In silico discovery of multi-targeting inhibitors for the COVID-19 treatment by molecular docking, molecular dynamics simulation studies, and ADMET predictions

Structural Chemistry - Tập 33 Số 5 - Trang 1645-1665 - 2022
Aso Hameed Hasan1,2, Narmin Hamaamin Hussen3, Sonam Shakya4, Joazaizulfazli Jamalis5, Mohammad Rizki Fadhil Pratama6,7, Subhash Chander8, Harsha Kharkwal8, Sankaranarayanan Murugesan9
1Universiti Teknologi Malaysia
2University of Garmian
3Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, University of Sulaimani, Sulaimani, Iraq
4Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh, India
5Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
6Department of Pharmacy, Universitas Muhammadiyah Palangkaraya, Central Kalimantan, Indonesia
7Doctoral Program of Pharmaceutical Sciences, Universitas Airlangga, Soekarno Kampus C UNAIR Mulyorejo, Surabaya, East Java, Indonesia
8Amity Inst Phytomedicine and Phytochemistry, Amity University, Amity University, Noida, India
9Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani, India

Tóm tắt

Từ khóa


Tài liệu tham khảo

Shahhosseini N, Babuadze G, Wong G, Kobinger GP (2021) Mutation signatures and in silico docking of novel SARS-CoV-2 variants of concern. Microorganisms 9(5):926

Rezaei M, Ziai SA, Fakhri S, Pouriran R (2021) ACE2: Its potential role and regulation in severe acute respiratory syndrome and COVID-19. J Cell Physiol 236(4):2430–2442. https://doi.org/10.1002/jcp.30041

Zaib S, Rana N, Noor A, Khan I (2021) Machine intelligence techniques for the identification and diagnosis of COVID-19. Curr Med Chem 28(26):5268–5283. https://doi.org/10.2174/0929867328666210106143307

World Health Organization (2021) Coronavirus (COVID-19) Dashboard. Available on: https://covid19.who.int/

Chen J, Lu H (2021) New challenges to fighting COVID-19: virus variants, potential vaccines, and development of antivirals. Biosci Trends 15(2):126–128. https://doi.org/10.5582/bst.2021.01092

Pavia CS, Wormser GP (2021) Passive immunization and its rebirth in the era of the COVID-19 pandemic. Int J Antimicrob Agents 57(3):106275. https://doi.org/10.1016/j.ijantimicag.2020.106275

Rehman M, Tauseef I, Aalia B, Shah SH, Junaid M, Haleem KS (2020) Therapeutic and vaccine strategies against SARS-CoV-2: past, present and future. Futur Virol. https://doi.org/10.2217/fvl-2020-0137.10.2217/fvl-2020-0137

Skariyachan S, Gopal D, Chakrabarti S, Kempanna P, Uttarkar A, Muddebihalkar AG, Niranjan V (2020) Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies- deciphering the scope of repurposed drugs. Comput Biol Med 126:104054. https://doi.org/10.1016/j.compbiomed.2020.104054

Ledford H (2021) Covid antiviral pills: what scientists still want to know. Nature 599(7885):358–359. https://doi.org/10.1038/d41586-021-03074-5

Awadasseid A, Wu Y, Tanaka Y, Zhang W (2021) Effective drugs used to combat SARS-CoV-2 infection and the current status of vaccines. Biomed Pharmacother 137:111330. https://doi.org/10.1016/j.biopha.2021.111330

Poduri R, Joshi G, Jagadeesh G (2020) Drugs targeting various stages of the SARS-CoV-2 life cycle: exploring promising drugs for the treatment of Covid-19. Cell Signal 74:109721. https://doi.org/10.1016/j.cellsig.2020.109721

Fakhri S, Nouri Z, Moradi SZ, Akkol EK, Piri S, Sobarzo-Sánchez E, Farzaei MH, Echeverría J (2021) Targeting multiple signal transduction pathways of SARS-CoV-2: approaches to COVID-19 therapeutic candidates. Molecules 26(10):2917. https://doi.org/10.3390/molecules26102917

Kumar S, Sharma PP, Upadhyay C, Kempaiah P, Rathi B, Poonam (2021) Multi-targeting approach for nsp3, nsp9, nsp12 and nsp15 proteins of SARS-CoV-2 by diosmin as illustrated by molecular docking and molecular dynamics simulation methodologies. Methods 195:44−56. https://doi.org/10.1016/j.ymeth.2021.02.017

Elhady SS, Abdelhameed RFA, Malatani RT, Alahdal AM, Bogari HA, Almalki AJ, Mohammad KA, Ahmed SA, Khedr AIM, Darwish KM (2021) Molecular docking and dynamics simulation study of Hyrtios erectus isolated scalarane sesterterpenes as potential SARS-CoV-2 dual target inhibitors. Biology 10(5):389. https://doi.org/10.3390/biology10050389

Su H, Xu Y, Jiang H (2021) Drug discovery and development targeting the life cycle of SARS-CoV-2. Fundam Res 1(2):151–165. https://doi.org/10.1016/j.fmre.2021.01.013

Zhang H, Zhang H (2021) Entry, egress and vertical transmission of SARS-CoV-2. J Mol Cell Biol 13(3):168–174. https://doi.org/10.1093/jmcb/mjab013

Hu X, Shrimp JH, Guo H, Xu M, Chen CZ, Zhu W, Zakharov AV, Jain S, Shinn P, Simeonov A, Hall MD, Shen M (2021) Discovery of TMPRSS2 inhibitors from virtual screening as a potential treatment of COVID-19. ACS Pharmacol Transl Sci 4(3):1124–1135. https://doi.org/10.1021/acsptsci.0c00221

Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu N-H, Nitsche A, Müller MA, Drosten C, Pöhlmann S (2020) SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181(2):271-280.e278. https://doi.org/10.1016/j.cell.2020.02.052

Vincent MJ, Bergeron E, Benjannet S, Erickson BR, Rollin PE, Ksiazek TG, Seidah NG, Nichol ST (2005) Chloroquine is a potent inhibitor of SARS coronavirus infection and spread. Virol J 2(1):69. https://doi.org/10.1186/1743-422X-2-69

Ren L, Xu W, Overton JL, Yu S, Chiamvimonvat N, Thai PN (2020) Assessment of chloroquine and hydroxychloroquine safety profiles: a systematic review and meta-analysis. Front Pharmacol. https://doi.org/10.3389/fphar.2020.562777

Yamamoto M, Matsuyama S, Li X, Takeda M, Kawaguchi Y, Inoue J-I, Matsuda Z (2016) Identification of nafamostat as a potent inhibitor of Middle East respiratory syndrome coronavirus S protein-mediated membrane fusion using the split-protein-based cell-cell fusion assay. Antimicrob Agents Chemother 60(11):6532–6539. https://doi.org/10.1128/AAC.01043-16

Trougakos IP, Stamatelopoulos K, Terpos E, Tsitsilonis OE, Aivalioti E, Paraskevis D, Kastritis E, Pavlakis GN, Dimopoulos MA (2021) Insights to SARS-CoV-2 life cycle, pathophysiology, and rationalized treatments that target COVID-19 clinical complications. J Biomed Sci 28(1):9. https://doi.org/10.1186/s12929-020-00703-5

Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S (2020) Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antiviral Res 178:104792. https://doi.org/10.1016/j.antiviral.2020.104792

Faheem BK, Kumar KVGC, Sekhar S, Kunjiappan J, Jamalis R, Balaña-Fouce BLT, Sankaranarayanan M (2020) Druggable targets of SARS-CoV-2 and treatment opportunities for COVID-19. Bioorg Chem 104:104269. https://doi.org/10.1016/j.bioorg.2020.104269

Kishk SM, Kishk RM, Yassen ASA, Nafie MS, Nemr NA, ElMasry G, Al-Rejaie S, Simons C (2020) Molecular insights into human transmembrane protease serine-2 (TMPS2) inhibitors against SARS-CoV2: homology modelling, molecular dynamics, and docking studies. Molecules 25(21):5007. https://doi.org/10.3390/molecules25215007

Vardhan S, Sahoo SK (2022) Computational studies on the interaction of SARS-CoV-2 Omicron SGp RBD with human receptor ACE2, limonin and glycyrrhizic acid. Comput Biol Med 144:105367. https://doi.org/10.1016/j.compbiomed.2022.105367

Alazmi M, Motwalli O (2021) In silico virtual screening, characterization, docking and molecular dynamics studies of crucial SARS-CoV-2 proteins. J Biomol Struct Dyn 39(17):6761–6771. https://doi.org/10.1080/07391102.2020.1803965

Sola I, Almazán F, Zúñiga S, Enjuanes L (2015) Continuous and discontinuous RNA synthesis in coronaviruses. Annu Rev Virol 2(1):265–288. https://doi.org/10.1146/annurev-virology-100114-055218

V’kovski P, Kratzel A, Steiner S, Stalder H, Thiel V (2021) Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 19(3):155–170. https://doi.org/10.1038/s41579-020-00468-6

Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, Wang Q, Xu Y, Li M, Li X, Zheng M, Chen L, Li H (2020) Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B 10(5):766–788. https://doi.org/10.1016/j.apsb.2020.02.008

Marinho EM, de Andrade Neto JB, Silva J, Rocha da Silva C, Cavalcanti BC, Marinho ES, Júnior HVN (2020) Virtual screening based on molecular docking of possible inhibitors of COVID-19 main protease. Microb Pathog 148:104365. https://doi.org/10.1016/j.micpath.2020.104365

Huseen NHA (2020) Docking study of naringin binding with COVID-19 main protease enzyme. Iraqi J Pharm Sci (P-ISSN: 1683–3597, E-ISSN: 2521–3512) 29(2):231–238. https://doi.org/10.31351/vol29iss2pp231-238

Gao X, Qin B, Chen P, Zhu K, Hou P, Wojdyla JA, Wang M, Cui S (2021) Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharmaceutica Sinica B 11(1):237–245. https://doi.org/10.1016/j.apsb.2020.08.014

Li X, Zhang L, Chen S, Ouyang H, Ren L (2021) Possible targets of pan-coronavirus antiviral strategies for emerging or re-emerging coronaviruses. Microorganisms 9(7):1479. https://doi.org/10.3390/microorganisms9071479

Abu-Melha S, Edrees MM, Riyadh SM, Abdelaziz MR, Elfiky AA, Gomha SM (2020) Clean grinding technique: a facile synthesis and in silico antiviral activity of hydrazones, pyrazoles, and pyrazines bearing thiazole moiety against SARS-CoV-2 main protease (Mpro). Molecules 25(19):4565

Kong R, Yang G, Xue R, Liu M, Wang F, Hu J, Guo X, Chang S (2020) COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19. Bioinformatics 36(20):5109–5111. https://doi.org/10.1093/bioinformatics/btaa645

Tang B, He F, Liu D, He F, Wu T, Fang M, Niu Z, Wu Z, Xu D (2022) AI-Aided Design of Novel Targeted Covalent Inhibitors against SARS-CoV-2. Biomolecules 12(6):746. https://doi.org/10.3390/biom12060746

Banerjee R, Perera L, Tillekeratne LMV (2021) Potential SARS-CoV-2 main protease inhibitors. Drug Discov Today 26(3):804–816. https://doi.org/10.1016/j.drudis.2020.12.005

Vandyck K, Deval J (2021) Considerations for the discovery and development of 3-chymotrypsin-like cysteine protease inhibitors targeting SARS-CoV-2 infection. Curr Opin Virol 49:36–40. https://doi.org/10.1016/j.coviro.2021.04.006

Dong L, Hu S, Gao J (2020) Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discov Ther 14(1):58–60. https://doi.org/10.5582/ddt.2020.01012

Cao B, Wang Y, Wen D, Liu W, Wang J, Fan G, Ruan L, Song B, Cai Y, Wei M, Li X, Xia J, Chen N, Xiang J, Yu T, Bai T, Xie X, Zhang L, Li C, Yuan Y, Chen H, Li H, Huang H, Tu S, Gong F, Liu Y, Wei Y, Dong C, Zhou F, Gu X, Xu J, Liu Z, Zhang Y, Li H, Shang L, Wang K, Li K, Zhou X, Dong X, Qu Z, Lu S, Hu X, Ruan S, Luo S, Wu J, Peng L, Cheng F, Pan L, Zou J, Jia C, Wang J, Liu X, Wang S, Wu X, Ge Q, He J, Zhan H, Qiu F, Guo L, Huang C, Jaki T, Hayden FG, Horby PW, Zhang D, Wang C (2020) A Trial of lopinavir-ritonavir in adults hospitalized with severe COVID-19. N Engl J Med 382(19):1787–1799. https://doi.org/10.1056/NEJMoa2001282

Anirudhan V, Lee H, Cheng H, Cooper L, Rong L (2021) Targeting SARS-CoV-2 viral proteases as a therapeutic strategy to treat COVID-19. J Med Virol 93(5):2722–2734. https://doi.org/10.1002/jmv.26814

Lin M-H, Moses DC, Hsieh C-H, Cheng S-C, Chen Y-H, Sun C-Y, Chou C-Y (2018) Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes. Antiviral Res 150:155–163. https://doi.org/10.1016/j.antiviral.2017.12.015

Yin W, Mao C, Luan X, Shen D-D, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S, Xie Y-C, Tian G, Jiang H-W, Tao S-C, Shen J, Jiang Y, Jiang H, Xu Y, Zhang S, Zhang Y, Xu HE (2020) Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science 368(6498):1499–1504. https://doi.org/10.1126/science.abc1560

de Wit E, Feldmann F, Cronin J, Jordan R, Okumura A, Thomas T, Scott D, Cihlar T, Feldmann H (2020) Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection. Proc Natl Acad Sci 117(12):6771–6776. https://doi.org/10.1073/pnas.1922083117

Sheahan TP, Sims AC, Leist SR, Schäfer A, Won J, Brown AJ, Montgomery SA, Hogg A, Babusis D, Clarke MO, Spahn JE, Bauer L, Sellers S, Porter D, Feng JY, Cihlar T, Jordan R, Denison MR, Baric RS (2020) Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nat Commun 11(1):222. https://doi.org/10.1038/s41467-019-13940-6

Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G (2020) Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res 30(3):269–271. https://doi.org/10.1038/s41422-020-0282-0

Singh TU, Parida S, Lingaraju MC, Kesavan M, Kumar D, Singh RK (2020) Drug repurposing approach to fight COVID-19. Pharmacol Rep 72(6):1479–1508. https://doi.org/10.1007/s43440-020-00155-6

Malone B, Campbell EA (2021) Molnupiravir: Coding for catastrophe. Nat Struct Mol Biol 28(9):706–708. https://doi.org/10.1038/s41594-021-00657-8

Naveed M, Tehreem S, Arshad S, Bukhari SA, Shabbir MA, Essa R, Ali N, Zaib S, Khan A, Al-Harrasi A, Khan I (2021) Design of a novel multiple epitope-based vaccine: an immunoinformatics approach to combat SARS-CoV-2 strains. J Infect Public Health 14(7):938–946. https://doi.org/10.1016/j.jiph.2021.04.010

Zhang S, Pei R, Li M, Su H, Sun H, Ding Y, Su M, Huang C, Chen X, Du Z, Jin C, Zang Y, Li J, Xu Y, Chen X, Zhang B, Ding K (2022) Cocktail polysaccharides isolated from Ecklonia kurome against the SARS-CoV-2 infection. Carbohyd Polym 275:118779. https://doi.org/10.1016/j.carbpol.2021.118779

Naydenova K, Muir KW, Wu L-F, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Löwe J, Barford D, Russo CJ (2021) Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Proc Natl Acad Sci 118(7):e2021946118. https://doi.org/10.1016/j.ultramic.2021.113396

Vardhan S, Sahoo SK (2020) In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19. Comput Biol Med 124:103936. https://doi.org/10.1016/j.compbiomed.2020.103936

Vijesh AM, Isloor AM, Telkar S, Arulmoli T, Fun H-K (2013) Molecular docking studies of some new imidazole derivatives for antimicrobial properties. Arab J Chem 6(2):197–204. https://doi.org/10.1016/j.arabjc.2011.10.007

Alfarisi S, Santoso M, Kristanti AN, Siswanto I, Puspaningsih NNT (2020) synthesis, antimicrobial study, and molecular docking simulation of 3,4-dimethoxy-β-nitrostyrene derivatives as candidate PTP1B inhibitor. Sci Pharm 88(3):37. https://doi.org/10.3390/scipharm88030037

Abu-Melha S, Edrees MM, Said MA, Riyadh SM, Al-Kaff NS, Gomha SM (2022) Potential COVID-19 drug candidates based on diazinyl-thiazol-imine moieties: synthesis and greener pastures biological study. Molecules 27(2):488. https://doi.org/10.3390/molecules27020488

Jain R, Mujwar S (2020) Repurposing metocurine as main protease inhibitor to develop novel antiviral therapy for COVID-19. Struct Chem 31(6):2487–2499. https://doi.org/10.1007/s11224-020-01605-w

Anand AV, Balamuralikrishnan B, Kaviya M, Bharathi K, Parithathvi A, Arun M, Senthilkumar N, Velayuthaprabhu S, Saradhadevi M, Al-Dhabi NA, Arasu MV, Yatoo MI, Tiwari R, Dhama K (2021) Medicinal plants, phytochemicals, and herbs to combat viral pathogens including SARS-CoV-2. Molecules 26(6):1775. https://doi.org/10.3390/molecules26061775

Fakhri S, Piri S, Majnooni MB, Farzaei MH, Echeverría J (2020) Targeting neurological manifestations of coronaviruses by candidate phytochemicals: a mechanistic approach. Front Pharmacol 11:621099. https://doi.org/10.3389/fphar.2020.621099

Parida PK, Paul D, Chakravorty D (2021) Nature’s therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants. Phytomedicine Plus 1(1):100002. https://doi.org/10.1016/j.phyplu.2020.100002

Lalani S, Poh CL (2020) Flavonoids as Antiviral Agents for Enterovirus A71 (EV-A71). Viruses. https://doi.org/10.3390/v12020184

Khan SL, Siddiqui FA, Jain SP, Sonwane GM (2021) Discovery of potential inhibitors of SARS-CoV-2 (COVID-19) main protease (Mpro) from Nigella Sativa (Black Seed) by molecular docking study. Coronaviruses 2(3):384–402. https://doi.org/10.2174/2666796701999200921094103

Ben-Shabat S, Yarmolinsky L, Porat D, Dahan A (2020) Antiviral effect of phytochemicals from medicinal plants: applications and drug delivery strategies. Drug Deliv Transl Res 10(2):354–367. https://doi.org/10.1007/s13346-019-00691-6

Kim C-H (2021) Anti–SARS-CoV-2 Natural products as potentially therapeutic agents. Front Pharmacol 12:1015. https://doi.org/10.3389/fphar.2021.590509

Fielding BC, Filho CDSMB, Ismail NSM, Sousa DP (2020) Alkaloids: therapeutic potential against human coronaviruses. Molecules. https://doi.org/10.3390/molecules25235496

Diniz LRL, Perez-Castillo Y, Elshabrawy HA, Filho CDSMB, de Sousa DP (2021) Bioactive terpenes and their derivatives as potential SARS-CoV-2 proteases inhibitors from molecular modeling studies. Biomolecules 11(1):74. https://doi.org/10.3390/biom11010074

Abdelmohsen UR, Albohy A, Abdulrazik BS, Bayoumi SAL, Malak LG, Khallaf ISA, Bringmann G, Farag SF (2021) Natural coumarins as potential anti-SARS-CoV-2 agents supported by docking analysis. RSC Adv 11(28):16970–16979. https://doi.org/10.1039/D1RA01989A

Wahedi HM, Ahmad S, Abbasi SW (2021) Stilbene-based natural compounds as promising drug candidates against COVID-19. J Biomol Struct Dyn 39(9):3225–3234. https://doi.org/10.1080/07391102.2020.1762743

Xu X-Y, Wang D-Y, Li Y-P, Deyrup ST, Zhang H-J (2021) Plant-derived lignans as potential antiviral agents: a systematic review. Phytochem Rev. https://doi.org/10.1007/s11101-021-09758-0

Pandey P, Rane JS, Chatterjee A, Kumar A, Khan R, Prakash A, Ray S (2021) Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development. J Biomol Struct Dyn 39(16):6306–6316. https://doi.org/10.1080/07391102.2020.1796811

Daoui O, Mazoir N, Bakhouch M, Salah M, Benharref A, Gonzalez-Coloma A, Elkhattabi S, Yazidi ME, Chtita S (2022) 3D-QSAR, ADME-Tox, and molecular docking of semisynthetic triterpene derivatives as antibacterial and insecticide agents. Struct Chem. https://doi.org/10.1007/s11224-022-01912-4

Akdemir A, Angeli A, Göktaş F, Eraslan Elma P, Karalı N, Supuran CT (2019) Novel 2-indolinones containing a sulfonamide moiety as selective inhibitors of candida β-carbonic anhydrase enzyme. J Enzyme Inhib Med Chem 34(1):528–531

Dassault Systèmes BIOVIA Discovery studio modeling environment, release 2017. Dassaul Systèmes, San Diego

Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14):1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14%3c1639::AID-JCC10%3e3.0.CO;2-B

Trott O, Olson AJ (2010) AutoDock Vina: 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

Pratama MRF, Poerwono H, Siswodiharjo S (2019) ADMET properties of novel 5-O-benzoylpinostrobin derivatives. J Basic Clin Physiol Pharmacol. https://doi.org/10.1515/jbcpp-2019-0251

Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31(4):671–690. https://doi.org/10.1002/jcc.21367

Yu W, He X, Vanommeslaeghe K, MacKerell AD Jr (2012) Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. J Comput Chem 33(31):2451–2468. https://doi.org/10.1002/jcc.23067

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935. https://doi.org/10.1063/1.445869

Allen MP, Tildesley DJ (2017) Computer simulation of liquids. Oxford university press

Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103(19):8577–8593. https://doi.org/10.1063/1.470117

Steinbach PJ, Brooks BR (1994) New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comput Chem 15(7):667–683. https://doi.org/10.1002/jcc.540150702

Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38. https://doi.org/10.1016/0263-7855(96)00018-5

DeLano WL (2002) Pymol: An open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr. 40(1):82–92

Su X, Kong L, Lei X, Hu L, Ye M, Zou H (2007) Biological fingerprinting analysis of traditional Chinese medicines with targeting ADME/Tox property for screening of bioactive compounds by chromatographic and MS methods. Mini Rev Med Chem 7(1):87–98. https://doi.org/10.2174/138955707779317830

Gil C, Ginex T, Maestro I, Nozal V, Barrado-Gil L, Cuesta-Geijo MÁ, Urquiza J, Ramírez D, Alonso C, Campillo NE, Martinez A (2020) COVID-19: drug targets and potential treatments. J Med Chem 63(21):12359–12386. https://doi.org/10.1021/acs.jmedchem.0c00606

Das G, Ghosh S, Garg S, Ghosh S, Jana A, Samat R, Mukherjee N, Roy R, Ghosh S (2020) An overview of key potential therapeutic strategies for combat in the COVID-19 battle. RSC Adv 10(47):28243–28266. https://doi.org/10.1039/D0RA05434H

Liu C, Zhou Q, Li Y, Garner LV, Watkins SP, Carter LJ, Smoot J, Gregg AC, Daniels AD, Jervey S, Albaiu D (2020) Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Cent Sci 6(3):315–331. https://doi.org/10.1021/acscentsci.0c00272

Hasan AH, Murugesan S, Amran SI, Chander S, Alanazi MM, Hadda TB, Shakya S, Pratama MRF, Das B, Biswas S, Jamalis J (2022) Novel thiophene Chalcones-Coumarin as acetylcholinesterase inhibitors: design, synthesis, biological evaluation, molecular docking, ADMET prediction and molecular dynamics simulation. Bioorg Chem 119:105572. https://doi.org/10.1016/j.bioorg.2021.105572

Prasanna S, Doerksen JR (2009) Topological polar surface area: a useful descriptor in 2D-QSAR. Curr Med Chem 16(1):21–41. https://doi.org/10.2174/092986709787002817

Banerjee P, Eckert AO, Schrey AK, Preissner R (2018) ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res 46(W1):W257–W263. https://doi.org/10.1093/nar/gky318

Chander S, Ashok P, Zheng Y-T, Wang P, Raja KS, Taneja A, Murugesan S (2016) Design, synthesis and in-vitro evaluation of novel tetrahydroquinoline carbamates as HIV-1 RT inhibitor and their antifungal activity. Bioorg Chem 64:66–73. https://doi.org/10.1016/j.bioorg.2015.12.005

Chander S, Wang P, Ashok P, Yang L-M, Zheng Y-T, Murugesan S (2016) Rational design, synthesis, anti-HIV-1 RT and antimicrobial activity of novel 3-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl)-1-(piperazin-1-yl)propan-1-one derivatives. Bioorg Chem 67:75–83. https://doi.org/10.1016/j.bioorg.2016.05.009

Kufareva I, Abagyan R (2012) Methods of protein structure comparison. Methods Mol Biol 857:231–257. https://doi.org/10.1007/978-1-61779-588-6_10

Wu S, Zhang Y (2008) A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 24(7):924–931. https://doi.org/10.1093/bioinformatics/btn069

Khan MD, Shakya S, Thi Vu HH, Habte L, Ahn JW (2021) Low concentrated phosphorus sorption in aqueous medium on aragonite synthesized by carbonation of seashells: optimization, kinetics, and mechanism study. J Environ Manag. 280:111652. https://doi.org/10.1016/j.jenvman.2020.111652

Alhomrani M, Alsanie WF, Alamri AS, Alyami H, Habeeballah H, Alkhatabi HA, Felimban RI, Haynes JM, Shakya S, Raafat BM, Refat MS, Gaber A (2022) Enhancing the antipsychotic effect of risperidone by increasing its binding affinity to serotonin receptor via picric acid: a molecular dynamics simulation. Pharmaceuticals 15(3):285. https://doi.org/10.3390/ph15030285