COVID-19: molecular targets, drug repurposing and new avenues for drug discovery

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious infection that may break the healthcare system of several countries. Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. Finally, we also discuss patent protection issues, cost effectiveness and scalability of synthetic routes for some of the most studied repurposing candidates since these are key aspects to meet global demand for COVID-19 treatment.

Key words:
COVID-19; SARS-CoV-2; drug repurposing; drug discovery; replication cycle; drug targets

Authorship

Mario Roberto Senger

Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz-FiocruzBrazilRio de Janeiro, RJ, BrazilFundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, Brasil

Tereza Cristina Santos Evangelista

Universidade Federal do Rio de Janeiro, Instituto de Química, Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ, BrasilUniversidade Federal do Rio de JaneiroBrazilRio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro, Instituto de Química, Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ, Brasil

Rafael Ferreira Dantas

Marcos Vinicius da Silva Santana

Luiz Carlos Saramago Gonçalves

Lauro Ribeiro de Souza Neto

Sabrina Baptista Ferreira

Floriano Paes Silva-Junior ⁺+ Corresponding author: floriano@ioc.fiocruz.br

http://orcid.org/0000-0003-4560-1291

+ Corresponding author: floriano@ioc.fiocruz.br

MRS, TCSE and RFD contributed equally to this work.

All authors contributed to writing, reviewing and editing the manuscript. MRS, TCSE and RFD contributed equally to this manuscript; FPS-Jr performed the manuscript conceptualisation and final review. The authors declare no conflict of interest concerning this manuscript.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables

Figures (17)
Tables (3)

Repurposed drug	Previous use	Predicted targets	Discovery origin	Experimental evidence	Reference
Pemirolast (30), nitrofurantoin (31), isoniazid pyruvate (32), eriodictyol (33), cepharanthine (34), ergoloid (35) and hypericin (36)	Multiple	Disrupting spike protein (S-protein) and ACE2 receptor interaction or inhibit S-protein and block ACE2 receptor	Ensemble docking	Natural products, such as eriodictyol (33), cepharanthin (34), ergoloid (35) and hypericin (36) have shown antiviral activity against coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV).^a	¹⁶⁰160. Pant S, Singh M, Ravichandiran V, Murty USN, Srivastava HK. Peptide-like and small-molecule inhibitors against Covid-19. J Biomol Struct Dyn. 2020: 1-10.
Mefuparib hydrochloride (CVL218) (37)	Cancer	Nucleocapsid (N protein)	Knowledge-graph docking in vitro and in vivo assays	Mefuparib (37) achieved an EC₅₀ of 5.12 μM.	¹⁶⁴164. Ge Y, Tian T, Huang S, Wan F, Li J, Li S, et al. A data-driven drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. 2020. Preprint available from: https://www.biorxiv.org/content/10.1101/2020.03.11.986836v1. https://www.biorxiv.org/content/10.1101/...
Atazanavir (12) and efavirenz (38)	HIV	SARS-CoV-2 3C-like protease (M^pro)	Molecule transformer drug-target interaction (MT-DTI)	Atazanavir (12) can been found in lungs after administration and have shown inhibitory activity against M^pro.^b	¹⁰³103. Beck BR, Shin B, Choi Y, Park S, Kang K. Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. Comput Struct Biotechnol J. 2020; 18: 784-90.
Baricitinib (39)	Rheumatoid arthritis	Human AP2-associated protein kinase 1 (AAK1)	Knowledge-graph	A pilot trial indicated that baricitinib (39) improved clinical parameters (e.g., cough and dyspnea) in a small group of patients.^c	¹⁶¹161. Richardson P, Griffin I, Tucker C, Smith D, Oechsle O, Phelan A, et al. Baricitinib as potential treatment for 2019-nCoV acute respiratory disease. Lancet. 2020; 395(10223): e30-1.
Toremifene (40), sirolimus (41), mercaptopurine (42), irbesartan (43)	Multiple	Multiple targets in humans and coronaviruses	Systems pharmacology-based network and human protein-protein (PPI) network	Antiviral activities against coronaviruses has been described for selective estrogen modulators toremifene (40), immunosuppressants sirolimus (41) and mercaptopurine (42) and angiotensin receptor blockers irbesartan (43).^d	⁵²52. Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F. Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. 2020; 6(1): 14.

Repurposed drug	Previous use	Targets	In vitro potency (EC₅₀)	Selectivity index	Reference
Remdesivir (8)	Ebola	RNA polymerase	0.77 μM	129.9	¹⁹⁴194. 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(3): 269-71.
Chloroquine (20) / Hydroxychloroquine (26)	Malaria / Lupus and rheumatoid arthritis	Acidification in endosomes and lysosomes, glycosylation of cellular virus receptors and modulation host immune response	1.13 μM / 0.72 μM	37.1 to 100.8 / 14.4 to 61.5 depending on multiplicities of infection	¹⁹⁴194. 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(3): 269-71. ^, ¹⁹⁵195. Cao B, Sheth MN, Mysorekar IU. To Zika and destroy: an antimalarial drug protects fetuses from Zika infection. Future Microbiol. 2018; 13(2): 137-9. ^, ¹⁹⁶196. Yao X, Ye F, Zhang M, Cui C, Huang B, Niu P, et al. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clin Infect Dis. 2020; 71(15): 732-9.
Ritonavir (2) + lopinavir (1)	HIV	3-chymotrypsin-like protease (3CL^pro) and papain-like protease (PL^pro)	6.6 to 17.1 μM for Lopinavir (1)	ND	¹⁹⁷197. Choy K-T, Wong AY-L, Kaewpreedee P, Sia SF, Chen D, Hui KPY, et al. Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro. Antiviral Res. 2020; 178: 104786.
Nitazoxanide (47)	Broad-spectrum antiparasitic and antiviral	Still needs confirmation	2.1 μM	16.8	¹⁹⁴194. 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(3): 269-71.
Ivermectin (48)	Broad-spectrum antiparasitic	Still needs confirmation	2 μM	ND	¹⁹⁸198. 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: 104787.
Teicoplanin (27)	Antibiotic for gram-positive bacteria	Still needs confirmation	1.7 μM	ND	¹⁹⁹199. Zhang J, Ma X, Yu F, Liu J, Zou F, Pan T, et al. Teicoplanin potently blocks the cell entry of 2019-nCoV. 2020. Preprint available from: https://www.biorxiv.org/content/10.1101/2020.02.05.935387v1. https://www.biorxiv.org/content/10.1101/...

Repurposed drug	Study characteristics	Estimated enrolment	Dosage	Characteristics of the study and conclusion	Clinical trial and recruitment status
Remdesivir (8)	Phase III, double-blind, randomised, placebo-controlled, multicentre	308 patients	200 mg Intravenously on the first day plus 100 mg once daily, for more nine consecutive days	Adult patients with mild and moderate COVID-19, no published results	NCT04252664 (suspended by epidemic control in China with no eligible patients)
		237 patients		Adult patients with severe COVID-19, remdesivir (8) was not associated with clinical benefits in severe forms. However, an observed numerical reduction in time to clinical improvement in patients treated earlier, but still requires confirmation	²¹⁵215. Wang Y, Zhang D, Du G, Du R, Zhao J, Jin Y, et al. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet. 2020; 395(10236): 1569-78.; NCT04257656 (terminated by epidemic control in China with no eligible patients)
		1063 patients		Remdesivir (8) treated patients with lower respiratory tract infection have a shorter time to recovery compared to placebo group (11 vs 15 days)	²¹⁶216. Beigel JH, Tomashek KM, Dodd LE, Mehta AK, Zingman BS, Kalil AC, et al. Remdesivir for the treatment of Covid-19 - Preliminary report. N Engl J Med [Internet]. 2020 [cited 2020 Aug 8]. Available from: https://doi.org/10.1056/NEJMoa2007764. https://doi.org/10.1056/NEJMoa2007764... ; NCT04280705
Chloroquine (20)	Multicentre	> 100 patients	500 mg per day, for 10 days	Compilation of various clinical studies that are in course, authors conclude that the dosage used could be sufficient	²¹⁷217. Gao J, Tian Z, Yang X. Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Biosci Trends. 2020; 14(1): 72-3.
Chloroquine (20)	Phase IIb Double-blind, randomised	81 patients	600 mg twice daily for 10 days and 450 mg twice on the first day, once daily for more 4 days	Higher dosage of chloroquine (20) has toxic effects and increased lethality, with any clinical benefit	²¹⁸218. Borba MGS, Val FFA, Sampaio VS, Alexandre MAA, Melo GC, Brito M, et al. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. JAMA Netw Open. 2020; 3(4): e208857.
Hydroxychloroquine (26)	non-randomised, non-double-blind, non-placebo-controlled	36 patients	600 mg of hydroxychloroquine (26) daily for 10 days	Hydroxychloroquine (26) significantly reduces viral load despite small sample size	²¹⁹219. Gautret P, Lagier J-C, Parola P, Hoang VT, Meddeb L, Mailhe M, et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int J Antimicrob Agents. 2020; 56(1): 105949.
Ritonavir (2)/lopinavir (1)	Randomised, controlled, open-label	199 patients	400 mg/100 mg twice a day for 14 days	No benefit was observed with lopinavir (1)-ritonavir (2) treatment compared to standard care in severe Covid-19 patients	²²⁰220. Cao B, Wang Y, Wen D, Liu W, Wang J, Fan G, et al. A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19. N Engl J Med. 2020; 382(19): 1787-99.
Ritonavir (2)/lopinavir (1) plus interferon	Phase II, randomised, controlled, open-label	127 participants	400 mg/100 mg twice a day for 14 days; Interferon Beta-1B plus 0.25 mg subcutaneous injection alternate day for three days	Completed with no published results until this moment	NCT04276688