In-Vitro Screening of Repurposed Drug Library against Severe Acute Respiratory Syndrome Coronavirus-2
Main Article Content
Abstract
The current pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) demands rapid identification of new antiviral molecules from the existing drugs. Drug repurposing is a significant alternative for pandemics and emerging diseases because of the availability of preclinical data, documented safety in clinic and possibility of immediate production and scalable capacity and supply. Several drugs such as ivermectin and hydroxy chloroquine have been repurposed as anti-SARS-CoV-2 agents, but the effect of these compounds in treating the COVID-19 patients remains sub-optimal. In the present study repurposed drug libraries consisting of 560 compounds from two different sources have been screened against SARS-CoV-2 isolate USA-WA1/2020 in Vero-E6 cell line and 24 compounds were found active. The SARS-CoV-2 virus propagated in Vero E6 cell line and used in screening the drug libraries was sequenced by Next Generation Sequencing to identify any mutations that may have accumulated in the virus genome. The whole genome sequencing data of SARS-CoV-2 showed 9 and 6 single nucleotide polymorphisms in spike protein with reference to Wuhan-Hu-1(NC045512.2) and USA/WA-CDC-WA1/2020 (MN985325.1) isolates respectively. The present study identified 24 compounds active against SARS-CoV-2 isolate USA-WA1/2020 out of 560 repurposed drugs from two libraries. The IC-50 values of the identified hits range from 0.4 µM to 16 µM. Further studies on the repurposed drugs identified in the present screen may be helpful in the rapid development of antiviral drugs against SARS-CoV-2.
Keywords:
COVID-19, dose response curve, IC-50, NGS, repurposed drugs, SARS-CoV-2, SNPs, Vero E6
Article Details
How to Cite
RUDRAMURTHY, Gudepalya Renukaiah; SHANDIL, Radha Krishan; NARAYANAN, Shridhar.
In-Vitro Screening of Repurposed Drug Library against Severe Acute Respiratory Syndrome Coronavirus-2.
Medical Research Archives, [S.l.], v. 11, n. 2, feb. 2023.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/3595>. Date accessed: 25 apr. 2024.
doi: https://doi.org/10.18103/mra.v11i2.3595.
Section
Research Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
References
1. Graham RL, Baric RS. Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission. J Virol. 2010;84(7). doi:10.1128/jvi.01394-09
2. Anthony SJ, Gilardi K, Menachery VD, et al. Further evidence for bats as the evolutionary source of middle east respiratory syndrome coronavirus. mBio. 2017;8(2). doi:10.1128/mBio.00373-17
3. Hu B, Ge X, Wang LF, Shi Z. Bat origin of human coronaviruses. Virol J. 2015;12(1). doi:10.1186/s12985-015-0422-1
4. Huynh J, Li S, Yount B, et al. Evidence Supporting a Zoonotic Origin of Human Coronavirus Strain NL63. J Virol. 2012;86(23). doi:10.1128/jvi.00906-12
5. Murgolo N, Therien AG, Howell B, et al. SARS-CoV-2 tropism, entry, replication, and propagation: Considerations for drug discovery and development. PLoS Pathog. 2021;17(2):1-18. doi:10.1371/JOURNAL.PPAT.1009225
6. Park SE. Epidemiology , virology , and clinical features of severe acute respiratory syndrome -coronavirus-2 ( SARS-CoV-2 ; Coronavirus Disease-19 ). 2020;63(4):119-124.
7. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet. 2020;395:497-506. doi:10.1016/S0140-6736(20)30183-5
8. Zhou Z, Ren L, Zhang L, et al. Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients. Cell Host Microbe. Published online 2020.
9. Krause PR, Fleming TR, Longini IM, et al. SARS-CoV-2 Variants and Vaccines.; 2021.
10. Takashita E, Kinoshita N, Yamayoshi S, et al. Efficacy of Antibodies and Antiviral Drugs against Covid-19 Omicron Variant. New England Journal of Medicine. 2022;386(10). doi:10.1056/nejmc2119407
11. Sheahan T, Sims A, Zhou S, et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus. 2020;5883:1-20. doi:10.1101/2020.03.19.997890
12. Kaptein SJ, Jacobs S, Langendries L, et al. Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine. Published online 2020. doi:10.1101/2020.06.19.159053
13. Zumla A, W Chan JF, Azhar EI, C Hui DS, Yuen KY. Coronaviruses — drug discovery and therapeutic options. Nature Publishing Group. Published online 2016. doi:10.1038/nrd.2015.37
14. Santoro MG, Carafoli E. Remdesivir: From Ebola to COVID-19. Published online 2020. doi:10.1016/j.bbrc.2020.11.043
15. Malin JJ, Suárez I, Priesner V, Fätkenheuer G, Rybniker J. Remdesivir against COVID-19 and Other Viral Diseases.; 2020. https://journals.asm.org/journal/cmr
16. Beigel JH, K.M. Tomashek, L.E. Dodd, et al. Remdesivir for the Treatment of Covid-19 — Final Report. Published online 2020. doi:10.1056/NEJMoa2007764
17. Wang Y, Zhang D, Du G, et al. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. www.thelancet.com. 2020;395:2020. doi:10.1016/S0140-6736(20)31022-9
18. Jason D. Goldman, David C.B. Lye, David S. Hui, et al. Remdesivir for 5 or 10 Days in Patients with Severe Covid-19. Published online 2020. doi:10.1056/NEJMoa2015301
19. Case JB, Bailey AL, Kim AS, Chen RE, Diamond MS. Growth, detection, quantification, and inactivation of SARS-CoV-2. Virology. 2020;548(June):39-48. doi:10.1016/j.virol.2020.05.015
20. Jureka AS, Silvas JA, Basler CF. Propagation, inactivation, and safety testing of SARS-CoV-2. Viruses. 2020;12(6). doi:10.3390/v12060622
21. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15). doi:10.1093/bioinformatics/btu170
22. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14). doi:10.1093/bioinformatics/btp324
23. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment / Map (SAM) Format and SAMtools 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009;25(16).
24. Cingolani P, Platts A, Wang LL, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2). doi:10.4161/fly.19695
25. Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11). doi:10.1038/s41564-020-0770-5
26. MMV’s COVID Box. MMV’s COVID Box. MMV’s COVID Box. Published 2021. https://www.mmv.org/mmv-open/covid-box/about-covid-box
27. Microsource, Discovery Systems, Inc. http://www.msdiscovery.com/
28. Mahmoud DB, Shitu Z, Mostafa A. Drug repurposing of nitazoxanide: can it be an effective therapy for COVID-19? Journal of Genetic Engineering and Biotechnology. 2020;18(1). doi:10.1186/s43141-020-00055-5
29. Mostafa A, Kandeil A, Elshaier YAMM, et al. Fda-approved drugs with potent in vitro antiviral activity against severe acute respiratory syndrome coronavirus 2. Pharmaceuticals. 2020;13(12):1-24. doi:10.3390/ph13120443
30. Ridi R el, Sharma D, Othman AA, Martinez MA. Lack of Effectiveness of Repurposed Drugs for COVID-19 Treatment. Frontiers in Immunology | www.frontiersin.org. 2021;1:635371. doi:10.3389/fimmu.2021.635371
31. Liu Z, Zheng H, Lin H, et al. Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. J Virol. 2020;94(17). doi:10.1128/jvi.00790-20
32. Vankadari N. Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution. Gene. 2020;752. doi:10.1016/j.gene.2020.144792
33. Chen Y, Liu MQ, Luo Y, et al. Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells. Virol Sin. Published online 2021. doi:10.1007/s12250
34. Ogando NS, Dalebout TJ, Zevenhoven-Dobbe JC, et al. SARS-coronavirus-2 replication in Vero E6 cells: Replication kinetics, rapid adaptation and cytopathology. Journal of General Virology. 2020;101(9):925-940. doi:10.1099/jgv.0.001453
35. Agostini ML, Andres EL, Sims AC, et al. Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. mBio. 2018;9(2). doi:10.1128/mBio.00221-18
36. Touret F, Gilles M, Barral K, et al. In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication. Sci Rep. 2020;10(1):1-8. doi:10.1038/s41598-020-70143-6
37. Manli W, Cao R, Zhang L, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30(3):269-271. doi:10.1038/s41422-020-0282-0
38. Kumar S, Singh B, Kumari P, et al. Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity. Comput Struct Biotechnol J. 2021;19:1998-2017. doi:10.1016/j.csbj.2021.04.014
39. Caly L, Druce JD, Catton MG, Jans DA, Wagstaff KM. The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Res. 2020;178(March):3-6. doi:10.1016/j.antiviral.2020.104787
40. Persoons L, Vanderlinden E, Vangeel L, et al. Available online 1. Antiviral Res. 2021;193:166-3542. doi:10.1016/j.antiviral.2021.105127
41. Rong Xiang, Zhengsen Yu, Yang Wang, et al. Recent advances in developing small-molecule inhibitors against SARS-CoV-2 | Elsevier Enhanced Reader. Published 2021. Accessed August 26, 2021. https://reader.elsevier.com/reader/sd/pii/S2211383521002483?token=8C6AEE438E6A0ABCF8981B2F43A8F6270BE50EBB830B32D7913D36A77054D81F9C95259481054E3D3EDBE4A04E1442C8&originRegion=eu-west-1&originCreation=20210826070723
42. Sacramento CQ, Fintelman-Rodrigues N, Temerozo JR, et al. In vitro antiviral activity of the anti-HCV drugs daclatasvir and sofosbuvir against SARS-CoV-2, the aetiological agent of COVID-19. Journal of Antimicrobial Chemotherapy. 2021;76(7). doi:10.1093/jac/dkab072
43. Xiao X, Wang C, Chang D, et al. Identification of Potent and Safe Antiviral Therapeutic Candidates Against SARS-CoV-2. Front Immunol. 2020;11. doi:10.3389/fimmu.2020.586572
44. Gonzalez JLB, Gámez MG, Enciso EAM, et al. Efficacy and Safety of Ivermectin and Hydroxychloroquine in Patients with Severe COVID-19: A Randomized Controlled Trial. Infect Dis Rep. 2022;14(2). doi:10.3390/idr14020020
45. Bakowski MA, Beutler N, Wolff KC, et al. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Nat Commun. 2021;12(1):1-14. doi:10.1038/s41467-021-23328-0
2. Anthony SJ, Gilardi K, Menachery VD, et al. Further evidence for bats as the evolutionary source of middle east respiratory syndrome coronavirus. mBio. 2017;8(2). doi:10.1128/mBio.00373-17
3. Hu B, Ge X, Wang LF, Shi Z. Bat origin of human coronaviruses. Virol J. 2015;12(1). doi:10.1186/s12985-015-0422-1
4. Huynh J, Li S, Yount B, et al. Evidence Supporting a Zoonotic Origin of Human Coronavirus Strain NL63. J Virol. 2012;86(23). doi:10.1128/jvi.00906-12
5. Murgolo N, Therien AG, Howell B, et al. SARS-CoV-2 tropism, entry, replication, and propagation: Considerations for drug discovery and development. PLoS Pathog. 2021;17(2):1-18. doi:10.1371/JOURNAL.PPAT.1009225
6. Park SE. Epidemiology , virology , and clinical features of severe acute respiratory syndrome -coronavirus-2 ( SARS-CoV-2 ; Coronavirus Disease-19 ). 2020;63(4):119-124.
7. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet. 2020;395:497-506. doi:10.1016/S0140-6736(20)30183-5
8. Zhou Z, Ren L, Zhang L, et al. Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients. Cell Host Microbe. Published online 2020.
9. Krause PR, Fleming TR, Longini IM, et al. SARS-CoV-2 Variants and Vaccines.; 2021.
10. Takashita E, Kinoshita N, Yamayoshi S, et al. Efficacy of Antibodies and Antiviral Drugs against Covid-19 Omicron Variant. New England Journal of Medicine. 2022;386(10). doi:10.1056/nejmc2119407
11. Sheahan T, Sims A, Zhou S, et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus. 2020;5883:1-20. doi:10.1101/2020.03.19.997890
12. Kaptein SJ, Jacobs S, Langendries L, et al. Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine. Published online 2020. doi:10.1101/2020.06.19.159053
13. Zumla A, W Chan JF, Azhar EI, C Hui DS, Yuen KY. Coronaviruses — drug discovery and therapeutic options. Nature Publishing Group. Published online 2016. doi:10.1038/nrd.2015.37
14. Santoro MG, Carafoli E. Remdesivir: From Ebola to COVID-19. Published online 2020. doi:10.1016/j.bbrc.2020.11.043
15. Malin JJ, Suárez I, Priesner V, Fätkenheuer G, Rybniker J. Remdesivir against COVID-19 and Other Viral Diseases.; 2020. https://journals.asm.org/journal/cmr
16. Beigel JH, K.M. Tomashek, L.E. Dodd, et al. Remdesivir for the Treatment of Covid-19 — Final Report. Published online 2020. doi:10.1056/NEJMoa2007764
17. Wang Y, Zhang D, Du G, et al. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. www.thelancet.com. 2020;395:2020. doi:10.1016/S0140-6736(20)31022-9
18. Jason D. Goldman, David C.B. Lye, David S. Hui, et al. Remdesivir for 5 or 10 Days in Patients with Severe Covid-19. Published online 2020. doi:10.1056/NEJMoa2015301
19. Case JB, Bailey AL, Kim AS, Chen RE, Diamond MS. Growth, detection, quantification, and inactivation of SARS-CoV-2. Virology. 2020;548(June):39-48. doi:10.1016/j.virol.2020.05.015
20. Jureka AS, Silvas JA, Basler CF. Propagation, inactivation, and safety testing of SARS-CoV-2. Viruses. 2020;12(6). doi:10.3390/v12060622
21. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15). doi:10.1093/bioinformatics/btu170
22. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14). doi:10.1093/bioinformatics/btp324
23. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment / Map (SAM) Format and SAMtools 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009;25(16).
24. Cingolani P, Platts A, Wang LL, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2). doi:10.4161/fly.19695
25. Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11). doi:10.1038/s41564-020-0770-5
26. MMV’s COVID Box. MMV’s COVID Box. MMV’s COVID Box. Published 2021. https://www.mmv.org/mmv-open/covid-box/about-covid-box
27. Microsource, Discovery Systems, Inc. http://www.msdiscovery.com/
28. Mahmoud DB, Shitu Z, Mostafa A. Drug repurposing of nitazoxanide: can it be an effective therapy for COVID-19? Journal of Genetic Engineering and Biotechnology. 2020;18(1). doi:10.1186/s43141-020-00055-5
29. Mostafa A, Kandeil A, Elshaier YAMM, et al. Fda-approved drugs with potent in vitro antiviral activity against severe acute respiratory syndrome coronavirus 2. Pharmaceuticals. 2020;13(12):1-24. doi:10.3390/ph13120443
30. Ridi R el, Sharma D, Othman AA, Martinez MA. Lack of Effectiveness of Repurposed Drugs for COVID-19 Treatment. Frontiers in Immunology | www.frontiersin.org. 2021;1:635371. doi:10.3389/fimmu.2021.635371
31. Liu Z, Zheng H, Lin H, et al. Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. J Virol. 2020;94(17). doi:10.1128/jvi.00790-20
32. Vankadari N. Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution. Gene. 2020;752. doi:10.1016/j.gene.2020.144792
33. Chen Y, Liu MQ, Luo Y, et al. Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells. Virol Sin. Published online 2021. doi:10.1007/s12250
34. Ogando NS, Dalebout TJ, Zevenhoven-Dobbe JC, et al. SARS-coronavirus-2 replication in Vero E6 cells: Replication kinetics, rapid adaptation and cytopathology. Journal of General Virology. 2020;101(9):925-940. doi:10.1099/jgv.0.001453
35. Agostini ML, Andres EL, Sims AC, et al. Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease. mBio. 2018;9(2). doi:10.1128/mBio.00221-18
36. Touret F, Gilles M, Barral K, et al. In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication. Sci Rep. 2020;10(1):1-8. doi:10.1038/s41598-020-70143-6
37. Manli W, Cao R, Zhang L, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30(3):269-271. doi:10.1038/s41422-020-0282-0
38. Kumar S, Singh B, Kumari P, et al. Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity. Comput Struct Biotechnol J. 2021;19:1998-2017. doi:10.1016/j.csbj.2021.04.014
39. Caly L, Druce JD, Catton MG, Jans DA, Wagstaff KM. The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Res. 2020;178(March):3-6. doi:10.1016/j.antiviral.2020.104787
40. Persoons L, Vanderlinden E, Vangeel L, et al. Available online 1. Antiviral Res. 2021;193:166-3542. doi:10.1016/j.antiviral.2021.105127
41. Rong Xiang, Zhengsen Yu, Yang Wang, et al. Recent advances in developing small-molecule inhibitors against SARS-CoV-2 | Elsevier Enhanced Reader. Published 2021. Accessed August 26, 2021. https://reader.elsevier.com/reader/sd/pii/S2211383521002483?token=8C6AEE438E6A0ABCF8981B2F43A8F6270BE50EBB830B32D7913D36A77054D81F9C95259481054E3D3EDBE4A04E1442C8&originRegion=eu-west-1&originCreation=20210826070723
42. Sacramento CQ, Fintelman-Rodrigues N, Temerozo JR, et al. In vitro antiviral activity of the anti-HCV drugs daclatasvir and sofosbuvir against SARS-CoV-2, the aetiological agent of COVID-19. Journal of Antimicrobial Chemotherapy. 2021;76(7). doi:10.1093/jac/dkab072
43. Xiao X, Wang C, Chang D, et al. Identification of Potent and Safe Antiviral Therapeutic Candidates Against SARS-CoV-2. Front Immunol. 2020;11. doi:10.3389/fimmu.2020.586572
44. Gonzalez JLB, Gámez MG, Enciso EAM, et al. Efficacy and Safety of Ivermectin and Hydroxychloroquine in Patients with Severe COVID-19: A Randomized Controlled Trial. Infect Dis Rep. 2022;14(2). doi:10.3390/idr14020020
45. Bakowski MA, Beutler N, Wolff KC, et al. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Nat Commun. 2021;12(1):1-14. doi:10.1038/s41467-021-23328-0