, 10.1006/dbio.2001.0176 Yoda, 2013, Systemic overexpression of TNFα-converting enzyme does not lead to enhanced shedding activity in vivo, PLoS One, 8, e54412, 10.1371/journal.pone.0054412 Ribeiro, 2019, Tumor necrosis factor alpha (TNF-α) and its soluble receptors are associated with disability, disability progression and clinical forms of multiple sclerosis, Inflamm. Res. Off. J. Eur. Histamine Res. Soc. ... [et al., 68, 1049 Holbrook, 2019, Tumour necrosis factor signalling in health and disease, F1000Research, 8, 10.12688/f1000research.17023.1 Dittrich, 2020, TNF-α signaling: TACE inhibition to put out the burning heart, PLoS Biol, 18, e3001037, 10.1371/journal.pbio.3001037 Tian, 2018, CASTp 3.0: computed atlas of surface topography of proteins, Nucleic Acids Res, 46, W363, 10.1093/nar/gky473 Hsu, 2011, iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis, BMC Bioinf, 12 Suppl 1, S33, 10.1186/1471-2105-12-S1-S33 Trott, 2010, “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J Comput Chem, 31, 455, 10.1002/jcc.21334 Vilar, 2008, Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery, Curr Top Med Chem, 8, 1555, 10.2174/156802608786786624 Adelusi, 2021, Exploring the inhibitory potentials of Momordica charantia bioactive compounds against Keap1-Kelch protein using computational approaches, silico Pharmacol., 9, 39, 10.1007/s40203-021-00100-2 Adelusi, 2021, Molecular dynamics , molecular mechanics , and density functional theory, J Mol Struct, 131879 Adelusi, 2021, 5, 778 Isaac, 2021, ( Mpro )– Molecular dynamics , molecular mechanics , and density functional theory investigations, J Mol Struct, xxxx, 131879 Radner, 2015, Anti-TNF in rheumatoid arthritis: an overview, Wien Med Wochenschr, 165, 3, 10.1007/s10354-015-0344-y Tzanavari, 2010, TNF-alpha and obesity, Curr Dir Autoimmun, 11, 145, 10.1159/000289203 He, 2005, Small-molecule inhibition of TNF-alpha, Science, 310, 1022, 10.1126/science.1116304 Boyenle, 2021, Direct Keap1-kelch inhibitors as potential drug candidates for oxidative stress-orchestrated diseases: a review on in silico perspective, Pharmacol Res, 167, 105577, 10.1016/j.phrs.2021.105577 dos Santos Maia, 2020, Consensus analyses in molecular docking studies applied to medicinal chemistry, Mini Rev Med Chem, 20, 1322, 10.2174/1389557520666200204121129 Halim, 2021, Structure-based virtual screening of tumor necrosis factor-α inhibitors by cheminformatics approaches and bio-molecular simulation, Biomolecules, 11, 10.3390/biom11020329 Sargsyan, 2017, How molecular size impacts RMSD applications in molecular dynamics simulations, J Chem Theor Comput, 13, 1518, 10.1021/acs.jctc.7b00028 Lobanov, 2008, [Radius of gyration is indicator of compactness of protein structure], Mol Biol, 42, 701, 10.1134/S0026893308040195 Chen, 2016, Regulation of protein-ligand binding affinity by hydrogen bond pairing, Sci Adv, 2, e1501240, 10.1126/sciadv.1501240 Fischer, 2021, Decision making in structure-based drug discovery: visual inspection of docking results, J Med Chem, 64, 2489, 10.1021/acs.jmedchem.0c02227 Thangsunan, 2020, Effective prediction model and determination of binding residues influential for inhibitors targeting HIV-1 integrase-LEDGF/p75 interface by employing solvent accessible surface area energy as key determinant, J Biomol Struct Dyn, 38, 460, 10.1080/07391102.2019.1580219 Ferreira, 2019, ADMET modeling approaches in drug discovery, Drug Discov Today, 24, 1157, 10.1016/j.drudis.2019.03.015 Di, 2003, Profiling drug-like properties in discovery research, Curr Opin Chem Biol, 7, 402, 10.1016/S1367-5931(03)00055-3 Lamothe, 2016, The human ether-a-go-go-related gene (hERG) potassium channel represents an unusual target for protease-mediated damage, J Biol Chem, 291, 20387, 10.1074/jbc.M116.743138 Walker, 1999, Inhibition of the human ether-a-go-go-related gene (HERG) potassium channel by cisapride: affinity for open and inactivated states, Br J Pharmacol, 128, 444, 10.1038/sj.bjp.0702774 Lipinski, 2004, Lead- and drug-like compounds: the rule-of-five revolution, Drug Discov Today Technol, 1, 337, 10.1016/j.ddtec.2004.11.007