COVID-19: Living Through Another Pandemic Essam Eldin A

pubs.acs.org/journal/aidcbc Viewpoint

COVID-19: Living through Another Pandemic Essam Eldin A. Osman, Peter L. Toogood, and Nouri Neamati*

Cite This: https://dx.doi.org/10.1021/acsinfecdis.0c00224 Read Online

ACCESS Metrics & More Article Recommendations *sı Supporting Information

ABSTRACT: Novel beta-coronavirus SARS-CoV-2 is the pathogenic agent responsible for coronavirus disease-2019 (COVID-19), a globally pandemic infectious disease. Due to its high virulence and the absence of immunity among the general population, SARS- CoV-2 has quickly spread to all countries. This pandemic highlights the urgent unmet need to expand and focus our research tools on what are considered “neglected infectious diseases” and to prepare for future inevitable pandemics. This global emergency has generated unprecedented momentum and scientificefforts around the globe unifying scientists from academia, government and the pharmaceutical industry to accelerate the discovery of vaccines and treatments. Herein, we shed light on the virus structure and life cycle and the potential therapeutic targets in SARS-CoV-2 and briefly refer to both active and passive immunization modalities, drug repurposing focused on speed to market, and novel agents against specific viral targets as therapeutic interventions for COVID-19.

s first reported in December 2019, a novel coronavirus, rate of seasonal influenza (flu), which is fatal in only ∼0.1% of A severe acute respiratory syndrome coronavirus 2 (SARS- infected patients.6 In contrast to previous coronavirus CoV-2), caused an outbreak of atypical pneumonia in Wuhan, epidemics (Table S1), COVID-19 is indiscriminately wreaking 1 China, that has since spread globally. The disease caused by havoc globally with no apparent end in sight due to its high this new virus has been named coronavirus disease-2019 virulence and the absence of resistance among the general (COVID-19) and on March 11, 2020 was declared a global population. pandemic by the World Health Organization (WHO).1 In general, all pandemics pass through three phases until Currently, there are seven known human coronaviruses fi “ ” classified into two broad genera of alpha- and beta- they become endemic. The rst phase of seeding or slow coronaviruses. The alpha-coronaviruses comprise HCoV- spread is often not noticed early enough, leading to NL63 and HCoV-229E, while the beta-coronaviruses comprise dissemination of the disease before effective countermeasures HCoV-OC43, HCoV-HKU1, SARS, Middle East Respiratory can be initiated. During the second phase, there is a rapid Syndrome virus (MERS), and SARS-CoV-2.2 The alpha- increase in cases until a peak occurs in the number of infected coronaviruses and HCoV-OC43 and HCoV-HKU1 are among individuals; parallel efforts to control and contain the virus can the causes of the common cold and have been circulating in mitigate this phase. In the third phase, the infection rate curve 2 Downloaded via 68.36.52.167 on May 10, 2020 at 16:42:22 (UTC). human and animal populations for many years. All these will start to decrease until the disease becomes extinct or viruses originate from a common ancestor and enter the endemic. The kinetics of increase and decrease in the rate of human population through zoonotic transfer or species infections can vary significantly between populations depend- jumping.3 Although the first four known human coronaviruses originated from birds, SARS, MERS, and SARS-CoV-2 appear, ing on the use of preventive measures and the availability of ff See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles. on the basis of gene sequence analysis, to have originated from e ective treatments. Previous coronavirus outbreaks and the bats.4 However, in each case, these more recent viruses appear current pandemic highlight the urgent unmet medical need to to have been transmitted through an intermediate host such as expand and focus our research tools on these long neglected a civet, a small nocturnal mammal native to tropical Asia and infectious diseases and to prepare for future inevitable Africa (SARS), a camel (MERS), or a pangolin (SARS-CoV-2) pandemics. Herein, we briefly recap the current and potential 2 after acquiring additional mutations. Bats harbor more strains future therapeutic interventions for SARS-CoV-2 and highlight of coronavirus than other mammals, estimated to range from 5 the recently published crystal structures of the SARS-CoV-2 5000 to 10,000 distinct subtypes. Therefore, additional main protease and its inhibitors as novel agents against SARS- epidemics are highly likely to occur in the future due to the CoV-2. abundant number of coronaviruses present in the bat population. As of May 6th, 2020, more than 3.7 million cases of SARS- Received: April 20, 2020 CoV-2 positive patients have been reported worldwide with over 260,000 deaths, reflecting a ∼6.8% case fatality rate. While the infection fatality rate is currently unknown, and likely to be lower than the current case fatality rate, estimates suggest it is close to 1%, or approximately 10 times the infection fatality

Figure 1. SARS-CoV-2 encoded proteins. ■ VIRUS STRUCTURE AND LIFE CYCLE airways.13 However, about 20% of infected patients will SARS-CoV-2 is an enveloped, nonsegmented single stranded, progress to develop a lower respiratory tract infection leading positive sense RNA virus. It has one of the largest genomes to hypoxia, and lung damage. These patients are liable to among all RNA viruses, comprising approximately 30 kilobases succumb to acute respiratory distress syndrome (ARDS), (kb) (NC_045512.2). SARS-CoV and SARS-CoV-2 belong to which is frequently fatal. Patients with comorbidities such as the same Coronaviridae family that also includes the highly fatal cardiovascular disease, diabetes mellitus, hypertension, chronic Middle East Respiratory Syndrome virus (MERS) that lung disease, cancer, chronic kidney disease, and obesity (body 7 ≥ 14 appeared in 2012. SARS-CoV-2 enters cells through the mass index 30) and ARDS are at increased risk of death. interaction of its surface Spike protein with the host receptor, The available data indicate that the viral infection can produce angiotensin-converting enzyme 2 (ACE2).8 Subsequent an excessive immune reaction known as cytokine release proteolytic cleavage by the host serine protease TMPRSS2 syndrome (CRS) or “cytokine storm” associated with elevated 15 or perhaps other proteases allows subsequent cell entry by levels of interleukin-6 (IL-6). Laboratory findings associated endocytosis.8 Upon membrane fusion and endocytosis, the with worse clinical outcomes include lymphopenia, and viral nucleocapsid with its genome payload is released into the elevations in liver enzymes, lactate dehydrogenase (LDH), cytoplasm of the infected cell. Following its release into the inflammatory markers (e.g., C-reactive protein [CRP], host cell, the virus usurps portions of the endoplasmic ferritin), D-dimer, prothrombin time (PT), troponin and 15 reticulum to form numerous double membrane vesicles.9 creatine phosphokinase (CPK), and acute kidney injury. These vesicles are perfect sanctuaries to protect the viral Chest CT scans in patients with COVID-19 commonly show genome and allow an efficient replication process to occur ground-glass opacification, consistent with viral pneumonia through a macromolecule complex called the replication− with abnormalities more likely to be bilateral with a peripheral transcription complex (RTC).10 The viral genome is distribution involving the lower lobes.16 While SARS-CoV-2 subsequently translated into viral polyproteins using the host entry is dependent on ACE2 in lung cells,8 ACE2 expression is cell protein translation machinery, which are then cleaved into not exclusive to the lungs, and higher relative ACE2 expression structural and nonstructural viral proteins by two viral is observed in heart, kidney, GIT, and testes (Gene ID: proteases, Mpro and PLpro.11 This step is followed by the 59272). The organ- and cell-specific expression of ACE2 assembly of viral particles (virions) in the endoplasmic suggests that it may play a role in the regulation of reticulum/golgi compartment.12 The packaged virions are cardiovascular and renal function as well as fertility. then transported to the cell surface, are released from the cells Surprisingly, the 2003 SARS-CoV infection was shown to through exocytosis, and proceed to infect other cells. downregulate the expression of ACE2 in lung tissue reducing transmissibility but increasing virulence.17 ACE2, a component ■ CLINICAL COURSE AND OUTCOMES OF COVID-19 of the renin-angiotensin system (RAS), catalyzes the cleavage SARS-CoV-2 likely binds to epithelial cells in the nasal cavity of angiotensin I into angiotensin 1−9 and angiotensin II into during the asymptomatic state of the disease (initial 1−2 days the vasodilator angiotensin 1−7.18 The balance between of infection) where there might be some local propagation of angiotensin II and angiotensin (1−7) is critical since the virus but with a limited innate immune response. Within angiotensin II elicits vasoconstriction via the angiotensin the next few days the infection starts in the upper airway and AT1 receptor, whereas angiotensin (1−7) exerts a vasodilatory during this stage the infection can be detected by nasal swabs effect mediated by AT2 with multiple beneficial effects on the or sputum as well as early markers of the innate immune cardiovascular and respiratory system.18 While ACE2 appears response. About 80% of infected patients show mild symptoms to be involved in the hypertension and respiratory manifes- that are mostly restricted to the upper and conducting tations of severely ill patients, the benefits and merits of ACE

B https://dx.doi.org/10.1021/acsinfecdis.0c00224 ACS Infect. Dis. XXXX, XXX, XXX−XXX ACS Infectious Diseases pubs.acs.org/journal/aidcbc Viewpoint inhibitors (ACEI) or angiotensin receptor 1 blockers (ARBs) might represent the most efficient, near-term therapeutic in the SARS-CoV-2 patient is still controversial.18 The priming intervention if regulatory and safety requirements can be of the S viral protein by TMPRSS2 is crucial for viral entry addressed. With over 1.3 million positive cases of COVID-19 where TMPRSS2 expression is very high in the lungs, kidneys, in the US based solely on the results of RNA molecular tests, and prostate tissue (Gene ID: 7113).8 TMPRSS2 is large-scale antibody testing should be expedited to identify predominantly expressed in the luminal cells of the prostate individuals who have been exposed to the virus but were never epithelium, where its expression is regulated positively by officially confirmed to have COVID-19. An understanding androgens and negatively regulated by estrogens. The what levels of antibody confer immunity postinfection could be hormonal regulation of TMPRSS2 has been suggested to be used to determine who may be less likely to transmit the virus linked to the fact that men are at higher risk than women to and thus may be able to go back safely to work. become seriously ill with COVID-19.19 TMPRSS2 knockout in Drug Repurposing. Developing highly selective SARS- mice is not lethal. In contrast, humans are intolerant to the loss CoV-2 specific new drugs will take many years. Alternatively, of function of ACE2.19 Concerns about the effect of ACEI and repurposing of existing, approved drugs can present a more AT receptor blockers in COVID-19 patients are actively being rapid strategy to identifying drugs effective in treating COVID- investigated in the clinic, with the most recent reports offering 19 (Tables S3 and S4 and Figure S1).11 Repurposing of drugs encouragement that they may have a beneficial effect. that would block SARS-CoV-2 entry and/or replication are urgently needed to mitigate the symptomatic burden of the ■ POTENTIAL DRUG TARGETS disease. Unfortunately, the HIV protease inhibitors ritonavir/ liponavir failed to show efficacy in SARS-CoV-2 infected SARS-CoV-2 viral RNA encodes several proteins that are patients.21 Hydroxychloroquine, which may act by increasing potentially druggable targets (Figure 1 and Table S2), the pH within lysosomes, was granted FDA authorization for including four structural proteins: the Spike (S), Envelope use in emergency cases. Several antiviral agents are being tested (E), Membrane (M), and Nucleocapsid (N).1 The 1273 amino such as the RdRp inhibitor remdesivir and the approved anti- acid, 141 kDa, Spike protein is heavily N-glycosylated and is a 8 influenza drug faviprivir. Remdesivir was previously tested in major inducer of host immune responses. The 222 amino acid humans with Ebola virus disease and also in animal models of M protein has three transmembrane domains and is the most 11 MERS and SARS-CoV. At least six clinical trials are abundant structural protein in the virion. The 75 amino acid E evaluating remdesivir in SARS-CoV-2 patients. Other drugs protein is important for assembly and release of the virus. The that might inhibit RdRp include the broad-spectrum antiviral 419 amino acid nucleocapsid protein forms a protective drug ribavirin. RdRp conservation among RNA virus families protein shell around the virus genetic material and is encased makes it an exciting target for the discovery of newer agents. in a lipid envelope that is usurped from the host cell. Matrix The Spike protein, ACE2, and TMPRSS2 may also represent protein connects the membrane to the nucleocapsid protein. interesting therapeutic targets for current drug repurposing There are also 16 nonstructural proteins (nsp1−16)1 including efforts. Camostat mesylate, approved in Japan for treatment of several for which there are X-ray crystallography-derived pancreatic inflammation, has been shown to block TMPRSS2 structural data: RNA dependent RNA polymerase (nsp12, activity.22 Arbidol, which is hypothesized to block Spike/ACE2 RdRp), a papain-like protease (nsp3, PLpro), the main binding, is being investigated clinically, and a clinical trial was protease (nsp5, 3CLpro,orMpro), and exonuclease/N7- recently launched to study the effect of thiazide, thiazide-like methyltransferase (nsp14, ExoN). RdRp catalyzes synthesis diuretics, calcium channel blockers, ACE inhibitors, and of the full length negative-strand RNA template used by RdRp angiotensin receptor blockers in COVID-19 to make more viral genomic RNA. The SARS-CoV-2 genome (NCT04330300). The availability of soluble recombinant also contains a number of open reading frames (ORFs): hACE2 encouraged its testing in two clinical trials; although namely, ORF 1a proposed to encode nsp1 to nsp11; ORF1b, is one was terminated (NCT04287686) the other is currently proposed to encode nsp12 to nsp16, essential for viral replication, and ORFs 3a, 3b, 6, 7a, 7b, 8, 9a, 9b, and 10, active (NCT04335136). Monoclonal antibodies, especially for which encode for accessory proteins1 (Table S2). interleukin-6 (IL-6) or its receptor, are also being considered for the control of SARS-CoV-2 associated respiratory exacerbations.11 Interestingly, several Janus Kinase (JAK) ■ TREATING VIRAL INFECTION inhibitors such as baricitinib and ruxolitinib are currently Immunization against SARS-CoV-2. The development being evaluated given their involvement in interleukin signaling of a manufacturable, safe, and effective vaccine may take 12− pathways. Another currently recruiting clinical trial is testing 18 months. Several phase I clinical trials are currently quinolone, macrolide, and β-lactam antibiotics against recruiting participants to test the safety, reactogenicity, and COVID-19 (NCT02735707). Multiple groups have tested immunogenicity of several investigational SARS-CoV-2 FDA approved drugs in various in vitro assays as well as in vaccines (Tables S3 and S4). An mRNA vaccine based on computational screens. Many of these drugs show inhibitory the Spike protein began human clinical trials within a record 63 activities, although not always at a concentration that may be days from first publication of the SARS-CoV-2 sequence safely achieved in patients.23 Controlled clinical trials of these (NCT04283461). It has been suggested that the mutation rate agents are mandatory to assess their efficacy and safety without for SARS-CoV-2 is expected to be low, raising hope that a creating false positive hope or depleting the supplies of drugs successful vaccine will provide life-long immunity.20 Hyper- needed to treat the diseases for which they were initially immune globulin isolated from the sera of convalescent approved. patients having high titers of antibodies against SARS-CoV-2 Novel Agents. Mpro and PLpro are cysteine proteases or even their whole blood may provide instant “passive” short- responsible for the cleavage of viral polypeptides into lived immunity mainly via viral neutralization. Antibody functional proteins for virus replication and packaging within dependent therapy, for example targeting the Spike protein host cells.24 These enzymes represent the best characterized

C https://dx.doi.org/10.1021/acsinfecdis.0c00224 ACS Infect. Dis. XXXX, XXX, XXX−XXX ACS Infectious Diseases pubs.acs.org/journal/aidcbc Viewpoint drug targets among coronaviruses and are currently the focus ■ CONCLUSIONS of attention among scientists seeking novel coronavirus small Since 2003, the three pandemics caused by SARS, MERS, and molecule therapeutics.25 Mpro is shared by all coronavirus pro SARS-CoV-2 are believed to have initiated as a result of bat genera and has similarity to the 3C of the Enterovirus genus coronaviruses crossing the species barrier. Therefore, other 24 pro ··· in the picornavirus family. M contains a Cys His catalytic epidemics are likely to occur in the future due to the effectively α dyad with an additional -helical domain involved in the unlimited supply of coronaviruses present in the bat dimerization of the protease, which is essential for its catalytic population. Equally concerning is the fact that RNA viruses 25 activity. The enteroviral 3Cpro functions as a monomer lack a genomic proof-reading mechanism and therefore are featuring a classical Cys···His···Glu/Asp catalytic triad.24 Yet, prone to mutation, raising the specter that once a new they share the almost absolute requirement for Gln in the P1 coronavirus begins circulating in the human population it will position of the substrate and space for only small residues such be extremely difficult to eliminate. Finally, for a drug to be as Gly, Ala, or Ser in the P1′ position. Since no human most effective, it must reach its site of action (e.g., lung tissues) proteases with a similar cleavage specificity are known, it may in sufficient quantity to clear the virus. With nearly three be possible to identify highly selective Mpro/3Cpro inhibitors, million reported cases, >260,000 deaths, millions out of work, which display minimal inhibition of host proteases.26 The 3-D and billions of dollars in lost revenue, it appears that SARS- structures of unliganded SARS-CoV-2 Mpro and of its complex CoV-2 has altered daily life for a sustained period of time. This with a peptidomimetic α-ketoamide inhibitor (11r) have been cascading effect has generated unprecedented momentum and 26 fi ff fi solved and were used to support the design of an optimized scienti ce ort around the globe to ght this virus. Success will derivative (13b) through docking studies (Figure S2). α- require creative thinking, new technologies, innovative Ketoamides can interact with the catalytic center of Mpro approaches, particularly focused on speed to market, and ff ff through two hydrogen bonding interactions rather than only combinations of di erent modalities to e ectively combat not one as with other warheads such as aldehydes or Michael just the current foe but also future coronaviruses. We remain 24 α hopeful that we will be more prepared for the emergence of a acceptors. Nucleophilic attack of the -keto group by the “ ” catalytic Cys residue results in reversible formation of a potential SARS-CoV-3 . thiohemiketal. These α-ketoamides feature a 5-membered rigid γ-lactam as a mimic of the P1 residue, glutamine, required for ■ ASSOCIATED CONTENT Mpro specificity, with the advantage of reducing the loss of *sı Supporting Information entropy upon binding.24 Follow up optimization efforts guided The Supporting Information is available free of charge at by docking to the SARS-CoV-2 Mpro co-crystal structure with https://pubs.acs.org/doi/10.1021/acsinfecdis.0c00224. 11r, included incorporation of the P3-P2 amide bond into a Tables showing viral outbreaks since year 2000, different pyridone ring as in 13a. The resulting half-life of 13a in plasma targets expressed in SARS-CoV-2 proteome, unique was enhanced by 3 fold relative to 11r, in vitro kinetic plasma ∼ therapeutic interventions in recruiting and nonrecruiting solubility improved by a factor of 19 and thermodynamic clinical studies for COVID-19, and structures of select solubility by a factor of ∼13. 13a inhibited purified pro pro approved or investigational drugs tested for drug recombinant SARS-CoV-2 M ,SARS-CoVM ,and repurposing against SARS-CoV-2; structures of the pro 26 fi MERS-CoV M in the submicromolar range. Modi cation novel inhibitors obtained from the PDB for SARS- ′ ff of the P1 and P3 moieties of 13a a orded an optimized CoV-2 Mpro (PDF) derivative 13b which was crystallized with SARS-CoV-2 Mpro (PDB: 6Y2G and 6Y2F). Both 13a and 13b displayed good stability in mouse and human microsomes. 13b (3 mg/kg) ■ AUTHOR INFORMATION showed longer t1/2, tmax, and residence time compared to 13a Corresponding Author (20 mg/kg) in CD-1 mice. Both compounds showed lung − fi Nouri Neamati Department of Medicinal Chemistry, College tropism which is thought to be bene cial. While the of Pharmacy, University of Michigan, Ann Arbor, Michigan development of these ketoamides into clinical candidates 48109, United States; orcid.org/0000-0003-3291-7131; requires additional safety studies, the availability of their crystal Email: [email protected] structures is of great importance in facilitating the discovery and development of other Mpro inhibitors. One of the Authors suggested agents for testing is the previously reported Essam Eldin A. Osman − Department of Medicinal Chemistry, Rhinovirus and SARS-CoV Mpro inhibitor clinical candidate College of Pharmacy, University of Michigan, Ann Arbor, rupintrivir (AG-7088) (Figure S2). In addition, other groups Michigan 48109, United States; Department of Pharmaceutical recently reported Mpro crystal structures with inhibitors such as Chemistry, Faculty of Pharmacy, Cairo University, Cairo the peptidomimetic Michael acceptor N3 (PDB: 6LU7) and 11562, Egypt the reversible inhibitor X77 (PDB: 6W63) (Figure S2).27 A Peter L. Toogood − Department of Medicinal Chemistry, large array of Mpro crystal structures with multiple covalent and College of Pharmacy and Michigan Drug Discovery, Life noncovalent fragments were solved through an exceptionally Sciences Institute, University of Michigan, Ann Arbor, Michigan large screen with vast opportunities for fragment growing and 48109, United States merging. The cryo EM structure of SARS-CoV-2 RdRp was Complete contact information is available at: recently solved, showing nearly an identical sequence to its https://pubs.acs.org/10.1021/acsinfecdis.0c00224 SARS-CoV homologue.28 RdRp should be another high priority target for therapeutic intervention given that lead Notes inhibitors such as remdesivir already exist. The authors declare no competing financial interest.

D https://dx.doi.org/10.1021/acsinfecdis.0c00224 ACS Infect. Dis. XXXX, XXX, XXX−XXX ACS Infectious Diseases pubs.acs.org/journal/aidcbc Viewpoint ■ REFERENCES Wuhan, China: a retrospective cohort study. Lancet 395 (10229), 1054−1062. (1) Wu, F., Zhao, S., Yu, B., Chen, Y. M., Wang, W., Song, Z. G., Hu, (16) Jiang, F., Deng, L., Zhang, L., Cai, Y., Cheung, C. W., and Xia, Y., Tao, Z. W., Tian, J. H., Pei, Y. Y., Yuan, M. L., Zhang, Y. L., Dai, F. Z. (2020) Review of the clinical characteristics of coronavirus disease H., Liu, Y., Wang, Q. M., Zheng, J. J., Xu, L., Holmes, E. C., and 2019 (COVID-19). J. Gen Intern Med.,1−5. Zhang, Y. Z. (2020) A new coronavirus associated with human − (17) Kuba, K., Imai, Y., Rao, S., Gao, H., Guo, F., Guan, B., Huan, Y., respiratory disease in China. Nature 579 (7798), 265 269. Yang, P., Zhang, Y., Deng, W., Bao, L., Zhang, B., Liu, G., Wang, Z., (2) Chan, J. F., Kok, K. H., Zhu, Z., Chu, H., To, K. K., Yuan, S., and Chappell, M., Liu, Y., Zheng, D., Leibbrandt, A., Wada, T., Slutsky, A. Yuen, K. Y. (2020) Genomic characterization of the 2019 novel S., Liu, D., Qin, C., Jiang, C., and Penninger, J. M. (2005) A crucial human-pathogenic coronavirus isolated from a patient with atypical − role of angiotensin converting enzyme 2 (ACE2) in SARS pneumonia after visiting Wuhan. Emerging Microbes Infect. 9 (1), 221 coronavirus-induced lung injury. Nat. Med. 11 (8), 875−879. 236. (18) Zhang, H., Penninger, J. M., Li, Y., Zhong, N., and Slutsky, A. S. (3) Parrish, C. R., Holmes, E. C., Morens, D. M., Park, E. C., Burke, (2020) Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 D. S., Calisher, C. H., Laughlin, C. A., Saif, L. J., and Daszak, P. receptor: molecular mechanisms and potential therapeutic target. (2008) Cross-species virus transmission and the emergence of new − − Intensive Care Med. 46 (4), 586 590. epidemic diseases. Microbiol. Mol. Biol. Rev. 72 (3), 457 470. (19) Wang, X., Dhindsa, R., Povysil, G., Zoghbi, A., Motelow, J., (4) Hu, B., Ge, X., Wang, L. F., and Shi, Z. (2015) Bat origin of Hostyk, J., and Goldstein, D. (2020) Transcriptional inhibition of human coronaviruses. Virol. J. 12, 221. host viral entry proteins as a therapeutic strategy for SARS-CoV-2. (5) Li, W., Shi, Z., Yu, M., Ren, W., Smith, C., Epstein, J. H., Wang, Preprints, 2020030360, DOI: 10.20944/preprints202003.0360.v1. H., Crameri, G., Hu, Z., Zhang, H., Zhang, J., McEachern, J., Field, H., (20) Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., and Daszak, P., Eaton, B. T., Zhang, S., and Wang, L. F. (2005) Bats are Garry, R. F. (2020) The proximal origin of SARS-CoV-2. Nat. Med. natural reservoirs of SARS-like coronaviruses. Science 310 (5748), − − 26 (4), 450 452. 676 679. (21) Cao, B., Wang, Y., Wen, D., Liu, W., Wang, J., Fan, G., Ruan, L., (6) Ejima, K., Omori, R., Cowling, B. J., Aihara, K., and Nishiura, H. Song, B., Cai, Y., Wei, M., Li, X., Xia, J., Chen, N., Xiang, J., Yu, T., (2012) The time required to estimate the case fatality ratio of Bai, T., Xie, X., Zhang, L., Li, C., Yuan, Y., Chen, H., Li, H., Huang, influenza using only the tip of an iceberg: joint estimation of the H., Tu, S., Gong, F., Liu, Y., Wei, Y., Dong, C., Zhou, F., Gu, X., Xu, J., virulence and the transmission potential. Comput. Math Methods Med. Liu, Z., Zhang, Y., Li, H., Shang, L., Wang, K., Li, K., Zhou, X., Dong, 2012, 978901. X., Qu, Z., Lu, S., Hu, X., Ruan, S., Luo, S., Wu, J., Peng, L., Cheng, F., (7) Coronaviridae Study Group of the International Committee on Pan, L., Zou, J., Jia, C., Wang, J., Liu, X., Wang, S., Wu, X., Ge, Q., He, Taxonomy of Viruses (2020) The species severe acute respiratory J., Zhan, H., Qiu, F., Guo, L., Huang, C., Jaki, T., Hayden, F. G., syndrome-related coronavirus: classifying 2019-nCoV and naming it − Horby, P. W., Zhang, D., and Wang, C. (2020) A trial of lopinavir- SARS-CoV-2. Nat. Microbiol. 5 (4), 536 544. ritonavir in adults hospitalized with severe COVID-19. N. Engl. J. (8) Hoffmann, M., Kleine-Weber, H., Schroeder, S., Kruger, N., Med., DOI: 10.1056/NEJMoa2001282. Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N. H., (22) Kawase, M., Shirato, K., van der Hoek, L., Taguchi, F., and Nitsche, A., Muller, M. A., Drosten, C., and Pohlmann, S. (2020) Matsuyama, S. (2012) Simultaneous treatment of human bronchial SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is − epithelial cells with serine and cysteine protease inhibitors prevents blocked by a clinically proven protease inhibitor. Cell 181 (2), 271 severe acute respiratory syndrome coronavirus entry. J. Virol 86 (12), 280. 6537−6545. (9) Knoops, K., Kikkert, M., Worm, S. H., Zevenhoven-Dobbe, J. C., (23) Jeon, S., Ko, M., Lee, J., Choi, I., Byun, S. Y., Park, S., Shum, D., van der Meer, Y., Koster, A. J., Mommaas, A. M., and Snijder, E. J. and Kim, S. (2020) Identiﬁcation of antiviral drug candidates against (2008) SARS-coronavirus replication is supported by a reticulove- SARS-CoV-2 from FDA-approved drugs. bioRxiv, DOI: 10.1101/ sicular network of modified endoplasmic reticulum. PLoS Biol. 6 (9), 2020.03.20.999730. No. e226. (24) Zhang, L., Lin, D., Kusov, Y., Nian, Y., Ma, Q., Wang, J., von (10) Hagemeijer, M. C., Verheije, M. H., Ulasli, M., Shaltiel, I. A., de Brunn, A., Leyssen, P., Lanko, K., Neyts, J., de Wilde, A., Snijder, E. J., Vries, L. A., Reggiori, F., Rottier, P. J., and de Haan, C. A. (2010) Liu, H., and Hilgenfeld, R. (2020) Alpha-ketoamides as broad- Dynamics of coronavirus replication-transcription complexes. J. Virol. − spectrum inhibitors of coronavirus and enterovirus replication: 84 (4), 2134 2149. structure-based design, synthesis, and activity assessment. J. Med. (11) Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. Chem., DOI: 10.1021/acs.jmedchem.9b01828. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., and Albaiu, D. (25) Hilgenfeld, R. (2014) From SARS to MERS: crystallographic (2020) Research and development on therapeutic agents and vaccines studies on coronaviral proteases enable antiviral drug design. FEBS J. for COVID-19 and related human coronavirus diseases. ACS Cent. Sci. − − 281 (18), 4085 4096. 6 (3), 315 331. (26) Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, (12) de Haan, C. A., Kuo, L., Masters, P. S., Vennema, H., and L., Becker, S., Rox, K., and Hilgenfeld, R. (2020) Crystal structure of Rottier, P. J. (1998) Coronavirus particle assembly: primary structure − SARS-CoV-2 main protease provides a basis for design of improved requirements of the membrane protein. J. Virol. 72 (8), 6838 6850. alpha-ketoamide inhibitors. Science, eabb3405. (13) Wu, Z., and McGoogan, J. M. J. J. (2020) Characteristics of and (27) Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, important lessons from the coronavirus disease 2019 (COVID-19) X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., outbreak in China: summary of a report of 72 314 cases from the Jiang, R., Yang, X., You, T., Liu, X., Yang, X., Bai, F., Liu, H., Liu, X., Chinese Center for Disease Control and Prevention. JAMA 323 (13), − Guddat, L. W., Xu, W., Xiao, G., Qin, C., Shi, Z., Jiang, H., Rao, Z., 1239 1242. and Yang, H. (2020) Structure of Mpro from COVID-19 virus and (14) Yang, X., Yu, Y., Xu, J., Shu, H., Xia, J., Liu, H., Wu, Y., Zhang, discovery of its inhibitors. Nature, DOI: 10.1038/s41586-020-2223-y. L., Yu, Z., Fang, M., Yu, T., Wang, Y., Pan, S., Zou, X., Yuan, S., and (28) Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Shang, Y. (2020) Clinical course and outcomes of critically ill patients Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., Yang, X., Li, J., Yang, H., retrospective, observational study. Lancet Respir. Med., DOI: 10.1016/ Liu, Z., Xu, W., Guddat, L. W., Wang, Q., Lou, Z., and Rao, Z. (2020) S2213-2600(20)30079-5. Structure of the RNA-dependent RNA polymerase from COVID-19 (15) Zhou, F., Yu, T., Du, R., Fan, G., Liu, Y., Liu, Z., Xiang, J., virus. Science, No. eabb7498. Wang, Y., Song, B., Gu, X., Guan, L., Wei, Y., Li, H., Wu, X., Xu, J., Tu, S., Zhang, Y., Chen, H., and Cao, B. (2020) Clinical course and risk factors for mortality of adult inpatients with COVID-19 in

E https://dx.doi.org/10.1021/acsinfecdis.0c00224 ACS Infect. Dis. XXXX, XXX, XXX−XXX Supporting Information

COVID-19: Living Through Yet Another Pandemic

Essam Eldin A. Osman,†,¶ Peter L. Toogood, †,‡ and Nouri Neamati†,*

†Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, and the ‡Michigan Drug Discovery, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 ¶Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt

* Corresponding author email: [email protected]

Table S1. Viral outbreaks since year 2000 Table S2. Different targets expressed in SARS-CoV-2 proteome (genome accession code: NC_045512.2 or MN908947.3), their length, potential functions extracted from Uniprot and crystal structures in Protein Data Bank (PDB) Table S3. Unique therapeutic interventions in recruiting clinical studies Table S4. Unique therapeutic interventions in non-recruiting clinical studies Figure S1. Structures of select approved or investigational drugs tested for drug repurposing against SARS-CoV2 Figure S2. Structures of the novel inhibitors obtained from the PDB for SARS-CoV-2 Mpro and rupintrivir

Table S1. Viral outbreaks since year 20001 Event Geographic Number of Direct morbidity or mortality extent cases SARS (2003) 4 continents, 37 8,098 744 deaths countries Swine flu influenza global Unknown 151,700–575,500 deaths (0.2–0.8 per (2009) 10,000 persons) MERS (2012) 22 countries 1,879 659 deaths West Africa Ebola 10 countries 28,646 11,323 deaths virus disease (2103- 2105) Zika virus (2015) 76 countries 2,656 2,656 cases of microcephaly or central nervous system malformation COVID-192 185 countries or >2,800,000 >195,000 regions

Table S2. Different targets expressed in SARS-CoV-2 proteome (genome accession code: NC_045512.2 or MN908947.3), their length, potential functions extracted from Uniprot and crystal structures in Protein Data Bank (PDB) Name of the Size Functiona X-ray structure Reference protein (PDB if available) PMIDc and Inhibitor (if reported)b Host translation 180 Inhibits host translation by interacting with the None 23035226 inhibitor Non- 40S ribosomal subunit. structural protein 1 (nsp1) Non-structural 638 May play a role in the modulation of host cell None 19640993 protein 2 (nsp2) survival signaling pathway by interacting with host Prohibitins (PHB and PHB2). Papain-like 1945 Has about 11 cleavage sites located at the N- 6VXS, 6W02, 23943763 proteinase (nsp3) terminus of the replicase polyprotein. 6W6Y, 6WCF, 19369340 Deubiquitinating/deISGylating activity and 6WEN, 6W9C processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates with nsp4 in the assembly of virally induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents host NF- kappa-B signaling. Non-structural 500 Participates in the assembly of virally induced None 23943763 protein 4 (nsp4) cytoplasmic double-membrane vesicles necessary for viral replication. Proteinase 3CL- 306 Cleaves the C-terminus of replicase 6Y7M (11r), 32198291 PRO (nsp5) polyprotein at 11 sites. 6Y2E, 6Y2G 32045235 (13b), 6Y2F (13b) 32272481 6LU7 (N3), 6W63 (X77), 6M03, 6M2N+6M2Q 6YB7, 6Y84, 6Y63 (unreleased) + +92 co-crystals (fragment screen) Non-structural 290 Plays a role in the initial induction of None 24991833 protein 6 (nsp6) autophagosomes from host endoplasmic reticulum. Non-structural 83 Forms a hexadecamer with nsp8 (8 subunits of 6M71 31138817 protein 7 each) that may participate in viral replication 7BTF 32277040 (nsp7). by acting as a primase. May synthesize substantially longer products than oligonucleotide primers. Non-structural 198 Forms a hexadecamer with nsp7 (8 subunits of 6M71 31138817 protein 8 (nsp8). each) that may participate in viral replication 7BTF 32277040 by acting as a primase. May synthesize substantially longer products than oligonucleotide primers. Non-structural 113 May participate in viral replication by acting 6W4B 14962394 protein 9 (nsp9). as a ssRNA-binding protein. 6W9Q Non-structural 139 Formerly known as growth-factor-like protein 6W61, 6W75, 29279395 protein 10 (nsp10). (GFL). Plays a pivotal role in viral 6W4H 26159422 transcription by stimulating both 3'-5' 21637813 exoribonuclease (nsp14) and 2'-O- methyltransferase (nsp16) activities. Therefore, plays an essential role in viral mRNAs cap methylation. Non-structural 13 Unknown function. None protein 11 (nsp11). RNA-directed RNA 932 Responsible for replication and transcription 6M71 31138817 polymerase (RdRp) of the viral RNA genome. 7BTF 32277040 (nsp12). Helicase (Hel). 601 Multi-functional protein with a zinc-binding None 31131400 (nsp13). domain in N-terminus displaying RNA and 28651017 DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium. Guanine-N7 527 Enzyme possessing two different activities: an None 26159422 methyltransferase exoribonuclease activity acting on both 29279395 (ExoN). (nsp14). ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Uridylate-specific 346 Mn2+-dependent, uridylate-specific enzyme, 6W01 16882730 endoribonuclease which leaves 2'-3'-cyclic phosphates 5' to the 6VWW 17409150 (NendoU) (nsp15). cleaved bond. 2'-O- 298 Methyltransferase that mediates mRNA cap 2'- 6W4H 21637813 methyltransferase O-ribose methylation to the 5'-cap structure of 6W75 18417574 (2'-O-MT). viral mRNAs. N7-methyl guanosine cap is a (nsp16). prerequisite for binding of nsp16. Therefore, plays an essential role in viral mRNAs cap methylation which is essential to evade immune system. Surface 1273 Spike protein S1 (residue 14-685): attaches the 6VSB, 6VW1, 32155444 glycoprotein (S). virion to the cell membrane by interacting 6VYB, 6VXX, 15496474 with host receptor, initiating the infection. 6VYB, 19321428 Binding to human ACE2 and CLEC4M/DC- 6M17,6M0J, 32245784 SIGNR receptors and internalization of the 6LZG, 6W41, virus into the endosomes of the host cell 6LXT, 6YLA, induces conformational changes in the S 6LVN glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes. Spike protein S2 (residue 686-1273): mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Spike protein S2' (residue 816-1273): acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis. ORF3a 275 Accessory protein. None E. 75 Component of the viral envelope that plays a None 29474890 central role in virus morphogenesis and 24668816 assembly via its interactions with other viral 15527857 proteins. M. 222 Component of the viral envelope that plays a None central role in virus morphogenesis and assembly via its interactions with other viral proteins. ORF6 61 Accessory protein. None ORF7a 121 Accessory protein. None Reported previously to induce apoptosis via a caspase-dependent pathway and in cell lines derived from different organs, including lung, kidney, and liver. ORF7b 43 Accessory protein. None May be an integral component of membrane ORF8 121 Accessory protein. None N. 419 Packages the positive strand viral genome 6M3M 17210170 RNA into a helical ribonucleocapsid (RNP) 6VYO and plays a fundamental role during virion 6YI3 assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription and replication. ORF9a and 9b Accessory protein. Overlapping with N. ORF10 38 Dubious/uncertain protein. Not currently clear None if this region translates into a functional protein. aPredicted functions were collected from Uniport server based on similar function in SARS-CoV or Bat-SARS bCrystal structures were obtained from protein data bank (PDB) on April 15, 2020. cReferences are listed as PubMed Identifiers (PMID)

Table S3. Unique therapeutic interventions in recruiting clinical studies Biologicals Phase mRNA-1273 vaccine Phase 1 LV-SMENP-DC vaccine Phase 1/2 BCG vaccine Phase 4 Antigen-specific CTLs vaccine Phase 1/2 ChAdOx1 (chimpanzee adenovirus vaccine vector vaccine) Phase 1/2 Pathogen-specific artificial antigen presenting cells (aAPCs) Phase 1 Umbilical cord-derived mesenchymal stem cells (UC-MSCs) Phase 2 Wharton's jelly derived mesenchymal stem cells (WJ-MSCs) Phase 1 Dental pulp mesenchymal stem cells Phase 1/2 NK Cells (IL15-NK, NKG2D CAR-NK, ACE2 CAR-NK, NKG2D-ACE2 CAR-NK) Phase 1/2 Human serum albumin Phase 1/2 Sargramostim (recombinant granulocyte macrophage colony-stimulating factor (GM-CSF) Phase 4 Human Amniotic Fluid Early Phase 1 Convalescent plasma Phase 3 Antiviral agents Remdesivir (RdRp inhibitor) Phase 3 Lopinavir/ritonavir (HIV protease inhibitor and CYP3A4 inhibitor) Phase 4 ASC09 (TMC-310911) (HIV protease inhibitor) Phase 3 Darunavir/Cobicistat (HIV protease inhibitor) Phase 3 Ritonavir (HIV protease inhibitor and CYP3A4 inhibitor) Phase 4 Oseltamivir (influenza neuraminidase inhibitor) Phase 4 Favipiravir (RdRp inhibitor) N/A Arbidol (broad spectrum antiviral, inhibitor of membrane fusion) Phase 4 Ribavirin (broad spectrum antiviral, purine synthesis inhibitor) Phase 2 Completed DAS181 (anti parainfluenza) Phase 3 Galidesivir (RNA polymerase inhibitor) Phase 1 Danoprevir (NS3/4A HCV protease inhibitor) Phase 4 Immunomodulatory agents Hydroxychloroquine (antimalarial) Phase 4 Chloroquine (antimalarial) Phase 2 GNS651 (chloroquine analog) Phase 2 Fingolimod (sphingosine-1-phosphate receptor modulator) Phase 2 Thymosin alpha 1 (peptide) Phase 3 Colchicine Phase 3 Interferon Beta-1b Phase 2 Interferon Beta-1a Phase 3 Recombinant human Interferon Alpha-1b Phase 3 Sirolimus (mTOR inhibitor) Phase 2 Tacrolimus (mTOR inhibitor) Phase 3 Ruxolitinib (inhibitor of Janus kinase (JAK)) Phase 1/2 Baricitinib (inhibitor of Janus kinase (JAK)) Phase 3 CD24Fc (CD24 extracellular domain-IgG1 Fc domain recombinant fusion protein) Phase 3 CM4620 (inhibitor of CRAC channels) Phase 2 Monoclonal antibody Bevacizumab (vascular endothelial growth factor A (VEGF-A) antibody) Phase 2/3 Tocilizumab (interleukin-6 receptor (IL-6R) antibody) Phase 4 Sarilumab (interleukin-6 receptor (IL-6R) antibody) Phase 2/3 Clazakizumab (humanized rabbit monoclonal antibody against IL-6) Phase 2/3 Siltuximab (chimeric monoclonal antibody for IL-6) Phase 3 Anakinra (recombinant human interleukin-1 receptor antagonist (IL-1Ra) Phase 4 Meplazumab (anti-CD147) Phase 1/2 IFX-1 (complement factor C5a) Phase 2/3 Emapalumab (immunoglobulin G1 monoclonal antibody for interferon-γ (IFN-γ)) Phase 2/3 Leronlimab (CCR5 Antagonist) Phase 2 Pembrolizumab (MK-3475) (PD-1 (programmed death-1) Phase 2 Nivolumab (PD-1 blocking antibody) Phase 2 TJ003234 (granulocyte-macrophage colony-stimulating factor antibody) Phase 1/2 Miscellaneous Camostat (serine protease inhibitor) Phase 4 Azithromycin (macrolide antibiotic) Phase 4 Levamisole (anthelmintic) Phase 2/3 Nitazoxanide (antiprotozoal) Phase 4 Defibrotide (mixture of single-stranded oligonucleotides for veno-occlusive diseases) Phase 2 Verapamil (calcium channel blocker) Phase 2/3 Amiodarone (class III antiarrhythmic) Phase 2/3 Valsartan (angiotensin receptor blocker, anti-hypertensive) Phase 4 Losartan (angiotensin receptor blocker, anti-hypertensive) Phase 4 Candesartan (angiotensin receptor blocker, anti-hypertensive) Phase 2/3 Sildenafil citrate (treatment for erectile dysfunction) Phase 3 Simvastatin (HMG-CoA inhibitor antilipidemic) Phase 2 Dapagliflozin (dipeptidyl peptidase inhibitor antidiabetic) Phase 3 Rivaroxaban (Factor XA inhibitor) N/A Clopidogrel (irreversible inhibitor of P2Y12 ADP receptor, Blood thinner) N/A Aspirin (thromboxane A2 synthesis inhibitor) N/A Fluvoxamine (selective serotonin reuptake inhibitor) Phase 2 Deferoxamine (iron chelator) Phase 1/ 2 Aescin (mixture of saponins) Phase 2/3 Vitamin C Phase 3 N-acetylcysteine Phase 2 Formoterol (bronchodilator) Phase 2/3 Methylprednisolone (corticosteroid) Phase 4 Dexamethasone (corticosteroid) Phase 4 Hydrocortisone (corticosteroid) Phase 4 Budesonide (corticosteroid) Phase 2/3 Nitric Oxide Phase 2 Hyperbaric oxygen N/A Fuzheng Huayu (Chinese herbal mixture) Phase 2 Data were collected from https://clinicaltrials.gov/ when searched for: covid-19, SARS-CoV-2, 2019-nCoV, and 2019 novel coronavirus (accessed on April 17, 2020). The Table represents the unique therapeutic entities that may be used as single agents or in combination. The recorded phases are the highest phase reached by each entity

Table S4. Unique therapeutic interventions in non-recruiting clinical studies Biologicals Phase NestCell® (mesenchymal stem cell) Phase 1 MSCs-derived exosomes Phase 1 Adipose tissue-derived mesenchymal stromal cells Phase 2 Heat killed (autoclaved) Mycobacterium w N/A ChAdOx1 (chimpanzee adenovirus vaccine vector vaccine) Phase 1/2 BCG vaccine Phase 4 Adenovirus Type 5 Vector vaccine Phase 1 BacTRL-Spike vaccine Phase 1 Stem Cell Educator-Treated Mononuclear Cells Apheresis Phase 2 Convalescent plasma Phase 3 Antiviral agents Lopinavir/ritonavir (HIV protease inhibitor) Phase 4 Clevudine (anti HBV) Phase 2 Emtricitabine (HIV nucleotide reverse transcriptase inhibitor) Phase 3 Tenofovir disoproxil (nucleotide reverse transcriptase inhibitor) Phase 3 ASC09 (TMC-310911) (HIV protease inhibitor) N/A Arbidol (broad spectrum antiviral, inhibitor of membrane fusion) Phase 4 Favipiravir (RdRp inhibitor) Phase 4 Oseltamivir (influenza neuraminidase inhibitor) Phase 4 Immunomodulatory agents Hydroxychloroquine (antimalarial) Phase 4 Chloroquine phosphate (antimalarial) Phase 4 Ruxolitinib (inhibitor of Janus kinase (JAK)) Phase 1/2 Tofacitinib (inhibitor of Janus kinase (JAK)) Phase 2 TD-0903 (inhibitor of Janus kinase (JAK)) Phase 1 Peginterferon Lambda-1a Phase 2 Recombinant human Interferon Early phase 1 Thalidomide Phase 2 PUL-042 (toll-like receptor2/6/9 (TLR) ligands) Phase 2 Thymosin alpha 1 (peptide hormone) Phase 2 Monoclonal antibody Sarilumab (interleukin-6 receptor (IL-6R)) Phase 2/3 Tocilizumab (interleukin-6 receptor (IL-6R)) Phase 3 Anakinra (recombinant human interleukin-1 receptor antagonist (IL-1Ra) Phase 4 BMS-986253 (IL-8 antibody) Phase 2 Mavrilimumab (granulocyte-macrophage colony-stimulating factor antibody) Phase 2 Lenzilumab (colony stimulating factor 2 /granulocyte-macrophage colony stimulating factor antibody) Phase 3 Nivolumab (PD-1 blocking antibody) Phase 2 Eculizumab (complement C5 antibody) Phase 2 LY3127804 (angiopoietin 2 antibody) Phase 2 Miscellaneous Atovaquone (antimalarial) N/A Azithromycin (macrolide antibiotic) Phase 4 Carrimycin (macrolide antibiotic) Phase 4 Ivermectin (anthelmintic) Phase 2/3 Niclosamide (anthelmintic) Phase 2/3 Triiodothyronine Phase 3 Prednisone (corticosteroid) Phase 2 Methylprednisolone (corticosteroid) Phase 3 Dexamethasone (corticosteroid) Phase 4 Ciclesonide (corticosteroid) Phase 2 Tradipitant (neurokinin 1 antagonist) Phase 3 Vazegepant (calcitonin gene-related peptide (CGRP) receptor antagonist) Phase 2/3 BLD-2660 (autotaxin inhibitor) Phase 2 Acalabrutinib (inhibitor of Bruton's tyrosine kinase) Phase 2 Nintedanib (tyrosine kinase inhibitor) Phase 2 Imatinib (tyrosine kinase inhibitor) Phase 2 Selinexor (exportin antagonist) Phase 2 Losartan (anti-hypertensive) Phase 2/3 Recombinant hACE2 Phase 2 Angiotensin 1-7 Phase 2/3 Aviptadil (analog of vasoactive intestinal polypeptide) Phase 2 Eicosapentaenoic acid Phase 3 Aspirin (thromboxane A2 synthesis inhibitor) Phase 3 Enoxaparin Phase 3 Tinzaparin Phase 2 Tranexamic acid Phase 2 Spironolactone (potassium sparing diuretic) Phase 4 Linagliptin (dipeptidyl peptidase 4 inhibitor antidiabetic) Phase 4 Piclidenoson (anti-inflammatory) Phase 2 Ibuprofen (anti-inflammatory) Phase 4 Naproxen (anti-inflammatory) Phase 3 Hyperbaric oxygen Phase 2 /3 Nitric Oxide Phase 2 Anluohuaxian (Chinese patent medicine) N/A Yinhu QingWen Granula (Chinese herbal medicine) N/A Wen Granula (Chinese herbal medicine) N/A Xiyanping injection (Chinese herbal medicine) N/A Huaier Granule (Chinese herbal medicine) Phase 2/3 T89 (botanical extracts) Phase 2 Vitamin C Phase 4 Vitamin D Phase 3 Zinc Phase 4 Data were collected from https://clinicaltrials.gov/ when searched for: covid-19, SARS-CoV-2, 2019-nCoV, and 2019 novel coronavirus (accessed on April 18, 2020). The Table represents the unique therapeutic entities that may be used as single agents or in combination. The recorded phases are the highest phase reached by each entity

Figure S1. Structures of select approved or investigational drugs tested for drug repurposing against SARS-CoV2

Figure S2. Structures of the novel inhibitors obtained from the PDB for SARS-CoV-2 Mpro and rupintrivir

References

1. Madhav, N.; Oppenheim, B.; Gallivan, M.; Mulembakani, P.; Rubin, E.; Wolfe, N., Pandemics: risks, impacts, and mitigation. In Disease Control Priorities: Improving Health and Reducing Poverty. 3rd edition, The International Bank for Reconstruction and Development/The World Bank: 2017. 2. Johns Hopkins Coronavirus Resource Center available at https://coronavirus.jhu. edu/ map.html (accessed April 24, 2020 ).