key: cord-1028044-btk6u9j4 authors: Sadia, Aatika; Basra, Muhammad Asim Raza title: Therapeutic dilemma in the repression of severe acute respiratory syndrome coronavirus‐2 proteome date: 2020-07-13 journal: Drug Dev Res DOI: 10.1002/ddr.21710 sha: 03f1852ee8e15b9bd3c477d12c2cd8ebebb76723 doc_id: 1028044 cord_uid: btk6u9j4 Currently, the pandemic coronavirus disease 2019 (COVID‐19) has unprecedentedly captivated its human hosts by causing respiratory illnesses because of evolution of the genetic makeup of novel coronavirus (CoV) known as severe acute respiratory syndrome coronavirus‐2 (SARS CoV‐2). As much as the researchers are inundated for the quest of effective treatments from available drugs, the discovery and trials of new experimental drugs are also at a threshold for clinical trials. There has been much concern regarding the new and targeted drugs considering the comprehensive ambiguity regarding the mechanism and pathway of the drug action with respect to the new and unpredictable structural and nonstructural proteins (NSPs) of SARS CoV‐2. This study was aimed to discuss functional pathways related to NSPs in CoVs with updated knowledge regarding SARS CoV‐2, mechanisms of action of certain approved and investigational drugs for correct orientation regarding the treatment strategies, including nucleotide analog mechanism, receptor analog mechanism, and peptide–peptide interactions, along with the impact of COVID‐19 on a global scale. Although there is a dire need for targeted drugs against SARS CoV‐2, the practical achievement of its cure is possible by only using effective drugs with appropriate mechanisms to eliminate the disease. The SARS CoV-2, which erupted originally from Wuhan city of China, has a reproductive number R o ranging from 2.24 to 3.58 as compared to 2.7 to 3.7 of MERS, and 2 to 5 of SARS, whereas the transmission rate of COVID-19 is considered 2.2% and the official case fatality rate is 3.17% in China (Sun, Lu, Xu, Sun, & Pan, 2020; Zhao et al., 2020) . The COVID-19 is characterized by SARS CoV-2 mediated sore throat, fever (38-39 C), cough, body fatigue, and viremia that might lead to pneumonia and eventually ventilator-associated pneumonia in severe cases (Rothan & Byrareddy, 2020) . The World Health Organization (WHO) has reported 6,535,354 confirmed cases of COVID-19 pandemic and 387,155 fatalities across the globe as of June 5, 2020, which is much higher than the combined fatalities (1632) for SARS and MERS, and the COVID-19 pandemic continues to rise (Mahase, 2020) . Owing to the lack of prophylaxis or curative treatment strategies against COVID-19, the WHO has recommended social distancing, restrictions on direct contact, self-isolation, use of alcohol-based hand sanitizers with ethanol (80%) or isopropyl alcohol (75%), and antiseptic products such as soaps to avoid the SARS CoV-2 transmission within humans (World Health Organization, 2020). Many countries have officially imposed partial to complete lockdown according to the prevalence of COVID-19 in their respective areas, aiming to flatten the curve of COVID-19 spike (Lau et al., 2020) . The historic engulfment of such a large number of people in the current pandemic COVID-19 has brought the medical setups and developing countries in the world under crisis. Above that, the lack of prophylaxis and drug resistance associated with SARS CoV-2 has rendered all the available antiviral management to undergo retrials, creating an enigma across the globe. The genome of CoVs ranges from 26 to 32 kbps in length with the open reading frames (ORFs) varying from 6 to 11; there are 14 ORFs in SARS CoV-2 (Song et al., 2019) . There are two parts of the first ORF in SARS CoV-2, ORF1a and ORF1b, constituting about 67% of the viral RNA and are translated into polyproteins, pp1a and pp1ab. The pp1a and pp1ab polyproteins encode 10 (NSPs 1-10) and 15 (NSPs 1-10 and NSPs 12-16) NSPs, respectively. These exhibit 72-99.8% homology with SARS CoV . ORFs 3, 6, 7a, 7b, 8, and 9b code for the accessory proteins (Dong et al. (2020); Shereen, Khan, Kazmi, Bashir, & Siddique, 2020) . ORFs 2, 4, 5, and 9a constitute about one-third of the CoVs RNA, which is translated into four structural proteins that ensemble as spike glycoprotein (S), envelope (E), membrane (M), and nucleocapsid (N), respectively (Dong et al. (2020) ; . Other than these ORFs, the viroid RNA comprises untranslated regions. NSPs play a role in replication and viability of the viroid and upregulate the cytokine storm, whereas the structural proteins mediate viral pathogenesis in the host (Wu, Peng, et al., 2020) . Structural proteins S, E, M, and N perform roles in host immune response such that the N-protein, one of the fundamental structural proteins, binds to the RNA genome to form a nucleocapsid that is imperative for virus replication. It inhibits the promotor of the nuclear factor kappa-B (NF-κB) and interferon-β (IFN-β), which eventually leads to disruption in the balance between biosynthesis of proinflammatory and anti-inflammatory cytokines. E is involved in host cell recognition as an integral component of the viroid envelope. M and E together manifest the transmembrane transportation, multiplication, assembly, and release of the viroids. Coronaviruses, especially SARS CoV and SARS CoV-2, attach to angiotensin converting enzyme receptor-2 (ACE-2) present on the lower respiratory-tract cells through S. Genetic mapping and phylogenetic analyses revealed the evolution of SARS CoV-2 because of mutations in its genome as F I G U R E 1 Phylogenetic family tree of coronaviruses infecting human hosts (Gao et al., 2020) . NSP9 is a replicase protein that catalyzes replication of viral RNA by the formation of dimers and preferential binding to single-stranded viroid RNA. Dimerization of NSP9 is essential for RNA binding and replication of viroid RNA (Figure 2 ) (Qiu & Xu, 2020; Wathelet, Orr, Frieman, & Baric, 2007) . NSP10 contains two zinc finger binding domains that are conserved in CoVs. It acts as a cofactor in viral replication through positive reinforcement of viroid RNA replicases and exonuclease NSP14, which provides the resistance of viroids against nucleotide analog drugs (Senanayake, 2020) . NSP11 is a relatively small protein and currently has no known functions. NSP12 is an RNA-dependent RNA polymerase (RDRP), which is the chief component of the viroid RTC and catalyzes the synthesis of viral RNA. NSP12 works in compliance with the cofactors NSP7 and NSP8 to carry out the polymerization and building of the RNA strand (Gao et al., 2020) . NSP13 contains an N-terminal zinc binding domain, whereas at the C-terminus it constitutes a helicase protein that performs its role in unwinding of the RNA or DNA; the NSP12-NSP13 interaction further promotes the unwinding activity (Shu et al., 2020) . NSP14 is a guanine-N7-methyltransferase with 3 0 -5 0 N terminus exonuclease activity that excises the nucleotide analogs from the viroid RNA transcripts and performs its role in proofreading of the synthesized viral RNA, leading to protein synthesis according to the RNA transcript. Furthermore, NSP14 eradicates the nucleoside analogs and interacts with the trimeric RNA polymerase complex (NSP12, NSP7, and NSP8) to perform its proofreading activity. The quality of the CoVs makes them resistant to nucleotide analog mechanism (NAM) treatment, causing uncontrollable growth and spread of the SARS CoV-2 in recent COVID-19 pandemic ( Figure 3a ) (Cao, Deng, & Dai, 2020; Ferron et al., 2018) . NSP15 is a hexameric, manganese-dependent, and uridine-specific endoribonuclease. It catalyzes the RNA replication process in RTC. It degenerates the single-or double-stranded RNA of the host to catalyze viral RNA polymerization Matsuyama et al., 2020) . The polyuridine sequences cleaved by NSP15 trigger the cytokine storm, with release of interleukin 1β, 4, and 10 (IL-1β, IL-4, and IL-10), monocyte chemoattractant protein-1 (MCP-1), interferon γ (IFN-γ), interferon γ-induced protein 10 (IP10), and CD 4+ and CD 6+ T-cells (Fu, Cheng, & Wu, 2020; Shang, Yang, Rao, & Rao, 2020) . NSP16 is a 2 0 O-methyltransferase that methylates the RNA cap 2 0 -O position of the ribose, bringing about the cap-1 form of the RNA. This proofreading strategy acquired by the CoVs helps them in overcoming the innate immune response and IFN-mediated antiviral responses (Decroly et al., 2011; Liao, Way, & Madahar, 2020) . The urgent requirement of potent drugs against COVID-19 is unmet because of limitations in drug design, targeted drug delivery, and controlled in vitro, in vivo, and clinical studies (Ahmadpoor & Rostaing, 2020; Dhama et al., 2020) . Researchers from the globe are putting efforts in the quest of an effective treatment for COVID-19. (Arabi et al., 2020; Carbajo-Lozoya et al., 2012; Chu et al., 2004; Matsuyama et al., 2020; Sheahan et al., 2020; Yang & Shen, 2020) . Chloroquine and hydroxychloroquine work efficiently by increasing the pH of the lysosome and inhibiting proteins E and N. Moreover, these drugs along with losartan and olmesartan are also under investigation for the inhibition of ACE-2 (Gurwitz, 2020; Liu et al., 2020 (Lau et al., 2020; Shannon et al., 2020) . However, the plausibility of RAM over NAM for inhibition of viral enzymes has an edge because of the NSP14 exonuclease that has the ability to proofread their synthesized RNA and polypeptide machinery (Figure 3a ,b) Dhama et al., 2020) . Convalescent plasma, which provides neutralizing antibodies to target protein S, has been under clinical investigation and is sought as a last resort for curing COVID-19 patients . PPI is also a promising tool for further investigation as NSP16 is another important drug target that protects the synthesized viral RNA from cleavage or recognition by the host immune response by methylation to the cap-1 form. The resistance of CoVs, including SARS CoV-2, because of the genetically evolving NSPs, proofreading capabilities of NSP14, severity of NSP15-dependent cytokine storm, and NSP16-mediated viral RNA-capping make them highly commendable drug targets. The lack of vaccine, oriented medicine and socio-economic burdens are escalating around the world, especially in underdeveloped countries. The resurgence of the COVID-19 might be increased if the official lockdowns are lifted in underdeveloped countries, ultimately increasing the risks of pandemic. Presently, providing financial support to underdeveloped countries and utilizing existing medicine and genetics of SARS CoV-2 can be helpful in treatment. NSPs and structural proteins are equally important in antiviral therapy, as NSP14 exonuclease and NSP16 2 0 O-methyl transferase are seemingly promising targets for anti-COVID-19 treatment. However, exceptional diligence is required for the selection of a suitable drug manifested by its mechanism of action against SARS CoV-2, along with the implementation of smart WHO recommended policies to effectively eradicate the current COVID-19 pandemic. This work was supported by the Institute of Chemistry, University of the Punjab, Lahore, Pakistan. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Aatika Sadia: Investigation; writing-original draft preparation. Muhammad Asim Raza Basra: Conceptualization; supervision; writing-review and editing. Muhammad Asim Raza Basra https://orcid.org/0000-0002-4242- Why the immune system fails to mount an adaptive immune response to a COVID-19 infection Membrane binding proteins of coronaviruses COVID-2019: The role of the nsp2 and nsp3 in its pathogenesis Treatment of Middle East respiratory syndrome with a combination of lopinavir/ritonavir and interferon-β1b (MIRACLE trial): Statistical analysis plan for a recursive twostage group sequential randomized controlled trial Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence Replication of human coronaviruses SARS-CoV, HCoV-NL63, and HCoV-229E is inhibited by the drug FK506. Virus Research Convalescent plasma as a potential therapy for COVID-19 Role of lopinavir/ritonavir in the treatment of SARS: Initial virological and clinical findings Severe acute respiratory syndrome coronavirus nonstructural protein 2 interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling Origin and evolution of pathogenic coronaviruses Cyclosporin a inhibits the replication of diverse coronaviruses Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex Arbidol combined with LPV/r versus LPV/r alone against Corona virus disease 2019: A retrospective cohort study COVID-19, an emerging coronavirus infection: Advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV) Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA Understanding SARS-CoV-2-mediated inflammatory responses: From mechanisms to potential therapeutic tools Structure of the RNA-dependent RNA polymerase from COVID-19 virus Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans Profiling early humoral response to diagnose novel coronavirus disease (COVID-19) The origin, transmission, and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak-An update on the status Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein The architecture of SARS-CoV-2 transcriptome Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2 The positive impact of lockdown in Wuhan on containing the COVID-19 outbreak in China Discovery of the first virus, the tobacco mosaic virus: 1892 or 1898? Comptes rendus de l'Académie des sciences. Série III, Sciences de la vie Molecular immune pathogenesis and diagnosis of COVID-19 Target virus or target ourselves for COVID-19 drugs discovery?-Lessons learned from anti-influenzas virus therapies Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Coronavirus: Covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral NSP15 Genotype and phenotype of COVID-19: Their roles in pathogenesis A history of influenza Functional studies of the coronavirus nonstructural proteins Baricitinib as potential treatment for 2019-nCoV acute respiratory disease The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak Mechanisms of action of hydroxychloroquine and chloroquine: Implications for rheumatology Drug repurposing strategies for COVID-19 The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines. npj Vaccines Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 exonuclease active-sites Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses SARS-coronavirus-2 nsp13 possesses NTPase and RNA helicase activities that can be inhibited by bismuth salts From SARS to MERS, thrusting coronaviruses into the spotlight Understanding of COVID-19 based on current evidence Human coronavirus NL63, a new respiratory virus Coronaviruses and the associated potential therapeutics for the viral infections Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities Coronavirus nsp10/nsp16 methyltransferase can be targeted by nsp10-derived peptide in vitro and in vivo to reduce replication and pathogenesis Severe acute respiratory syndrome coronavirus evades antiviral signaling: Role of nsp1 and rational design of an attenuated strain A coronavirus E protein is present in two distinct pools with different effects on assembly and the secretory pathway Considerations for quarantine of individuals in the context of containment for coronavirus disease (COVID-19): Interim guidance Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods Targeting the endocytic pathway and autophagy process as a novel therapeutic strategy in COVID-19 Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A datadriven analysis in the early phase of the outbreak A pneumonia outbreak associated with a new coronavirus of probable bat origin How to cite this article: Sadia A, Basra MAR. Therapeutic dilemma in the repression of severe acute respiratory syndrome coronavirus-2 proteome