Integrated virtual screening and molecular dynamics simulation revealed promising drug candidates of p53-MDM2 interaction

Journal of Molecular Modeling - Tập 28 Số 6 - 2022
Abdul-Quddus Kehinde Oyedele1, Temitope Isaac Adelusi1, Abdeen Tunde Ogunlana1, Rofiat Adeyemi1, Opeyemi Emmanuel Atanda1, Musa Oladayo Babalola2, Mojeed Ayoola Ashiru3, Isong Josiah Ayoola4, Ibrahim Damilare Boyenle5
1Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
2Department of Biochemistry, University of Lagos, Lagos, Nigeria
3Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Science, Fountain University, Osogbo, Nigeria
4Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
5College of Health Sciences, Crescent University, Abeokuta, Nigeria

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Adelusi TI, Abdul-Hammed M, Idris MO, Kehinde OQ, Boyenle ID, Divine UC, Adedotun IO, Folorunsho AA, Kolawole OE (2021) Exploring the inhibitory potentials of Momordicacharantia bioactive compounds against Keap1-Kelch protein using computational approaches. In Silico Pharmacol 9(1):39. https://doi.org/10.1007/s40203-021-00100-2

Adelusi TI, Abdul-Hammed M, Idris MO, Oyedele QK, Adedotun IO (2021) Molecular dynamics, quantum mechanics and docking studies of some Keap1 inhibitors - an insight into the atomistic mechanisms of their antioxidant potential. Heliyon 7(6):e07317. https://doi.org/10.1016/j.heliyon.2021.e07317

Adelusi TI, Abdul-Hammed M, Ojo EM, Oyedele QK, Boyenle ID, Adedotun IO, Olaoba OT, Folorunsho AA, Kolawole OE (2021) Molecular docking assessment of clinically approved antiviral drugs against mpro, spike glycoprotein and angiotensin converting enzyme-2 revealed probable anti-SARS-CoV-2 potential. Trop J Nat Prod Res. 5(4):778–791

Adelusi TI, Oyedele AK, Monday OE, Boyenle ID, Idris MO, Ogunlana AT, Ayoola AM, Fatoki JO, Kolawole OE, David KB, Olayemi AA (2021) Dietary polyphenols mitigate SARS-CoV-2 main protease (Mpro) - molecular dynamics, molecular mechanics, and density functional theory investigations. J Mol Struct 11:131879. https://doi.org/10.1016/j.molstruc.2021.131879

Adelusi TI, Oyedele AK, Boyenle ID, Ogunlana AT, Adeyemi RO, Ukachi CD, Idris MO, Olaoba OT, Adedotun IO, Kolawole OE, Xiaoxing Y, Abdul-Hammed M (2022) Molecular modeling in drug discovery. Inform Med Unlocked 29:100880. https://doi.org/10.1016/j.imu.2022.100880

Allen JG, Bourbeau MP, Wohlhieter GE, Bartberger MD, Michelsen K, Hungate R, Gadwood RC, Gaston RD, Evans B, Mann LW, Matison ME, Schneider S, Huang X, Yu D, Andrews PS, Reichelt A, Long AM, Yakowec P, Yang EY, Lee TA, Oliner JD (2009) Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction. J Med Chem 52(22):7044–7053. https://doi.org/10.1021/jm900681h

Almerico AM, Tutone M, Pantano L, Lauria A (2012) Molecular dynamics studies on Mdm2 complexes: an analysis of the inhibitor influence. Biochem Biophys Res Commun 424(2):341–347. https://doi.org/10.1016/j.bbrc.2012.06.138

Boyenle ID, Divine UC, Adeyemi R, Ayinde KS, Olaoba OT, Apu C, Du L, Lu Q, Yin X, Adelusi TI (2021) Direct Keap1-kelch inhibitors as potential drug candidates for oxidative stress-orchestrated diseases: a review on Insilico perspective. Pharmacol Res 167:105577. https://doi.org/10.1016/j.phrs.2021.105577

Boyenle ID, Adelusi TI, Ogunlana AT, Oluwabusola RA, Ibrahim NO, Tolulope A, Okikiola OS, Adetunji BL, Abioye IO, Oyedele AQ (2022) Consensus scoring-based virtual screening and molecular dynamics simulation of some TNF-alpha inhibitors. Inform Med Unlocked 28:100833. https://doi.org/10.1016/j.imu.2021.100833

Brindisi M, Brogi S, Relitti N, Vallone A, Butini S, Gemma S, Novellino E, Colotti G, Angiulli G, Di Chiaro F, Fiorillo A, Ilari A, Campiani G (2015) Structure-based discovery of the first non-covalent inhibitors of Leishmania major tryparedoxin peroxidase by high throughput docking. Sci Rep 5:9705. https://doi.org/10.1038/srep09705

Carry JC, Garcia-Echeverria C (2013) Inhibitors of the p53/hdm2 protein-protein interaction-path to the clinic. Bioorg Med Chem Lett 23(9):2480–2485. https://doi.org/10.1016/j.bmcl.2013.03.034

Chemi G, Gemma S, Campiani G, Brogi S, Butini S, Brindisi M (2017) Computational tool for fast in silico evaluation of hERG K+ channel affinity. Front Chem 5:7. https://doi.org/10.3389/fchem.2017.00007

Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC (2016) Regulation of protein-ligand binding affinity by hydrogen bond pairing. Sci Adv 2(3):e1501240. https://doi.org/10.1126/sciadv.1501240

Chen J, Wang J, Xu B, Zhu W, Li G (2011) Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: molecular dynamics simulation and free energy analysis. J Mol Graph Model 30:46–53. https://doi.org/10.1016/j.jmgm.2011.06.003

Chen J, Wang J, Zhu W, Li G (2013) A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. J Comput Aided Mol Des 27(11):965–974. https://doi.org/10.1007/s10822-013-9693-z

Chen J, Wang J, Zhang Q, Chen K, Zhu W (2015) Probing origin of binding difference of inhibitors to MDM2 and MDMX by polarizable molecular dynamics simulation and QM/MM-GBSA calculation. Sci Rep 5:17421. https://doi.org/10.1038/srep17421

Gao Y, Mei Y, Zhang JZ (2015) Treatment of hydrogen bonds in protein simulations. In: Liu J (ed) Advanced materials for renewable hydrogen production, storage and utilization. IntechOpen, pp 121–136

Grasberger BL, Lu T, Schubert C, Parks DJ, Carver TE, Koblish HK, Cummings MD, LaFrance LV, Milkiewicz KL, Calvo RR, Maguire D, Lattanze J, Franks CF, Zhao S, Ramachandren K, Bylebyl GR, Zhang M, Manthey CL, Petrella EC, Pantoliano MW, Deckman IC, Spurlino JC, Maroney AC, Tomczuk BE, Molloy CJ, Bone RF (2005) Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells. J Med Chem 48(4):909–912. https://doi.org/10.1021/jm049137g

Hosea NA, Jones HM (2013) Predicting pharmacokinetic profiles using in silico derived parameters. Mol Pharm 10(4):1207–1215. https://doi.org/10.1021/mp300482w

Hsu KC, Chen YF, Lin SR, Yang JM (2011) iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinformatics 12 Suppl 1(Suppl 1):S33. https://doi.org/10.1186/1471-2105-12-S1-S33

Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH (2016) PubChem substance and compound databases. Nucleic Acids Res 44(D1):D1202–D1213. https://doi.org/10.1093/nar/gkv951

Lauria A, Tutone M, Ippolito M, Pantano L, Almerico AM (2010) Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: the investigation of p53-MDM2 interaction and its inhibition by small molecules. Curr Med Chem 17(28):3142–3154. https://doi.org/10.2174/092986710792232021

Leão M, Gomes S, Pedraza-Chaverri J, Machado N, Sousa E, Pinto M, Inga A, Pereira C, Saraiva L (2013) Α-mangostin and gambogic acid as potential inhibitors of the p53-MDM2 interaction revealed by a yeast approach. J Nat Prod 76(4):774–778. https://doi.org/10.1021/np400049j

Leão M, Pereira C, Bisio A, Ciribilli Y, Paiva AM, Machado N, Palmeira A, Fernandes MX, Sousa E, Pinto M, Inga A, Saraiva L (2013) Discovery of a new small-molecule inhibitor of p53-MDM2 interaction using a yeast-based approach. Biochem Pharmacol 85(9):1234–1245. https://doi.org/10.1016/j.bcp.2013.01.032

Leão M, Soares J, Gomes S, Raimundo L, Ramos H, Bessa C, Queiroz G, Domingos S, Pinto M, Inga A, Cidade H, Saraiva L (2015) Enhanced cytotoxicity of prenylatedchalcone against tumour cells via disruption of the p53-MDM2 interaction. Life Sci 142:60–65. https://doi.org/10.1016/j.lfs.2015.10.015

Lee JH, Zhang Q, Jo S, Chai SC, Oh M, Im W, Lu H, Lim HS (2011) Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions. J Am Chem Soc 133(4):676–679. https://doi.org/10.1021/ja108230s

Liao KH, Chen KB, Lee WY, Sun MF, Lee CC, Chen CY (2014) Ligand-based and structure-based investigation for Alzheimer’s disease from traditional Chinese medicine. Evid Based Complement Alternat Med 2014:364819. https://doi.org/10.1155/2014/364819

Liu K, Watanabe E, Kokubo H (2017) Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. J Comput Aided Mol Des 31(2):201–211. https://doi.org/10.1007/s10822-016-0005-2

Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X (2018) Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 13(1):23–37. https://doi.org/10.1080/17460441.2018.1403419

Lynch T, Price A (2007) The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects. Am Fam Physician 76(3):391–396

Macchiarulo A, Giacchè N, Carotti A, Baroni M, Cruciani G, Pellicciari R (2008) Targeting the conformational transitions of MDM2 and MDMX: insights into dissimilarities and similarities of p53 recognition. J Chem Inf Model 48(10):1999–2009. https://doi.org/10.1021/ci800146m

Mazola Y, Guirola O, Palomares S, Chinea G, Menéndez C, Hernández L, Musacchio A (2015) A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes. J Mol Model 21(9):228. https://doi.org/10.1007/s00894-015-2772-4

Patel S, Player MR (2008) Small-molecule inhibitors of the p53-HDM2 interaction for the treatment of cancer. Expert Opin Investig Drugs 17(12):1865–1882. https://doi.org/10.1517/13543780802493366

Pires DE, Blundell TL, Ascher DB (2015) pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem 58(9):4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104

Raj BV, Rao MR, Acharya Y (2017) Structure based virtual screening, docking and molecular dynamic simulation studies to identify potent mdm2-p53 inhibitors: future implications for cancer therapy. Acta Med Int 4:11–21. https://doi.org/10.5530/ami.2017.4.3

Rew Y, Sun D, Gonzalez-Lopez De Turiso F, Bartberger MD, Beck HP, Canon J, Chen A, Chow D, Deignan J, Fox BM, Gustin D, Huang X, Jiang M, Jiao X, Jin L, Kayser F, Kopecky DJ, Li Y, Lo MC, Long AM, Michelsen K, Oliner JD, Osgood T, Ragains M, Saiki AY, Schneider S, Toteva M, Yakowec P, Yan X, Ye Q, Yu D, Zhao X, Zhou J, Medina JC, Olson SH (2012) Structure-based design of novel inhibitors of the MDM2-p53 interaction. J Med Chem 55(11):4936–54. https://doi.org/10.1021/jm300354j

Riaz M, Ashfaq UA, Qasim M, Yasmeen E, UlQamar MT, Anwar F (2017) Screening of medicinal plant phytochemicals as natural antagonists of p53-MDM2 interaction to reactivate p53 functioning. Anticancer Drugs 28(9):1032–1038. https://doi.org/10.1097/CAD.0000000000000548

Schüttelkopf AW, van Aalten DM (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D BiolCrystallogr 60(Pt 8):1355–1363. https://doi.org/10.1107/S0907444904011679

Sirous H, Chemi G, Campiani G, Brogi S (2019) An integrated in silico screening strategy for identifying promising disruptors of p53-MDM2 interaction. Comput Biol Chem 83:107105. https://doi.org/10.1016/j.compbiolchem.2019.107105

Tovar C, Rosinski J, Filipovic Z, Higgins B, Kolinsky K, Hilton H, Zhao X, Vu BT, Qing W, Packman K, Myklebost O, Heimbrook DC, Vassilev LT (2006) Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy. Proc Natl Acad Sci USA 103(6):1888–1893. https://doi.org/10.1073/pnas.0507493103

Trott O, Olson AJ (2010) AutoDockVina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455–461. https://doi.org/10.1002/jcc.21334

Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701–1718. https://doi.org/10.1002/jcc.20291

Vassilev LT, Vu BT, Graves B, Carvajal D, Podlaski F, Filipovic Z, Kong N, Kammlott U, Lukacs C, Klein C, Fotouhi N, Liu EA (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303(5659):844–848. https://doi.org/10.1126/science.1092472

Warner WA, Sanchez R, Dawoodian A, Li E, Momand J (2012) Identification of FDA-approved drugs that computationally bind to MDM2. Chem Biol Drug Des 80(4):631–637. https://doi.org/10.1111/j.1747-0285.2012.01428.x

Watson AF, Liu J, Bennaceur K, Drummond CJ, Endicott JA, Golding BT, Griffin RJ, Haggerty K, Lu X, McDonnell JM, Newell DR, Noble ME, Revill CH, Riedinger C, Xu Q, Zhao Y, Lunec J, Hardcastle IR (2011) MDM2-p53 protein-protein interaction inhibitors: a-ring substituted isoindolinones. Bioorg Med Chem Lett 21(19):5916–5919. https://doi.org/10.1016/j.bmcl.2011.07.084

Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C, Yin M, Zeng X, Wu C, Lu A, Chen X, Hou T, Cao D (2021) ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res 49(W1):W5-W14. https://doi.org/10.1093/nar/gkab255

Zaccagnini L, Brogi S, Brindisi M, Gemma S, Chemi G, Legname G, Campiani G, Butini S (2017) Identification of novel fluorescent probes preventing PrPSc replication in prion diseases. Eur J Med Chem 127:859–873. https://doi.org/10.1016/j.ejmech.2016.10.064

Zhao Y, Aguilar A, Bernard D, Wang S (2015) Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 Inhibitors) in clinical trials for cancer treatment. J Med Chem 58(3):1038–1052. https://doi.org/10.1021/jm501092z

Zhao Y, Bernard D, Wang S (2013) Small molecule inhibitors of MDM2-p53 and MDMX-p53 interactions as new cancer therapeutics. BioDiscovery 8(8):4. https://doi.org/10.7750/BioDiscovery.s

Zhuang C, Miao Z, Zhu L, Dong G, Guo Z, Wang S, Zhang Y, Wu Y, Yao J, Sheng C, Zhang W (2012) Discovery, synthesis, and biological evaluation of orally active pyrrolidone derivatives as novel inhibitors of p53-MDM2 protein-protein interaction. J Med Chem 55(22):9630–9642. https://doi.org/10.1021/jm300969t