key: cord-0795906-9pbqdiku
authors: Kumar, Devendra; Chauhan, Gaurav; Kalra, Sourav; Kumar, Bhupinder; Singh Gill, Manjinder
title: A Perspective on Potential Target Proteins of COVID-19: Comparison with SARS-CoV for Designing New Small Molecules
date: 2020-09-29
journal: Bioorg Chem
DOI: 10.1016/j.bioorg.2020.104326
sha: 63fbf6aeb36e933ff7e6f38872d39fdb098cf4fc
doc_id: 795906
cord_uid: 9pbqdiku

SARS-CoV-2 (COVID-19) epidemic has created an unprecedented medical and economic crisis all over the world. SARS-CoV-2 is found to have more contagious character as compared to MERS-CoV and is spreading in a very fast manner all around the globe. It has affected over 31 million people all over the world till date. This virus shares around 80% of genome similarity with SARS-CoV. In this perspective, we have explored three major targets namely; SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or Mpro Protease for the inhibition of SARS-CoV-2. These targets have attracted attention of the medicinal chemists working on computer-aided drug design in developing new small molecules that might inhibit these targets for combating COVID-19 disease. Moreover, we have compared the similarity of these target proteins with earlier reported coronavirus (SARS-CoV). We have observed that both the coronaviruses share around 80% similarity in their amino acid sequence. The key amino acid interactions which can play a crucial role in designing new small molecule inhibitors against COVID-19 have been reported in this perspective. Authors believe that this study will help the medicinal chemists to understand the key amino acids essential for interactions at the active site of target proteins in SARS-CoV-2, based on their similarity with earlier reported viruses. In this review, we have also described the lead molecules under various clinical trials for their efficacy against COVID-19.

Coronaviruses (CoVs) tend to have a high zoonotic potential and according to the World Health Organization (WHO), these viral diseases have emerged as a serious health issue to the world [1] .

Two previously identified coronaviruses (CoVs), severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV), have dominated medical, science, and media attention over the past two decades due to their dangerous epidemic potential [2, 3] . The first SARS case was found in Foshan, China, in November 2002 [4] , and the first case of MERS died in June 2012 in a hospital in Jeddah, Saudi Arabia. Both zoonotic diseases remain on the list of priority diseases of the World Health Organization (WHO) as they pose a major threat to the global public health security [5, 6] . The novel coronavirus pneumonia of 2019, called COVID-19 by the World Health Organization (WHO), triggered by SARS-CoV-2, first emerged in Wuhan City in December 2019 and emerged as an epidemic overworld [7] [8] [9] . This new virus shares 80% of its genome with SARS-CoV but more contagious which leads to very fast spreading all over the globe and presented a great challenge to the health system of the whole world [10, 11] .

Various studies on COVID-19 reported its epidemiological and clinical characteristics. Most patients effected from it were found to develop fever and cough while some patients experienced acute respiratory failure, ARDS, septic shock, and other serious complications. Critical patients tend to have poor outcome and high mortality as compared with other forms of CoV [12] [13] [14] .

Currently, the diagnosed therapy of COVID-19 relies primarily on a consensus guideline involving epidemic communication history, laboratory testing, and CT imaging analysis [15, 16] . Since the first case in China, the epidemic has spread to a total of 213 countries and regions, with more than 31 million confirmed cases as reported till 23 September 2020.

Coronaviruses are Nidovirales single-strand RNA viruses which are spherical or pleomorphic in shape with bear's club-shaped glycoprotein projections. These are classified into four genera: alpha, beta, gamma, and delta coronaviruses [17] . Gamma and delta CoVs are primarily associated with avian hosts, while alpha and beta CoVs contain many human and domestic pathogens that are likely to be associated with the transmission events of cross-species [18, 19] . Both SARS-CoV and MERS-CoV belong to the genus beta coronavirus and are associated with a severe infection of the respiratory tract with mortality rates of 10% and 35% respectively [20] . The SARS pandemic was managed rapidly through an unparalleled global containment campaign, and since May 2004, the virus has not been identified in humans [4] . Despite this rapid eradication, nearly 800 deaths in 27 countries were caused by SARS-CoV, with persistent outbreaks in 18 countries on three continents (WHO). Rhinolophid bats are gradually serving as natural reservoirs for SARS-related CoVs with a potential spill-over to the non-flying mammals. For example, as with the SARS coronavirus, some bat CoVs may use angiotensin-converting enzyme 2 (ACE2) as a cell receptor [21] [22] [23] [24] . In comparison, the role of bats in MERS-CoV epidemiology is less well explained, since this human viruse is mostly linked to the viruses found in dromedary camels [25] . In addition, while similar viruses have been identified in bats, they are divergent in their spike sequences and appear ineffective in the use of human dipeptidyl peptidase 4 (DPP4) as a receptor cell [23, 26, 27] . The MERS epidemic is ongoing in the Middle East, with travel-related cases recorded in 27 countries around the world [28] . Lastly, Alphacoronaviruses 229E and NL63, which induce a mild human influenza-like syndrome, share a common ancestor with Hipposideros and Triaenops batsampled viruses, respectively [29] [30] [31] .

Bats are considered to have high rates of CoV diversity with geographical range and prevalence in almost every species investigated. It supports the theory that bats played a major role in the evolution of CoV [18, 32] . Additionally, bat CoVs are interspersed taxonomically with other associated mammals including humans and domestic animals which is consistent with the theory that bats are a significant genetic reservoir of CoVs [31, 33] . The long-term evolutionary relations between bats and coronaviruses are also confirmed by phylogenetic evidence that CoVs display such tropisms unique to species and genus [34, 35] , and those taxonomically-based viruses are identified independently of the sampling position in different bat species. Conversely, that CoVs are not always shared among bat species that co-roost suggests that there are some barriers to transmission across species [18, 26, [35] [36] [37] [38] . Due to the topological similarity between the phylogenetic trees of CoVs and their mammalian hosts, it has been proposed that the diversity of CoVs represents primarily the long-term co-divergence between bats and CoVs [35] . Indeed, recent studies of unique bat taxa from different locations indicate that the role of virus-host codivergence in the evolutionary history of CoVs may have been overestimated relative to other events like host-jumping [31, 32, 39] .

In SARS-CoV-2 to date, three targets have been explored namely the SARS-CoV-2 spike (S) protein [40] , RNA dependent RNA polymerase [41] , and 3CL or M pro Protease [42] with several mechanisms for the inhibition of the SARS-CoV-2. Out of these two targets, RNA dependent RNA polymerase and 3CL/M pro Protease are reported with their inhibitors while the antibody-based inhibition was reported for the SARS-CoV-2 spike protein receptor-binding domain (RBD) [43] .

Other than these three targets, some host-based targets, their role in SARS-CoV-2 transmission and problems in targeting them are also discussed in this manuscript. However it is also known that SARS-CoV-2, as well as SARS-CoV, are identical (80%) [44, 45] , So the information about the structural similarity and identical amino acids of targets has unlocked the pathways of the medicinal chemists working in the area of computer-aided drug design in generating new small molecules and structural biologists to design the antibodies that might interact with these targets to combat the COVID-19 disease.

In 1960, the coronavirus was first reported for causing the common cold [46, 47] . More than 500 patients have emerged with flu-like the symptoms in one study conducted in Canada in 2001.

Virologic analysis has shown that 3.6 percent of these cases were polymerase chain reaction (PCR) positive for the HCoV-strain [48] . Coronavirus was considered as a fairly safe, non-virus until   2002. Before 2003, there were only 2 CoVs reported to cause human disease, human CoV 229E (HCoV-229E), and HCoV-OC43 [48] which present mild symptoms such as common cold in adults and more severe illness in children and elders along with the weakened immune system. In November 2002, rare cases of unknown cause of "atypical pneumonia" occurred in Foshan City, Guangdong Province, China, where many health care workers were infected [49] identified as a cause of these cases of atypical pneumonia [51] . Therefore, a state of emergency was declared in 2004 by the Centers for Disease Control and Prevention (CDC) and WHO [50, 52, 53] . The evolution of this virus has shown that coronavirus is not a stable virus as well as it can adapt to humans to become more virulent, even lethal. Indeed, another outbreak in Saudi Arabia 

In SARS-CoV-2 till date, three targets have been explored namely the SARS-CoV-2 spike (S) protein [40] , RNA dependent RNA polymerase [41] , and 3CL or M pro Protease [42] with several mechanisms for the inhibition of SARS-CoV-2. Out of these two targets, RNA dependent RNA polymerase and 3CL or M pro Protease are reported with their inhibitors while the antibody-based inhibition is reported for the SARS-CoV-2 spike protein receptor-binding domain (RBD) [43] . So the information about the structural similarity and identical amino acids of these targets has 

The entry of the virus in the host cell is an important step towards infection of SARS-CoV and SARS-CoV-2. This entry is facilitated by the ACE 2 receptor. The Spike glycoprotein (S Protein) of these viruses is a trimer of about 1300 amino acids that splits into S1 (700 amino acids) and S2

(600 amino acids) subunits [54] [55] [56] [57] . The S1 contains the receptor-binding domain (RBD) that interacts with the peptidase domain (PD) of ACE 2 while S2 subunit is cleaved by the host proteases in post interaction and facilitates membrane fusion and hence important step in viral infection [55, [58] [59] [60] . The interaction with the ACE 2 is facilitated by polar interactions such as hydrogen bonding, pi-pi stacking, and salt bridge interactions. The PD arc-shaped helix of ACE 2 binds to the loop region of the RBD of S protein. The amino acid interactions that helped in binding were observed between the RBD of SARS-CoV-2 and PD of ACE 2 and are considered as important aspects for the interaction inhibitor design [61] . There are 17 amino acids of SARS-CoV-2 and 20 amino acids of ACE 2. Out of these 14 amino acid interactions of SARS-CoV-2 namely Tyr449, Tyr453, Leu455, Phe456, Phe486, Asn487, Tyr489, Gln493, Gly496, Gln498, Thr500, Asn501, Gly502, and Tyr505 are considered to be important. The 5 amino acid interactions are explored to be more critical as these amino acids interact with 18 amino acids of ACE 2. These critical amino acid interactions involved Leu455 interaction with Asp30, Lys31, and His34; Phe486 with Gln24, Leu79, Met82, Tyr83, and Leu472; Gln493 with ACE 2 Lys31, His34 and Glu35; GLN498 of SARS-CoV-2 with Asp38, Tyr41, Gln42, Leu45, and Lys353.

Amino acid Asn501 has a similar type of interactions with ACE2 Lys353, Gly354, and Asp355 while H-bond interaction is observed with Tyr41. The binding affinity of the RBD domain of SARS-CoV-2 and PD of ACE2 is 4.7nM which is strong as compared to the 31nM in SARS-CoV.

It was reported that in SARS-CoV-2 the amino acid Lys417 showed a salt bridge interaction with Asp30 of ACE-2. The positive patch on the surface of RBD of SARS-CoV-2 was added by Lys417 that contributed towards the electrostatic potential. The structure of the SARS-CoV-2 and ACE 2 interaction was reported (PDB ID: 6M0J) and the interactions of the residues are shown in Figure   3 . 

The transcription of the mRNA and replication is an important process in the viral life cycle that is carried out by the RNA dependent RNA polymerase (RdRp) [69] . The major part of the RdRp is viral non-structural proteins 12 (nsp12) which is a major catalytic subunit [70, 71] . Nonstructural protein 12 (nsp12) itself is less active and require nsp7 and nsp8 for the binding of the template and processing of the mRNA [72, 73] . The structure of the complex of nsp12-nsp7-nsp8

has been determined (RdRp complex) [73] [74] [75] [76] [77] . Nsp 12 consists of β-hairpin with residues from 31-50, and is extended with seven helices and three β-strands [73, 77] to nidovirus RdRp-associated nucleotidyl-transferase domain (NiRAN) that contains residues from 115-250 [78] . The NiRAN domain connects to an interface domain that contains three helices and five β-strands from the residues 251-365 [79] . This interface domain is followed by the main RdRp domain (residues 366-920) (Figure 7) . The RdRp domain contains the finger subdomain that runs from 397-581 residues and 621-679 residues, followed by palm subdomain from 680-815 residues and connecting to the thumb subdomain from 819-920 residues. The complex of nsp12 was stabilized by the binding of nsp7 and nsp8 ( Figure 8) . The motifs F and G in the finger subdomain interacts with the RNA with residues Lys545 and ARG 555. Remdesivir is a prodrug that gets converted to RTP (Remdesivir triphosphate) binds covalently to the mRNA strand and stops the mRNA transcription and replication of SARS-CoV-2.

It also interacts with the magnesium ions present in the active site. The residues Asp760 and Asp761 also interact with the Remdesivir triphosphate via hydrogen bond interactions. The nsp12

of the SARS-CoV-2 and SARS-CoV are subjected to clustalW alignment and found to be 94% identical and 96% similar ( Figure 9 ). 3. Specificity and key different amino acids residues in these target proteins Table 1 shows the two types of columns, one column represents the binding residues and the other represents the residues that affect the specificity. The two columns are segregated based on differences/similarities in the binding site of SARS-CoV and SARS-CoV-2. It was observed that many of the residues in SARS-CoV and SARS-CoV-2 are similar in the case of S protein-ACE2

interaction, M pro , and RNA dependent RNA polymerase (RdRp) i.e. more than 96 %. So the specificity can be explained based on the difference between the active site residues, binding residues in case of (S1 subunit and ACE2 interaction), nature of residues, and the conformation of the residues in or near to the active site hence providing the insights to the specific inhibitor design for the SARS-CoV-2 as compared to SARS-CoV [80] . Only conformational in the residues Firstly the difference and similarities are highlighted in between the S1 subunits of the SARS-CoV and SARS-CoV-2 ( Figure 4 ). These helped in the shortlisting of the residues that are involved in the interaction of S1 with the ACE2. Although the binding is affected by the residues, some of the residues play an important role and contribute towards the binding affinities in case of SARS-CoV which contributes towards the binding affinities of the S1 subunits towards ACE2. These differences in the residues and nature also affect the specificity and binding towards ACE2 and useful for the medicinal chemists to design a strategy for inhibition of the interaction between S1

and ACE2. The representations of the difference between the active site residues, the nature of residues, and conformation ( Figure 10 ) depicts the specificity and may help in designing new inhibitors to stop S-protein-ACE2 interaction. 

This type II transmembrane enzyme belongs to the serine protease family. Some studies reported that SARS-CoV-2 uses TMPRSS2 for S protein priming [84] . SARS-CoV-2 initiate the cleavage of S protein and these TMPRSS2 inhibitors such as camostat were found to prevent the coronavirus infection [85] . CoV-2. A study in TMPRSS2 knockout mice revealed that these knockout mice were immune to coronavirus [88] . Some studies suggest that TMPRSS2 expression is controlled by estrogens or androgen, thus to target by which pathway is still under consideration [89] . Moreover, there is no crystal structure of TMPRSS2 reported to date. It is another problem in target-based drug designing as it can be done only via homology modeling from other similar serine protease enzymes.

Cathepsin L is found to play a key role in the entry of SARS-CoV-2 to host cells via endocytosis [90] . Cathepsin L inhibitors prevent pulmonary fibrosis. This fact indicates the importance of Cathepsin L as a target for the treatment of SARS-CoV-2 [91] . A research study on HEK 293/hACE2 cells in which these cells were treated with specific Cathepsin L inhibitor demonstrated very low chances of SARS-CoV-2 entry to host cells. It decreased the entry rate by more than 76%. It showed the key role of Cathepsin L in S protein priming by SARS-CoV-2 in lysosomes [92] . Earlier, Cathepsin L inhibitors were also found effective in the treatment of SARS-CoV [93] which also describes it as a potential target for the treatment of novel coronavirus.

The main problem behind designing Cathepsin L inhibitors for the treatment of SARS-CoV-2 is their specificity. There are different types of cathepsins reported which can play a key role in entry of the virus to cells via endocytosis. Although, targeting Cathepsin L with other target proteins can provide some beneficial effects in SARS-CoV-2 patients.

site is cleaved during biosynthesis and is reported as a key feature to differentiate SARS-CoV-2 from SARS-CoV [94, 95] . Furin is found highly expressed in various tissues like lungs by which SARS-CoV-2 can successfully infect the respiratory system via this convertase and initiate activation of its surface glycoprotein [96] . Similarly, in some sample studies obtained from SARS-CoV-2 infected persons in China, various mutations in the furin cleavage site were observed which ultimately affect the binding ability of S-protein to surface [97] . Thus, this site is an important feature in the pathogenicity of SARS-CoV-2. As furin is also overexpressed in the liver, kidney, and glands, it may play a role in infecting these tissues too with the novel coronavirus.

The major issue in targeting furin for treatment of SARS-CoV-2 is their role in various cellular processes. Thus, inhibition of these furin-like enzymes in our body can lead to the various side or adverse effects. Different kinds of mechanisms of furin activation reported are also still confusing in designing novel furin inhibitors.

Other host-based targets that can play a key role in the treatment of SARS-CoV-2 in the future [98, 99] . Recently, an AAK1 and GAK inhibitor is reported to decrease the entry of SARS-CoV-2 to cells but still, no mechanism is reported for this study [100] . This inhibitor, baricitinib, is also beneficial in relief from inflammation which might be advantageous in the treatment of SARS-CoV-2 caused lung inflammation also [101] . For targeting AAK1 and GAK in COVID-19 patients still, a lot of clinical studies are required as these inhibitors are also found to increase the chances of lung infection in clinical trials which is too risky for COVID-19 patients [102] .

Phosphatidylinositol 3-Phosphate 5-Kinase (PIKfyve) is another enzyme that sought to play a key role in the endocytosis process and its dynamical control [103, 104] . A study on treatment with PIKfyve, IL-12, and IL-23 inhibitors (apilimod and YM201636) of 293/hACE2 cells showed the reduced entry of SARS-CoV-2 virus to cells [105, 106] . Thus, PIKfyve can be an important target in the treatment of COVID-19 but major problem is that its 3D crystal structure is still unavailable.

The target-based drug designing for this protein is still difficult.

The fast spread of infectious COVID-19 in the world outbroken the surge of clinical trials against it in search of treatment. The race to find a treatment of this deadly viral infectious disease has started all over the world [107] [108] [109] . More than one thousand trials of various synthetic small molecules, natural molecules, antibodies, or vaccines are under progress in search of effective treatment against this deadly disease (clinicaltrials.gov) [110] [111] [112] [113] . Hydroxychloroquine, an antimalarial drug, is sought to play a key role in treated patients of COVID-19 [114] . This drug molecule is under multiple phase-III clinical trials (NCT04345692, NCT04342221, NCT04322123) against this disease by different health improvement agencies and companies ( Table 2 ). In combination with antibiotic azithromycin, hydroxychloroquine is under phase-II (NCT04329832) and phase-III (NCT04322123) clinical trials. Hydroxychloroquine is found to show a significant reduction in the viral carriage at D6-post inclusion with lower carrying duration as compared to control and untreated patients. In combination with azithromycin, the efficiency was increased and the viral elimination rate was significantly higher [115] . Lopinavir and ritonavir, anti-HIV drugs, are two other molecules that are sought as future treatment of this COVID-19 disease. These drug molecules are also in alone or in combination with other molecules are under different clinical trials for determining their effectiveness in COVID-19 patients (NCT04330690, NCT04307693, NCT04315948). These studies will also determine if these drugs reduce the viral load from the respiratory system in COVID-19 patients or not. Similarly, in various studies effectiveness of Lopinavir/ritonavir is reported against COVID-19 [116, 117] . Remdesivir, drug for ebola virus, is the first drug which is observed in clinical trials to show effectiveness in COVID-19 patients and treated patients with 30% more rapidly as compared to placebo and treated the first patient in US successfully [118] . It has shown possibility in various in vitro studies against COVID-19 and MERS viral infections [119] [120] [121] . The efficiency of this drug against SARS-CoV and MERS-CoV also increased expectations from it against COVID-19 [120, 122] . During some in vitro studies, remdesivir is efficiently found to inhibit this novel coronavirus COVID-19 [123] . Favipiravir, an RNA polymerase inhibitor [124] , is under phase-III clinical trial (NCT04336904) to determine its safety and performance in the treatment of COVID-19 patients by Giuliano Rizzardini, ASST Fatebenefratelli Sacco. Fujifilm Pharmaceuticals U.S.A., Inc. is conducting another phase-II trial of Favipiravir in hospitalized patients of COVID-19 for 14 days treatment (NCT04358549). In one study, against lopinavir, ritonavir, and control groups, Favipiravir receiving patients showed shorter viral clearance time along with improvement in chest imaging [125] . Ruxolitinib, a Janus kinase inhibitor approved for the treatment of myelofibrosis, polycythemia vera, and graft-versus-host disease [126] , is under different phase-I, II, and III trials (NCT04348071, NCT04334044) by various agencies to learn its effect on the progression of COVID-19, inflammation caused by this virus and its severity. Losartan, an orally available angiotensin-receptor antagonist [127] , is under phase-I clinical trials (NCT04335123) for evaluation of its safety in the failure of respiratory system of COVID-19 patients. Dapagliflozin, an antidiabetic drug [128] , is under phase-III studies (NCT04350593) by Saint Luke's Health System in US and high prevalence countries to determine its role in reducing the progression of COVID-19, its complication and mortality due to this disease. Tocilizumab, a recombinant human monoclonal antibody [129] , is gone to phase-III study on 310 patients (NCT04317092) for determining its clinical benefits in COVID-19 patients with risk of the cytokine storm. Although in initial studies, tocilizumab treatment was found associated with an increase in CRP (C-reactive proteins) in few patients, it was also found to clinically stabilize the patients with risk of complications of cytokine storm [130] . Zhang et al. reported the successful treatment of COVID-19 patients with multiple myeloma with tocilizumab treatment [131] . Further, tocilizumab is under various phase-II and III studies by various health agencies to determine its efficacy in the early treatment of COVID-19 patients with evaluation of its safety parameters and role in the prevention of inflammation (NCT04331795, NCT04346355, NCT04320615). Sirolimus, an immunosuppressive agent [132] , under phase-II, double-blind, placebo controlled trial to determine its benefits in hospitalized patients with COVID-19 pneumonia (NCT04341675). [133, 134] . Thus, these supplements are also sought to play a key role in the intervention of COVID-19 and need to be evaluated. To determine the short-term effect of colchicine in COVID-19 patients, it is under phase-III trial by Montreal Heart Institute (NCT04322682). 

SARS-CoV-2 (COVID-19) has emerged as a more contagious virus compared to earlier found CoVs and was declared as pandemic by World Health Organization. It is challenging the health system of the world. The information about its structural similarity with SARS-CoV has unlocked pathways for the rapid development of new molecules for targeting this virus. The exploration of the X-ray crystal structure of SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or M pro Protease has provided critical information for developing small molecule inhibitors for the SARS-CoV-2. The sequencing of SARS-CoV-2 and SARS-CoV was found around 80% similar and key amino acids responsible for the interactions of these proteins have been reported. In case of spike proteins, the important residue like Phe486 is present in the active site of SARS-CoV-2 while absent in the case of SARS-CoV. The other residues such as Tyr442,

Leu443, Asn479, Tyr484, Thr487 are present in SARS-CoV while Leu455, Phe456, Gln493, Gln498, Asn501 are present in SARS-CoV-2 which contributes towards the binding affinities of the S1 subunits towards ACE2. Similarly, in 3CL or M pro target, the conformation of the residues in the active site was found different and the binding site entry residues such as Ala46 in SARS-CoV while Ser46 in SARS-CoV-2 were found to affect the entry as well as binding of ligands to the M pro active site. Further, in case of RdRp (RNA dependent RNA polymerase), the only conformational difference of the residues in the active site. These findings will help medicinal chemists to understand the binding mechanism and key interactions of these proteins responsible for the virus cycle. Further, it will help the medicinal chemists to design new small molecules to target these enzymes of COVID-19 and help in its treatment. Authors also believe that this perspective will help the chemists and biologists to understand the key proteins to target for finding the cure of this epidemic.

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SARS-like WIV1-CoV poised for human emergence

Isolation and characterization of a novel bat coronavirus closely related to the direct progenitor of severe acute respiratory syndrome coronavirus

Bat severe acute respiratory syndrome-like coronavirus WIV1 encodes an extra accessory protein, ORFX, involved in modulation of the host immune response

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia

Further evidence for bats as the evolutionary source of Middle East respiratory syndrome coronavirus

Cross host transmission in the emergence of MERS coronavirus

Middle East respiratory syndrome coronavirus (MERS-CoV)-update

Evidence for an ancestral association of human coronavirus 229E with bats

Link of a ubiquitous human coronavirus to dromedary camels

Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history

Global patterns in coronavirus diversity

Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus

Evolutionary Insights into the Ecology of

Evolutionary relationships between bat coronaviruses and their hosts

Highly diversified coronaviruses in neotropical bats

Coronavirus infection and diversity in bats in the Australasian region

Prevalence and genetic diversity of coronaviruses in bats from China

Extensive diversity of coronaviruses in bats from China

Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein

Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir

Structure of M pro from SARS-CoV-2 and discovery of its inhibitors

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

A pneumonia outbreak associated with a new coronavirus of probable bat origin

COVID-19): current status and future perspectives

Laboratory diagnosis of emerging human coronavirus infections-the state of the art

Epidemiology, genetic recombination, and pathogenesis of coronaviruses

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Summary of probable SARS cases with onset of illness from 1

Coronavirus as a possible cause of severe acute respiratory syndrome

Update: outbreak of severe acute respiratory syndrome-worldwide

31-Coronavirus never before seen in humans is the cause of SARS

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Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry

Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2

Structure of SARS coronavirus spike receptor-binding domain complexed with receptor

Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis

Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Novel inhibitors of severe acute respiratory syndrome coronavirus entry that act by three distinct mechanisms

Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor

Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design

Structure of main protease from human coronavirus NL63: insights for wide spectrum anti-coronavirus drug design

Design of wide-spectrum inhibitors targeting coronavirus main proteases

The coronavirus replicase

Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates

The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent

One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities

Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors

Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer

Structural genomics of the severe acute respiratory syndrome coronavirus: nuclear magnetic resonance structure of the protein nsP7

NMR structure of the SARS-CoV nonstructural protein 7 in solution at pH 6.5

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses

RNA synthetic mechanisms employed by diverse families of RNA viruses

Structural insights of cyclin dependent kinases: implications in design of selective inhibitors

Nanotechnology for COVID-19: therapeutics and vaccine research

Molecular mechanism of evolution and human infection with sars-cov-2

Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies

SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor

Virtual Screening of Natural Products against Type II Transmembrane Serine Protease (TMPRSS2), the Priming Agent of Coronavirus

Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells

SARS-CoV-2 receptor ACE 2 and TMPRSS 2 are primarily expressed in bronchial transient secretory cells

TMPRSS2 contributes to virus spread and immunopathology in the airways of murine models after coronavirus infection

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A novel cathepsin L inhibitor prevents the progression of idiopathic pulmonary fibrosis

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Novel inhibitors of severe acute respiratory syndrome coronavirus entry that act by three distinct mechanisms

Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein

A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells

The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

Virus strain of a mild COVID-19 patient in Hangzhou representing a new trend in SARS-CoV-2 evolution related to Furin cleavage site

Anticancer kinase inhibitors impair intracellular viral trafficking and exert broad-spectrum antiviral effects

The Serine/Threonine Kinase AP2-Associated Kinase 1 Plays an Important Role in Rabies Virus Entry

Baricitinib as potential treatment for 2019-nCoV acute respiratory disease

COVID-19: combining antiviral and anti-inflammatory treatments

Janus kinase inhibitor baricitinib is not an ideal option for management of COVID-19

Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic

PIKfyve regulation of endosome-linked pathways

YM201636, an inhibitor of retroviral budding and PIKfyve-catalyzed PtdIns (3, 5) P2 synthesis, halts glucose entry by insulin in adipocytes

Apilimod inhibits the production of IL-12 and IL-23 and reduces dendritic cell infiltration in psoriasis

The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak-an update on the status

Current Drugs with Potential for Treatment of COVID-19: A Literature Review

Therapeutic options for the 2019 novel coronavirus (2019-nCoV)

Discovering drugs to treat coronavirus disease 2019 (COVID-19)

Ongoing clinical trials for the management of the COVID-19

Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review

Systematic Review of the Registered Clinical Trials of Coronavirus Diseases 2019 (COVID-19), medRxiv Accepted

Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro

Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial

A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19

Case of the index patient who caused tertiary transmission of COVID-19 infection in Korea: the application of lopinavir/ritonavir for the treatment of COVID-19 infected pneumonia monitored by quantitative RT-PCR

First case of 2019 novel coronavirus in the United States

Compassionate use of remdesivir for patients with severe Covid-19

Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection

Remdesivir as a possible therapeutic option for the COVID-19

Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses

Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro

Favipiravir (T-705), a novel viral RNA polymerase inhibitor

Experimental treatment with favipiravir for COVID-19: an open-label control study

Clinical pharmacokinetics of losartan

Tocilizumab treatment in COVID-19: A single center experience

First case of COVID-19 in a patient with multiple myeloma successfully treated with tocilizumab

Sirolimus: its discovery, biological properties, and mechanism of action

Can early and high intravenous dose of vitamin C prevent and treat coronavirus disease 2019 (COVID-19)?

Evidence that vitamin D supplementation could reduce risk of influenza and COVID-19 infections and deaths

Graphical Abstract

The authors are thankful to Chairman