Table Info

Table 2.

Mechanism of action for the available compound and their COVID-19-related targets

Compound	Binding affinity (kcal/mol)	Target	Mechanism of action	Ref.
ATV	WT-ATV –20.05 DLT-ATV –15.88 LMB-ATV –17.58	S-protein WT, delta, and lambda variant	Potent inhibitors targeting RBD of the S-protein	[45]
PRZ	WT-PRZ –17.81 DLT-PRZ –19.52	S-protein WT and delta variant	Potent inhibitors targeting RBD of the S-protein	[45]
14 Herbal isolates 10 Approved drugs	Below –8.10	S-protein	Inhibit the SARS-CoV-2 S-protein	[46]
28 Bioactive compounds	Below –5.60	Mpro or 3CLpro	Anti-SARS-CoV-2 activity	[47]
Saquinavir	–74.41	3CLpro	Inhibitors against the SARS-CoV-2	[48]
TCM5280805	–29.49	3CLpro	Inhibitors against the SARS-CoV-2	[48]
Binifibrate	–69.04	Mpro	Bind strongly to the enzyme active site and hence they can be repurposed against SARS-CoV-2	[49]
Bamifylline	–63.19	Mpro		[49]
Simeprevir	–10.30	Mpro	Anti-SARS-CoV-2 activity	[50]
Ergotamine	–9.80
Bromocriptine	–9.60
Boceprevir	–13.60	Mpro	Inhibitors against the SARS-CoV-2	[2]
Epirubicin	–11.40
Nelfinavir	–13.40
Rutin	–14.90
X77 “control”	–17.00
Beclabuvir	–10.40	Mpro	Inhibit the replication of the virus	[75]
Nilotinib	–9.90
Tirilazad	–9.60
Trametinib	–9.50
Glecaprevir	–9.40
Hydroxychloroquine	Between –4.40 and –8.80	Multiple Mpros of SARS-CoV-2	Demonstrate efficacy against SARS-CoV-2	[52]
Chloroquine
Remdesivir
Lopinavir
Ritonavir
Umifenovir
Favipiravir
Epclusa (velpatasvir/sofosbuvir)	Between –9.00 and –10.10	Mpro	Very effective inhibitory actions on viral enzymes	[53]
Harvoni (ledipasvir/sofosbuvir)	Between –9.00 and –10.10	Mpro	Very effective inhibitory actions on viral enzymes	[53]
9 compounds	Between –6.05 and –11.23	S-protein (S-RBD)	Anti-SARS-CoV-2 activity	[54]
9 compounds	Between –6.05 and –11.23	ACE2	Anti-SARS-CoV-2 activity	[54]
Bedaquiline	-	Mpro	Inhibitors against the SARS-CoV-2	[76]
Glibenclamide
Miconazole
7 Drugs	-	Mpro	Inhibitors against the SARS-CoV-2	[55]
Vaborbactam	Below –5.40	Mpro	Anti-SARS-CoV-2 activity	[56]
Cimetidine
Ixazomib
Scopolamine
Bicalutamide
Riociguat
9 Nucleoside triphosphate analogs	Below –8.70	RdRp	Anti-viral activity	[57]
Ibrutinib and zanubrutinib	Below –7.00	S-protein (S-RBD)	Inhibitors against the SARS-CoV-2	[58]
		Mpro
		RdRp
		ACE2
		BTK
		TMPRSS2
		PLpro
9 Currently approved molecules daunorubicin	Between –0.50 and –138.80	Mpro	Potential inhibitors of SARS-CoV-2.	[59]
Oxytetracycline	–9.30	3CLpro	Inhibitors against the SARS-CoV-2	[60]
Bemcentinib	–78.46	PLpro 3CLpro	Inhibitors against the SARS-CoV-2	[63]
Clofazimine	–165.60
Abivertinib	–301.37
Dasabuvir	–166.16
MFCD00832476	–158.66
Leuconicine F	–224.32
Indinavir	Between –26.27 and –69.23	MPPs, spike ecto-domain, spike RBD, Nsp9 RNA binding protein, and HR2 domain	Fight SARS-CoV-2 infection	[64]
Sorivudine
Cidofovir
Darunavir
Ledipasvir	Below –10.00	ACE2	Anti-SARS-CoV-2 activity	[30]
Estradiol benzoate		CD147
Vancomycin		RdRp
Paritaprevir and vancomycin		ACE2 and RdRp
Lividomycin	–2,145.79	ACE2	Potential ACE2 inhibitors	[65]
Burixafor	–2,108.82
Quisinostat	–1,998.77
Fluprofylline	–1,785.00
Pemetrexed	–1,602.58
Spirofylline	–1,541.73
Edotecarin	–1,312.19
Diniprofylline	–1,292.42
10 Molecules	Below –4.32	S1-RBD and the ACE2 receptor	Inhibitors of S-protein S1 domain and ACE2 interaction	[10]
Ribavirin	- (Relative docking Score below 2.80)	Mpro	Inhibitors of Mpro	[20]
Telbivudine
Vitamin B12
Nicotinamide
Apixaban	-	Mpro	Anti-SARS-CoV-2 activity	[66]
Lapatinib	Approximately –30.00	3CLpro	Inhibit SARS-CoV-2 3CLpro	[67]
16 Potent inhibitors	Below –5.30	Mpro	Inhibitors of Mpro	[33]
Omipalisib/remdesivir	-	RdRp	Inhibitors against the SARS-CoV-2	[16]
Tipifarnib/omipalisib
Tipifarnib/remdesivi
Saquinavir	Below –6.00	Mpro	Inhibitors against the SARS-CoV-2	[70]
Beclabuvir	Below –6.00	Mpro	Inhibitors against the SARS-CoV-2	[70]
Diammonium Glycyrrhizinate Digitoxin	–11.75 –11.25	S1-RBD and the ACE2 receptor	Inhibitors against the SARS-CoV-2	[71]
Ivermectin Rapamycin (Sirolimus)	–10.86 –10.56
Rifaximin Amphotericin B	–10.54 –10.50
Ritonavir	–8.01	Mpro	Mpro inhibitors	[72]
Nelfinavir	–7.62
Saquinavir	–7.50
Pralmorelin	–9.17
Iodixanol	–15.77
Iotrolan	–14.36
Hesperidin	–10.30	Nsp16 2’-O-MTase	Potential inhibitors of 2’-O-ribose MTase	[73]
Rebastinib	–10.20
Losulazine	–10.27
Cep-32496	–10.20
R428	–10.40
Entrectinib	–10.57
Osi-027	–10.50
MK3207	–10.97
Rimegepant	–10.77
Bolazine	–10.47
Paritaprevir, Simeprevir and Velpatasvir	Below –10.0	S-protein	Anti-SARS-CoV-2 activity	[61]
		Nucleocapsid protein
		2’-O-ribose MTase
Gonadorelin	–9.40	RBD-ACE2	Inhibiting the virus infection	[62]
Fondaparinux	–8.50
Atorvastatin	–7.30

Ref.: reference; WT: wild type; ATV: atovaquone; DLT: delta mutated RBD of S-protein; LMB: lambda mutated RBD of S-protein; PRZ: praziquantel; TMPRSS2: transmembrane serine protease 2; MPPs: main protease proteins; MTase: methyltransferase; -: blank cell

Declarations

Author contributions

BS: Conceptualization, Investigation, Writing—original draft, Writing—review & editing, Validation, Supervision.

Conflicts of interest

The author declares that he have no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Not applicable.

Copyright

References

Payne S. Chapter 17 - Family coronaviridae. In: Payne S, editor. Viruses. Academic Press; 2017. pp. 149–58. [DOI] [PMC]

Mandour YM, Zlotos DP, Alaraby Salem M. A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn. 2022;40:2327–38. [DOI] [PubMed] [PMC]

Pushpakom S, Iorio F, Eyers PA, Escott KJ, Hopper S, Wells A, et al. Drug repurposing: progress, challenges and recommendations. Nat Rev Drug Discov. 2019;18:41–58. [DOI] [PubMed]

Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–73. [DOI] [PubMed] [PMC]

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al.; China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727–33. [DOI] [PubMed] [PMC]

Tahir Ul Qamar M, Alqahtani SM, Alamri MA, Chen LL. Structural basis of SARS-CoV-2 3CL^pro and anti-COVID-19 drug discovery from medicinal plants. J Pharm Anal. 2020;10:313–9. [DOI] [PubMed] [PMC]

Cinatl J, Morgenstern B, Bauer G, Chandra P, Rabenau H, Doerr HW. Glycyrrhizin, an active component of liquorice roots, and replication of SARS-associated coronavirus. Lancet. 2003;361:2045–6. [DOI] [PubMed] [PMC]

Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, et al. Structure of M^pro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582:289–93. [DOI] [PubMed]

Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020;26:450–2. [DOI] [PubMed] [PMC]

10.

Prajapat M, Shekhar N, Sarma P, Avti P, Singh S, Kaur H, et al. Virtual screening and molecular dynamics study of approved drugs as inhibitors of spike protein S1 domain and ACE2 interaction in SARS-CoV-2. J Mol Graph Model. 2020;101:107716. [DOI] [PubMed] [PMC]

11.

Wang W, Yue RF, Jin Z, He LM, Shen R, Du D, et al. Efficiency comparison of apigenin-7-O-glucoside and trolox in antioxidative stress and anti-inflammatory properties. J Pharm Pharmacol. 2020;72:1645–56. [DOI] [PubMed]

12.

Yu J, Ouyang W, Chua MLK, Xie C. SARS-CoV-2 Transmission in patients with cancer at a tertiary care hospital in Wuhan, China. JAMA Oncol. 2020;6:1108–10. [DOI] [PubMed] [PMC]

13.

Onder G, Rezza G, Brusaferro S. Case-fatality rate and characteristics of patients dying in relation to COVID-19 in Italy. JAMA. 2020;323:1775–6. Erratum in: JAMA. 2020;323:1619. [DOI] [PubMed]

14.

Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science. 2020;368:409–12. [DOI] [PubMed] [PMC]

15.

Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, et al. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 2020;587:657–62. [DOI] [PubMed] [PMC]

16.

Jang WD, Jeon S, Kim S, Lee SY. Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay. Proc Natl Acad Sci U S A. 2021;118:e2024302118. [DOI] [PubMed] [PMC]

17.

Li YH, Hu CY, Wu NP, Yao HP, Li LJ. Molecular characteristics, functions, and related pathogenicity of MERS-CoV proteins. Engineering (Beijing). 2019;5:940–7. [DOI] [PubMed] [PMC]

18.

Zumla A, Chan JF, Azhar EI, Hui DS, Yuen KY. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov. 2016;15:327–47. [DOI] [PubMed] [PMC]

19.

Pillaiyar T, Meenakshisundaram S, Manickam M. Recent discovery and development of inhibitors targeting coronaviruses. Drug Discov Today. 2020;25:668–88. [DOI] [PubMed] [PMC]

20.

Kandeel M, Al-Nazawi M. Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sci. 2020;251:117627. [DOI] [PubMed] [PMC]

21.

Li G, De Clercq E. Therapeutic options for the 2019 novel coronavirus (2019-nCoV). Nat Rev Drug Discov. 2020;19:149–50. [DOI] [PubMed]

22.

Lu H. Drug treatment options for the 2019-new coronavirus (2019-nCoV). Biosci Trends. 2020;14:69–71. [DOI] [PubMed]

23.

Fan HH, Wang LQ, Liu WL, An XP, Liu ZD, He XQ, et al. Repurposing of clinically approved drugs for treatment of coronavirus disease 2019 in a 2019-novel coronavirus-related coronavirus model. Chin Med J (Engl). 2020;133:1051–6. [DOI] [PubMed] [PMC]

24.

Kruse RL. Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China. F1000Res. 2020;9:72. [DOI] [PubMed] [PMC]

25.

Bouyahya A, El Omari N, Elmenyiy N, Hakkour M, Balahbib A, Guaouguaou E, et al. Therapeutic strategies of COVID-19: From natural compounds to vaccine trials. Biointerface Res Appl Chem. 2020;11:8318–73. [DOI]

26.

Simmons G, Gosalia DN, Rennekamp AJ, Reeves JD, Diamond SL, Bates P. Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry. Proc Natl Acad Sci U S A. 2005;102:11876–81. [DOI] [PubMed] [PMC]

27.

Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30:269–71. [DOI] [PubMed] [PMC]

28.

Zhang H, Yang Y, Li J, Wang M, Saravanan KM, Wei J, et al. A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro. PLoS Comput Biol. 2020;16:e1008489. [DOI] [PubMed] [PMC]

29.

Kirchdoerfer RN, Ward AB. Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nat Commun. 2019;10:2342. [DOI] [PubMed] [PMC]

30.

Mahdian S, Zarrabi M, Panahi Y, Dabbagh S. Repurposing FDA-approved drugs to fight COVID-19 using in silico methods: targeting SARS-CoV-2 RdRp enzyme and host cell receptors (ACE2, CD147) through virtual screening and molecular dynamic simulations. Inform Med Unlocked. 2021;23:100541. Erratum in: Inform Med Unlocked. 2023:101263. [DOI] [PubMed] [PMC]

31.

Almeida JSFD, Botelho FD, de Souza FR, Dos Santos MC, Goncalves ADS, Rodrigues RLB,et al. Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets. J Biomol Struct Dyn. 2022;40:5229–42. [DOI] [PubMed] [PMC]

32.

Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, et al. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002;58:899–907. [DOI] [PubMed]

33.

Li Z, Li X, Huang YY, Wu Y, Liu R, Zhou L, et al. Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs. Proc Natl Acad Sci U S A. 2020;117:27381–7. [DOI] [PubMed] [PMC]

34.

Sokouti B. A systems biology approach for investigating significantly expressed genes among COVID-19, hepatocellular carcinoma, and chronic hepatitis B. Egypt J Med Hum Genet. 2022;23:146. [DOI] [PubMed] [PMC]

35.

Sokouti M, Sadeghi R, Pashazadeh S, Eslami S, Sokouti M, Ghojazadeh M, et al. Comparative global epidemiological investigation of SARS-CoV-2 and SARS-CoV diseases using Meta-MUMS tool through incidence, Mortality, and Recovery Rates. Arch Med Res. 2020;51:458–63. [DOI] [PubMed] [PMC]

36.

Sokouti M, Sadeghi R, Pashazadeh S, Eslami S, Sokouti M, Ghojazadeh M, et al. Meta-MUMS COVID-19 web server: an online daily monitoring server for comparative and cumulative epidemiological analysis. Z Gesundh Wiss. 2023;31:37–9. [DOI] [PubMed] [PMC]

37.

Gujar S, Pol JG, Kim Y, Kroemer G. Repurposing CD8⁺ T cell immunity against SARS-CoV-2 for cancer immunotherapy: a positive aspect of the COVID-19 pandemic? Oncoimmunology. 2020;9:1794424. [DOI] [PubMed] [PMC]

38.

Borcherding N, Jethava Y, Vikas P. Repurposing anti-cancer drugs for COVID-19 treatment. Drug Des Devel Ther. 2020;14:5045–58. [DOI] [PubMed] [PMC]

39.

Sonkar C, Doharey PK, Rathore AS, Singh V, Kashyap D, Sahoo AK, et al. Repurposing of gastric cancer drugs against COVID-19. Comput Biol Med. 2021;137:104826. [DOI] [PubMed] [PMC]

40.

Pingali MS, Singh A, Singh V, Sahoo AK, Varadwaj PK, Samanta SK. Docking and molecular dynamics simulation for therapeutic repurposing in small cell lung cancer (SCLC) patients infected with COVID-19. J Biomol Struct Dyn. 2023;41:16–25. [DOI] [PubMed]

41.

García-Trejo JJ, Ortega R, Zarco-Zavala M. Putative repurposing of lamivudine, a nucleoside/nucleotide analogue and antiretroviral to improve the outcome of cancer and COVID-19 patients. Front Oncol. 2021;11:664794. [DOI] [PubMed] [PMC]

42.

Ashrafizadeh M, Mirzaei S, Gholami MH, Hashemi F, Zabolian A, Raei M, et al. Hyaluronic acid-based nanoplatforms for Doxorubicin: a review of stimuli-responsive carriers, co-delivery and resistance suppression. Carbohydr Polym. 2021;272:118491. [DOI] [PubMed]

43.

Paskeh MDA, Entezari M, Mirzaei S, Zabolian A, Saleki H, Naghdi MJ, et al. Emerging role of exosomes in cancer progression and tumor microenvironment remodeling. J Hematol Oncol. 2022;15:83. [DOI] [PubMed] [PMC]

44.

Mirzaei S, Gholami MH, Hashemi F, Zabolian A, Farahani MV, Hushmandi K, et al. Advances in understanding the role of P-gp in doxorubicin resistance: molecular pathways, therapeutic strategies, and prospects. Drug Discov Today. 2022;27:436–55. [DOI] [PubMed]

45.

Ebrahimi M, Karami L, Alijanianzadeh M. Computational repurposing approach for targeting the critical spike mutations in B.1.617.2 (delta), AY.1 (delta plus) and C.37 (lambda) SARS-CoV-2 variants using exhaustive structure-based virtual screening, molecular dynamic simulations and MM-PBSA methods. Comput Biol Med. 2022;147:105709. [DOI] [PubMed] [PMC]

46.

de Oliveira OV, Rocha GB, Paluch AS, Costa LT. Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening. J Biomol Struct Dyn. 202;39:3924–33. [DOI] [PubMed] [PMC]

47.

Tsuji M. Potential anti-SARS-CoV-2 drug candidates identified through virtual screening of the ChEMBL database for compounds that target the main coronavirus protease. FEBS Open Bio. 2020;10:995–1004. [DOI] [PubMed] [PMC]

48.

Khan A, Ali SS, Khan MT, Saleem S, Ali A, Suleman M, et al. Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro). J Biomol Struct Dyn. 2021;39:4659–70. [DOI] [PubMed] [PMC]

49.

Arun KG, Sharanya CS, Abhithaj J, Francis D, Sadasivan C. Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target. J Biomol Struct Dyn. 2021;39:4647–58. [DOI] [PubMed] [PMC]

50.

Rahman MM, Saha T, Islam KJ, Suman RH, Biswas S, Rahat EU, et al. Virtual screening, molecular dynamics and structure-activity relationship studies to identify potent approved drugs for Covid-19 treatment. J Biomol Struct Dyn. 2021;39:6231–41. [DOI] [PubMed] [PMC]

51.

Yang Y, Zhou D, Zhang X, Shi Y, Han J, Zhou L, et al. D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19. Brief Bioinform. 2022;23:bbac147. [DOI] [PubMed] [PMC]

52.

Liang H, Zhao L, Gong X, Hu M, Wang H. Virtual screening FDA approved drugs against multiple targets of SARS-CoV-2. Clin Transl Sci. 2021;14:1123–32. [DOI] [PubMed] [PMC]

53.

Chen YW, Yiu CB, Wong KY. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL^pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates [version 2; peer review: 3 approved]. F1000Res. 2020;9:129. [DOI] [PubMed] [PMC]

54.

Choudhary S, Malik YS, Tomar S. Identification of SARS-CoV-2 cell entry inhibitors by drug repurposing using in silico structure-based virtual screening approach. Front Immunol. 2020;11:1664. [DOI] [PubMed] [PMC]

55.

Federico LB, Silva GM, da Silva Hage-Melim LI, Gomes SQ, Barcelos MP, Galindo Francischini IA, et al. Identification of known drugs as potential SARS-CoV-2 Mpro inhibitors using ligand- and structure-based virtual screening. Future Med Chem. 2021;13:1353–66. [DOI] [PubMed] [PMC]

56.

Vázquez-Mendoza LH, Mendoza-Figueroa HL, García-Vázquez JB, Correa-Basurto J, García-Machorro J. In slico drug repositioning to target the SARS-CoV-2 main protease as covalent inhibitors employing a combined structure-based virtual screening strategy of pharmacophore models and covalent Docking. Int J Mol Sci. 2022;23:3987. [DOI] [PubMed] [PMC]

57.

Tsuji M. Virtual screening and quantum chemistry analysis for SARS-CoV-2 RNA-dependent RNA polymerase using the ChEMBL database: reproduction of the remdesivir-RTP and favipiravir-RTP binding modes obtained from Cryo-EM experiments with high binding affinity. Int J Mol Sci. 2022;23:11009. [DOI] [PubMed] [PMC]

58.

Kaliamurthi S, Selvaraj G, Selvaraj C, Singh SK, Wei DQ, Peslherbe GH. Structure-based virtual screening reveals ibrutinib and zanubrutinib as potential repurposed drugs against COVID-19. Int J Mol Sci. 2021;22:7071. [DOI] [PubMed] [PMC]

59.

Jiménez-Alberto A, Ribas-Aparicio RM, Aparicio-Ozores G, Castelán-Vega JA. Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Comput Biol Chem. 2020;88:107325. [DOI] [PubMed] [PMC]

60.

Meyer-Almes FJ. Repurposing approved drugs as potential inhibitors of 3CL-protease of SARS-CoV-2: virtual screening and structure based drug design. Comput Biol Chem. 2020;88:107351. [DOI] [PubMed] [PMC]

61.

Kadioglu O, Saeed M, Greten HJ, Efferth T. Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Comput Biol Med. 2021;133:104359. [DOI] [PubMed] [PMC]

62.

Kumar V, Liu H, Wu C. Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulations. Comput Biol Med. 2021;135:104634. [DOI] [PubMed] [PMC]

63.

Jade D, Ayyamperumal S, Tallapaneni V, Joghee Nanjan CM, Barge S, Mohan S, et al. Virtual high throughput screening: Potential inhibitors for SARS-CoV-2 PLPRO and 3CLPRO proteases. Eur J Pharmacol. 2021;901:174082. [DOI] [PubMed] [PMC]

64.

Rahman MR, Banik A, Chowdhury IM, Sajib EH, Sarkar S. Identification of potential antivirals against SARS-CoV-2 using virtual screening method. Inform Med Unlocked. 2021;23:100531. [DOI] [PubMed] [PMC]

65.

Teralı K, Baddal B, Gülcan HO. Prioritizing potential ACE2 inhibitors in the COVID-19 pandemic: insights from a molecular mechanics-assisted structure-based virtual screening experiment. J Mol Graph Model. 2020;100:107697. [DOI] [PubMed] [PMC]

66.

Hage-Melim LIDS, Federico LB, de Oliveira NKS, Francisco VCC, Correia LC, de Lima HB, et al. Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19. Life Sci. 2020;256:117963. [DOI] [PubMed] [PMC]

67.

Sanachai K, Somboon T, Wilasluck P, Deetanya P, Wolschann P, Langer T, et al. Identification of repurposing therapeutics toward SARS-CoV-2 main protease by virtual screening. PLoS One. 2022;17:e0269563. [DOI] [PubMed] [PMC]

68.

Mazzini S, Musso L, Dallavalle S, Artali R. Putative SARS-CoV-2 M^pro inhibitors from an in-house library of natural and nature-inspired products: a virtual screening and molecular docking study. Molecules. 2020;25:3745. [DOI] [PubMed] [PMC]

69.

Manelfi C, Gossen J, Gervasoni S, Talarico C, Albani S, Philipp BJ, et al. Combining different docking engines and consensus strategies to design and validate optimized virtual screening protocols for the SARS-CoV-2 3CL protease. Molecules. 2021;26:797. [DOI] [PubMed] [PMC]

70.

Talluri S. Molecular docking and virtual screening based prediction of drugs for COVID-19. Comb Chem High Throughput Screen. 2021;24:716–28. [DOI]

71.

Kalhor H, Sadeghi S, Abolhasani H, Kalhor R, Rahimi H. Repurposing of the approved small molecule drugs in order to inhibit SARS-CoV-2 S-protein and human ACE2 interaction through virtual screening approaches. J Biomol Struct Dyn. 2022;40:1299–315. [DOI] [PubMed] [PMC]

72.

Kanhed AM, Patel DV, Teli DM, Patel NR, Chhabria MT, Yadav MR. Identification of potential Mpro inhibitors for the treatment of COVID-19 by using systematic virtual screening approach. Mol Divers. 2021;25:383–401. [DOI] [PubMed] [PMC]

73.

Nand M, Maiti P, Joshi T, Chandra S, Pande V, Kuniyal JC, et al. Virtual screening of anti-HIV1 compounds against SARS-CoV-2: machine learning modeling, chemoinformatics and molecular dynamics simulation based analysis. Sci Rep. 2020;10:20397. [DOI] [PubMed] [PMC]

74.

Jiang Y, Liu L, Manning M, Bonahoom M, Lotvola A, Yang Z, et al. Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2’-O-ribose methyltransferase of SARS-CoV-2 coronavirus. J Biomol Struct Dyn. 2022;40:1331–46. [DOI] [PubMed] [PMC]

75.

Chtita S, Belhassan A, Aouidate A, Belaidi S, Bouachrine M, Lakhlifi T. Discovery of potent SARS-CoV-2 inhibitors from approved antiviral drugs via docking and virtual screening. Comb Chem High Throughput Screen. 2021;24:441–54. [DOI] [PubMed]

76.

Ferraz WR, Gomes RA, S Novaes AL, Goulart Trossini GH. Ligand and structure-based virtual screening applied to the SARS-CoV-2 main protease: an in silico repurposing study. Future Med Chem. 2020;12:1815–28. [DOI] [PubMed] [PMC]

77.

Verma N, Qu X, Trozzi F, Elsaied M, Karki N, Tao Y, et al. SSnet: a deep learning approach for protein-ligand interaction prediction. Int J Mol Sci. 2021;22:1392. [DOI] [PubMed] [PMC]

78.

Negru PA, Miculas DC, Behl T, Bungau AF, Marin RC, Bungau SG. Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses. Biomed Pharmacother. 2022;153:113432. [DOI] [PubMed] [PMC]

79.

Pantsar T, Poso A. Binding affinity via docking: fact and fiction. Molecules. 2018;23:1899. [DOI] [PubMed] [PMC]

80.

Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J Med Chem. 2004;47:45–55. [DOI] [PubMed]

81.

Feher M, Williams CI. Effect of input differences on the results of docking calculations. J Chem Inf Model. 2009;49:1704–14. [DOI] [PubMed]

82.

Pinzi L, Rastelli G. Molecular docking: shifting paradigms in drug discovery. Int J Mol Sci. 2019;20:4331. [DOI] [PubMed] [PMC]

83.

Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, et al. A critical assessment of docking programs and scoring functions. J Med Chem. 2006;49:5912–31. [DOI] [PubMed]

84.

Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov. 2015;10:449–6. [DOI] [PubMed] [PMC]