key: cord-1047958-rf0kblv0
authors: Konwar, Manashjyoti; Sarma, Diganta
title: Advances in Developing Small Molecule SARS 3CL(pro) Inhibitors as Potential Remedy for Corona Virus Infection
date: 2020-11-19
journal: Tetrahedron
DOI: 10.1016/j.tet.2020.131761
sha: 73ea1b34e49f640b93773e5c813f3cf3a31c4b4e
doc_id: 1047958
cord_uid: rf0kblv0

Originated in China, coronavirus disease 2019 (COVID-19)- the highly contagious and fatal respiratory disease caused by SARS-CoV-2 has already infected more than 29 million people worldwide with a mortality rate of 3.15% (according to World Health Organization’s (WHO’s) report, September 2020) and the number is exponentially increasing with no remedy whatsoever discovered till date. But it is not the first time this infectious viral disease has appeared, in 2002 SARS-CoV infected more than 8000 individuals of which 9.6% patients died and in 2012 approximately 35% of MERS-CoV infected patients have died. Literature reports indicate that a chymotripsin-like cystein protease (3CL(pro)) is responsible for the replication of the virus inside the host cell. Therefore, design and synthesis of 3CL(pro) inhibitor molecules play a great impact in drug development against this COVID-19 pandemic. In this review, we are discussing the anti-SARS effect of some small molecule 3CL(pro) inhibitors with their various binding modes of interactions to the target protein.

lower respiratory area of human body in which S-glycoprotein of coronavirus attaches to replicate the virus and regulates human-to-human transmission. 29 The two subunits, S1 and S2 of S-glycoprotein of coronavirus are mainly responsible for the various activities of the SARS-CoV-2. The S1 subunit is mainly responsible for the determination of range of the virus-host ability and cellular tropism whereas S2 subunit intercedes the fusion ability of the virus-cell membrane by two simultaneous domains, heptad repeats 1 and 2 (HR 1 and 2). [30] [31] Following the virus-cell membrane fusion, the viral RNA is liberated into the cytoplasm and the two replicase polyproteins, pp1a and pp1ab which convert the non-structural virus proteins to form replication complex (RTC) to infect the host cell and thus the replication goes on. 32 For proteolytic and replication processing of SARS-CoV and SARS-CoV-2, they have to encode a protease, known as chymotripsin-like cystein protease (3CL pro ) or more commonly known as Main protease (M pro ). 33 3CL pro is a part of the replicase polyproteins (similar to the 3C protease of main picoronavirus) which plays the major role in the viral imitation through proteolysis releasing replicative proteins from their polyproteins precursor to the infected host cell at 11 different cleavage sites. 34 Therefore, for viral replication and infection process of the coronavirus inside the host cell, 3CL pro is very much requisite. 35 The practical congregation of 3CL pro is believed to be in the form of dimer where each monomer contains one independent active site making 3CL pro dimer more active than the monomer. 36 Moreover, in the active site of the enzyme 3CL pro , cysteine acts as a nucleophile and histidine residue acts as a base. 37 The key steps during the viral entry of the SARS-CoV-2 include the binding interaction of the host cells receptor, ACE2 with the spike protein of virus From medicinal chemistry perspectives, an imperative and promising advance to fight with COVID-19 is to develop molecules that can inhibit the essential major polyprotein processing, 3CL pro . As 3CL pro is very much crucial for the viral replication, it is widely regarded as a major drug target for the development of SARS treatment. 45 Several synthetic inhibitors for the 3CL pro have been reported but they are relatively weak in nature. 46 The inhibitors initially bind with the 3CL pro through covalent bonding with the active site of the cysteine 145 residue leading to the deactivation of 3CL pro 's enzymatic activity. 47 The binding of S-glycoprotein of the virus and ACE2 receptor is a decisive step for virus entry and the virus-receptor binding affinity is under intensive study through different approaches.

Additionally this approach also suggests that the S pockets of 3CL pro have been the principal targeting sites for anti-SARS molecules which can block the cysteine site and do not make them free to attach with the ACE2 receptor molecule. The reasons behind the choice of 3CL pro inhibition as the target are a) 3CL pro has the predetermined crystal structure which makes them more approachable in the study, b) 3CL pro is the most studied enzyme of coronavirus which is also common in various bacterial systems and its functional examination such as proteolytic activity is very much easy in presence of inhibitor molecules, c) practical importance of 3CL pro in the life cycle of coronavirus make them more practically superlative as a target for antiviral drug design. [48] [49] In this review, we are trying to analyse the various small molecules/drugs developed as cysteine protease inhibitors or anti-SARS therapy. As COVID-19 is virus infected disease and till now there is not a single commercially available protective drug/vaccine present in zone with mechanical ventilation. 51 Moreover in case of severe breathing problems of patient a high dose of steroid is also needed. In addition to that patients with SARS may also have severe damage of their immune systems due to which various other diseases may also occur.

Therefore, people are advised to keep away from the SARS infected patients or the probable SARS infected people to diminish the infection of SARS.

Most of the human diseases are directly or indirectly linked to the cysteine protease; the nucleophilic sulphur atom of Cys145 forms covalent bond with the receptor of the human body causing the disease. 52 Now if we block this nucleophilic centre with some other small molecule drugs or inhibitors, this will lead to the deactivation of the enzymatic activity of 3CL pro . After this covalent binding with the small molecule inhibitors, 3CL pro is not free to bind with the ACE2 receptor of the human body causing no infection of SARS CoV (Scheme 2). Literature reports clearly state that the principal targeting site for the anti-SARS molecules/drugs is the S pockets of the SARS-CoV 3CL pro . 53 The conventional method of finding the biologically pronounced small molecule inhibitors is primarily based on the rigorous screening of the chemical libraries which is actually very time consuming as well as involves laborious work. In this lengthy process the success of finding the drug molecules also greatly relies on the superiority of the existing libraries. Consequently, at the initial stage most of the researchers tried different protease inhibitors which were previously used to cure and prevent various infectious diseases to inhibit the COVID-19 infection. Out of all well-known drugs, chloroquine (antimalarial drug)

is the foremost drug that comes into the mind which has the ability to hold back the SARS-CoV replication through various pH-dependent steps. 55 Moreover, chloroquine has the ability to modify the various functions related to the immune system such as antibody formation and hence it is known as immunomodulatory drug. (Figure 1 ) Various literature reports reveal that functioning cellular receptors of SARS-CoV-2 was impeded by chloroquine (through glycosylation) for the entrance of the virus into the Vero E6 cells of human to keep away the COVID-19 infection from human body. 56 Similarly, teicoplanin, 57 an antibiotic used for prophylaxis had also proven efficacy (less than that of the chloroquine) through in vitro manner to hold back the SARS-CoV replication. 58 But the results obtained are not so much effective towards the inhibition of the SARS-CoV, only lowers the fever of the patient as a secondary treatment.

J o u r n a l P r e -p r o o f Several other drug molecules which have the ability to inhibit/reduce the SARS-CoV are cinanserin, 59 ribavirin, 60 corticosteroids, 61 lopinavir/ritonavir, 62 Use of cinanserin significantly reduces the replication of SARS-CoV in cell culture with the evidence of negligibly lower cytotoxicity at the inhibitory concentrations. Cinanserin is also available in the form of water soluble hydrochloride salt form but its hydrochloride salt form is less active than the neutral molecule. This is due to the fact that cinanserin has less hydrophilic nature making it more efficient to penetrate the cell membrane and inhibit the viral replication. 59 Furthermore, the inhibition of SARS-CoV in tissue culture can also be shown by individual use of ribavirin (a nucleoside analogue), corticosteroids, lopinavir and type I interferon (INF α) [64] [65] which were proved by the clinical trial methods and in vitro studies but J o u r n a l P r e -p r o o f their applications in human body is still not beneficial. [66] [67] [68] But the combined use of ribavirin and corticosteroids proved to be a beneficial antiviral agent against SARS. 69 A well known naturally occurring alkaloid reserpine which was originally used as sedative and antihypertensive drug also has a potential ability against SARS-CoV. 70 A significant inhibitory efficiency against the replication of SARS-CoV was analyzed by He et al. 71 by the use of aurintricarboxylic acid (ATA) in cell culture. The drastic efficiency of the ATA compound as anti-SARS-CoV agent was attributed due to its polymerization ability in aqueous solution forming a stable free radical which prevents the binding of the protease enzyme to the human cell. In their study, they found that aurintricarboxylic acid has the EC 50 value of 0.2 mg/ml which implies that the use of 0.2 mg per ml (concentration) of ATA gave 50% of its maximal effect. (Figure 4 ) While comparing aurintricarboxylic acid with the Interferon α and β (INF α and β), it was observed that aurintricarboxylic acid is 10 and 100 times more effective than IFN α and interferon β respectively against SARS-CoV replication.

J o u r n a l P r e -p r o o f 

Because of the less effectiveness of the commercially available drugs against SARS-CoV-2, the current interest of research in the various fields is to develop more effectual and potent anti-SARS-CoV-2 inhibitors. Various techniques such as structure based discovery, virtual and experimental screening have been utilized by the researchers in the search for small molecules cysteine protease inhibitors and their implication in the mammalian cells. 73 J o u r n a l P r e -p r o o f 14 In search of the cysteine protease inhibitors, we reported a research article describing the inhibitory effect of peptidic compounds bearing a several heteroatom ketone groups such as benzothaizoyl or thaizolyl and trifluoromethyl ketone groups as SARS-CoV 3CL protease inhibitors. 74 In our study, we found that in the series of trifluoromethyl ketones containing peptidic compounds, the compound with N-morpholine groups as substituent, 1 was found to be most potent with the inhibition constant (K i ) value of 21.0 μM. In the second series of compounds bearing benzothaizoyl or thaizolyl ketone group, the compound with P1pyrrolidone and thaizolyl warhead, 2 was found to be the most potent against 3CL protease with the inhibition constant (K i ) value of 2.20 μM while the compound containing benzothaizoyl warhead, 3 was observed to be little less effective with 49.3 μM. From this report we can assure that the presence/introduction of such groups (fluorine atom, heterocyclic aromatic ring with two or more than two heteroatoms, naturally occurring compounds with such type of rings etc.) in different small molecules may be effective as anti-SARS-CoV agent or cysteine protease inhibitors. 53 (Figure 6 ) As peptide chemistry is very complex and broad in nature, researchers usually utilized various techniques such as structure based discovery, virtual and experimental screening in the search for small molecules cysteine protease inhibitors bearing such kind of warhead groups, effectiveness and its implication in the mammalian cells. Ikejiri et al. 75 developed and evaluated the biological activity against SARS-CoV using nucleoside analogues based on 6-chloropurine derivatives. This kind of nucleoside based purine derivatives have already been reported as antiviral compounds and also show potent as anti-SARS-CoV activity. 76 Out of several synthesized nucleoside analogues, two compounds (4 and 5) exhibited major significant activity as anti-SARS-CoV agent with the IC 50 values 48.7 and 14.5 μM respectively. (Figure 7) The structure-activity relationship of these compounds revealed that the presence of 6-chloropurine motif in both the compounds, unprotected 5 / -hydroxyl group in 4 and protected (benzoylated) 5 / -hydroxyl group in 5 mainly enhanced the antiviral activities in these compounds. Similarly, Niu et al. 39 also synthesized non-peptidic 3-chloropyridine derivatives which are structurally similar to that of MAC-5576 and evaluated the biological activity of these compounds as chymotripsin-like proteinase inhibitors to diminish the SARS infection.

The molecular docking study of these compounds proved that the chloropyridine moieties of these inhibitors initially bind inside the S1 pocket of the inhibitor to the enzyme through in vitro manner whereas ester part specially binds to the S1 substrate binding site of 3CL pro . In their report they summarized all the molecules in the different groups of chloropyridine molecules. Group I compounds contained chloropyridine ester moiety as well as heterocyclic furan moiety (7 and 8) which is found to be more potent for 3CL pro inhibitor than the group II compounds containing simply chloropyridine ester moieties (9) along with fused rings such as naphthalene and coumarin (10 and 11 respectively). The best potent compounds of both the groups are shown in the figure with the IC 50 Chen et al. 83 initially synthesized N-Substituted isatin derivatives by the simple reaction of isatin molecule (2,3-dioxindole) and various bromides sources. The SARS-CoV 3CL pro inhibition assays were conducted via fluorescence resonance energy transfer (FRET) followed by HPLC analysis of the fragment peaks cleaved by 3CL pro . The two thiophene containing isatin derivatives such as thiophenecarboxylic 7-bromo-3-pyridinol ester, 24 and thiophenecarboxylic 5-iodo-3-pyridinol ester, 25 are reported as the most potent SARS-CoV 3CL pro inhibitors with the IC 50 values 0.98 and 0.95 μM respectively. (Figure 14 ) Molecular docking of these molecules showed that the isatin scaffold was located in the S1 site whereas S2 site was blocked by the N-substituted side chain. Moreover it also showed that both the oxygen atoms of the carbonyl group of the synthesized isatin derivative was bonded through hydrogen bond to the-NH groups of the different protein chain residues such as Cys145, His41, Ser144, and Gly143. Similarly, in 1-benzyl-5-[(4-methylpiperidin-1-yl)sulfonyl]-1H-indole-2,3-dione, 28 the carbonyl group of C2-position also formed hydrogen bonds with Gly143 and Ser144 residue of the protease while Asn142 residue binds with the nitrogen atom at the 1-postion of isatin molecule. Moreover, molecular docking revealed that the S1 / site of SARS CoV 3CL pro was blocked by the isatin scaffold while the S2 and S1 sites are booked by the side chain of R 2 and R 3 of the newly synthesized 5-sulfonyl isatin derivatives respectively.

Zhou et al. 85 inhibitors with IC 50 value 13.9-18.2 μM (30 and 31). (Figure 17 ) These inhibitors bind the S1 site of the His163 and Glu166 residues through hydrogen bonding interactions while hydrophobic S2 site was booked with Met, Asp, His, Pro and Tyr residues. Moreover two additional aromatic/hydrophobic interactions were also found in the S1 and S2 sites close to the catalytic cysteine residue where a donor site interacts with residues His163 and His164 in the S1 site. Herein, the S2 pocket originated by the residues such as His41, Met49, Met165 and Asp187 side chains of the protease was occupied by the novel decahydroisoquinoline scaffold of 33. Simialrly, the S1 site which was originated by the residues Phe-140, Leu-141 and Glu-166 was occupied by the P1 site nitrogen atom of the imidazole of 33 and it forms hydrogen bonding interaction with the His-163 residue of the protease.

Ramajayam et al. 89 developed a series of 1,6-dihydropyrimidine derivatives as SARS-CoV 3CL protease inhibitors and their effectiveness was appraised by in vitro protease inhibitor analyses. These 1,6-dihydropyrimidine derivatives were synthesized by the two step reaction of substituted benzaldehyde, ethyl cyanoacetate and thiourea followed by the slow addition of different halide derivatives in DMF as solvent and K 2 CO 3 as base at 0-5 °C. In In the molecular docking study, the pocket created by Thr25, His41, Cys44, Thr45, and Ala46 residues was occupied by the 2-chloro-4-nitroanilide moiety of 56. In addition to that, the nitro group in 56 is envisaged to be bonded with the -NH of Ala46 residue of 3CL pro through hydrogen bonding, while the S-atom of Cys145 and N2 atom of His41 residues was fitted with the chlorine atom of the compound 56. Similarly, the site formed by Gln189-Gln192 and Met165-Pro68 residues was filled by the dimethylaminophenyl group of the compound.

A series of benzoquinoline compounds were designed, synthesized and evaluated against 3C-like protease (3CL pro ) inhibitors by Ahn et al. 98 They found that alkylated benzoquinolines with N-phenoltetrazole moieties linked through sulphur atom, 57 was found to be more potent than the non-alkylated derivative, 58 with the IC 50 In the compound bearing oxazole motif, 59 the free rotation of the phenyl and oxazole moiety was restricted by the 1,2-steric interaction between the N-aryl imino group and the acetate group. Based on the molecular modelling interactions, the S1, S2 and S3 sites of 3CL pro are fitted with the N-aryl imino group, phenyl ring and acetate group respectively.

Moreover the carbonyl oxygen of the acetate group binds with the Glu166 residue of 3CL pro through hydrogen bonding interaction. In the molecular docking study, it was found that the molecule (Sabadinine) 66 is sited n ext to the residues His44 and Cys144 covering the catalytic dyad of the protease.

Moreover, hydrogen bonding interactions was also found between the hydroxyl oxygen at 

In summary, the use of small molecules as cysteine protease inhibitor reduces the feasible replication of SARS corona virus. There is no report of corona virus protease inhibitors developed as drug candidate until now, but the approach of targeting 3CLpro to find novel anti-SARS CoV protease inhibitor with drug like properties is expected to lead the drug discovery approach against COVID-19 and other SARS related disease. Therefore, we J o u r n a l P r e -p r o o f hope that the summarization of all these small molecule cysteine protease inhibitors in this review will undeniably help medicinal chemists for further development/modification of the new/ existing structures in near future to find effective therapy for corona viruses.

Corresponding Author * E-mail: konwarmanashjyoti@gmail.com; dsarma22@dibru.ac.in, Tel: +91 9854403297

The authors declare no competing financial interest.

Chemistry and Medicinal Chemistry. He has published more than 50 articles in international journal of high repute. He has also authored a Green Chemistry Book published by Kalyani

Publications. In addition to that three more book chapters are in press which are going to be published soon; two book chapters in Elsevier and one in Spinger. His is also the recipient of 

Literature report suggested that the advancement of SARS-CoV and SARS-CoV-2 was emerged from the non-human sources (bat) while there is probably an unidentified intermediary reservoir for SARS-CoV-2 (intermediary reservoir for SARS-CoV was Civet cat while camel was the intermediary reservoir for MERS-CoV). 20 The key feature for the human-to-human transmission involves the transfer of respiratory droplets, direct contact, J o u r n a l P r e -p r o o f fecal-oral route, suspected mother to the new born baby, through aerosols etc. 21 Moreover, reports also suggested that SARS-CoV-2 was also independently introduced from the animals to human with or without the involvement of carrier. As reported, bat coronavirus and SARS-CoV-2 might assign the identical precursor as bats are recognized to be host reservoir for more than 30 coronaviruses with more than 90% nucleotide resemblance. 22

1. Both of them have 86% structural genome similarity.

2. Bat is the primary reservoir of the both of them.

3. Pneumonia is the most common symptoms in both of them with the fever above 38° C.

4. Both of them have the structurally similar to the bat coronavirus.

5. Both of them are β-coronavirus.

6. Pandemic potential is very high in both the cases.

7. Highly efficient human-to-human transmission.

8. Incubation period is 1-14 days in both the cases while the initial 3-8 days are most potent to infection.

9. Fatality rate is around 9% in both the cases.* * For SARS-CoV-2 it is increasing day by day.

SARS-CoV-2 is a mono-stranded RNA virus surrounded with positive-sense containing club-shaped spikes pointing upwards from its surface. These spikes are actually a type of glycoprotein and named as spikes proteins (S). 23 precursor to the infected host cell at 11 different cleavage sites. 34 Therefore, for viral replication and infection process of the coronavirus inside the host cell, 3CL pro is very much requisite. 35 The practical congregation of 3CL pro is believed to be in the form of dimer where each monomer contains one independent active site making 3CL pro dimer more active than the monomer. 36 Moreover, in the active site of the enzyme 3CL pro , cysteine acts as a nucleophile and histidine residue acts as a base. 37 The key steps during the viral entry of the SARS-CoV-2 include the binding interaction of the host cells receptor, ACE2 with the spike protein of virus S protein, subsequent changes in the conformation of the S protein followed by proteolysis for the activation of the COVID-19 in the human cells. 38 In addition to that, the two replicase polyproteins, pp1a and pp1ab which are also known as the promoters for viral replication are arranged perpendicularly to one another and both of them contain three domains I, II and III. Domains I and II have similar structural β-patterns as present in picoronavirus 3C proteinases. 39 These domains are mainly responsible for the substrate binding and the autocatalytic ability containing Cys145 and His41 residues. In addition, domain III attaches to the domain II via five different α-helices with an exterior circle which primarily preserves the accurate conformation of the dimer after proteolytic activity of SARS-CoV 3CL pro .

As mentioned earlier, SARS is mainly distinguished by a high fever above 38° C or From medicinal chemistry perspectives, an imperative and promising advance to fight with COVID-19 is to develop molecules that can inhibit the essential major polyprotein processing, 3CL pro . As 3CL pro is very much crucial for the viral replication, it is widely regarded as a major drug target for the development of SARS treatment. 45 Several synthetic inhibitors for the 3CL pro have been reported but they are relatively weak in nature. 46 The inhibitors originally bind with the 3CL pro through covalent bonding with the active site of the cysteine 145 residue leading to the deactivation of 3CL pro 's enzymatic activity. 47 The binding of S-glycoprotein of the virus and ACE2 receptor is a decisive step for virus entry and the virus-receptor binding affinity is under intensive study through different approaches.

Additionally this approach also suggests that the S pockets of 3CL pro have been the principal targeting sites for anti-SARS molecules which can block the cysteine site and do not make Literature reports clearly state that the principal targeting site for the anti-SARS molecules/drugs is the S pockets of the SARS-CoV 3CL pro . [53] [54] Treatment:

a) Use of commercially available drugs as potent inhibitors:

The conventional method of finding the biologically pronounced small molecule inhibitors is primarily based on the rigorous screening of the chemical libraries which is actually very time overwhelming as well as involves laborious work. In this lengthy process the success of finding the drug molecules also greatly relies on the superiority of the existing libraries. Consequently, at the initial stage most of the researchers tried different protease inhibitors which were previously used to cure and prevent various infectious diseases to inhibit the COVID-19 infection. Out of all renowned drugs, chloroquine (antimalarial drug) is the foremost drug that comes into the mind which has the ability to hold back the SARS-CoV replication through various pH-dependent steps. 55 Moreover, chloroquine has the ability to modify the various functions related to the immune system such as antibody formation and hence it is known as immunomodulatory drug. (Figure 1 Similarly, Niu et al. 39 also synthesized non-peptidic 3-chloropyridine derivatives which are structurally similar to that of MAC-5576 and evaluated the biological activity of these compounds as chymotripsin-like proteinase inhibitors to diminish the SARS infection.

The molecular docking study of these compounds proved that the chloropyridine moieties of these inhibitors initially bind inside the S1 pocket of the inhibitor to the enzyme through in vitro manner whereas ester part specially binds to the S1 substrate binding site of 3CL pro . In their report they summarized all the molecules in the different groups of chloropyridine molecules. Group I compounds contained chloropyridine ester moiety as well as heterocyclic furan moiety (7 and 8) which is found to be more potent for 3CL pro inhibitor than the group II compounds containing simply chloropyridine ester moieties (9) along with fused rings such as naphthalene and coumarin (10 and 11 respectively). The best potent compounds of both the groups are shown in the figure with the IC 50 value. (Figure 9) J o u r n a l P r e -p r o o f inhibitors with IC 50 value 13.9-18.2 μM (30 and 31). (Figure 17 ) These inhibitors bind the S1 site of the His163 and Glu166 residues through hydrogen bonding interactions while hydrophobic S2 site was booked with Met, Asp, His, Pro and Tyr residues. Moreover two additional aromatic/hydrophobic interactions were also found in the S1 and S2 sites close to the catalytic cysteine residue where a donor site interacts with residues His163 and His164 in the S1 site. In the molecular docking study, the pocket created by Thr25, His41, Cys44, Thr45, and Ala46 residues was occupied by the 2-chloro-4-nitroanilide moiety of 56. In addition to that, the nitro group in 56 is envisaged to be bonded with the -NH of Ala46 residue of 3CL pro through hydrogen bonding, while the S-atom of Cys145 and N2 atom of His41 residues was fitted with the chlorine atom of the compound 56. Similarly, the site formed by Gln189-Gln192 and Met165-Pro68 residues was filled by the dimethylaminophenyl group of the compound.

A series of benzoquinoline compounds were designed, synthesized and evaluated against 3C-like protease (3CL pro ) inhibitors by Ahn et al. 98 They found that alkylated benzoquinolines with N-phenoltetrazole moieties linked through sulphur atom, 57 was found to be more potent than the non-alkylated derivative, 58 with the IC 50 nitrogen and N3 nitrogen of tetrazole ring are located in the S1 / and S1 subsite of the 3CL pro .

Furthermore the N3 nitrogen of tetrazole ring also binds to the Gly145 residue through hydrogen bonding. In the compound bearing oxazole motif, 59 the free rotation of the phenyl and oxazole moiety was restricted by the 1,2-steric interaction between the N-aryl imino group and the acetate group. Based on the molecular modelling interactions, the S1, S2 and S3 sites of 3CL pro are fitted with the N-aryl imino group, phenyl ring and acetate group respectively.

Moreover the carbonyl oxygen of the acetate group binds with the Glu166 residue of 3CL pro through hydrogen bonding interaction. interactions. In compound 63, two hydrogen bonds are formed between the terminal amino group and the Thr190 and Gln192 residues whereas in the compound 62 the hydrogen bond interaction was found between the carbonyl group linked to the Michael system and the His163 residue of the protein which make the compound 63 more potent than compound 62. In the molecular docking study, it was found that the molecule (Sabadinine) 66 is sited n ext to the residues His44 and Cys144 covering the catalytic dyad of the protease.

Moreover, hydrogen bonding interactions was also found between the hydroxyl oxygen at C(20) position of sabadinine and the nitrogen atom of His44 residue.

Park et al. 103 

In summary, the use of small molecules as cysteine protease inhibitor reduces the feasible replication of SARS corona virus. There is no report of corona virus protease inhibitors developed as drug candidate until now, but the approach of targeting 3CLpro to find novel anti-SARS CoV protease inhibitor with drug like properties is expected to lead the drug discovery approach against COVID-19 and other SARS related disease. Therefore, we hope that the summarization of all these small molecule cysteine protease inhibitors in this review will undeniably help medicinal chemists for further development/modification of the new/ existing structures in near future to find effective therapy for corona viruses.

Corresponding Author * E-mail: konwarmanashjyoti@gmail.com; dsarma22@dibru.ac.in, Tel: +91 9854403297

The authors declare no competing financial interest. published 11 research articles in international journals from his green, medicinal chemistry work so far. He is also a co-author of one of the book chapters along with Dr. Diganta Sarma in the Elsevier publishing house which will be published soon.

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

COVID-19 epidemic: disease characteristics in children

Another decade, another coronavirus

The different clinical characteristics of corona virus disease cases between children and their families in China-the character of children with COVID-19

COVID-19 pandemic: perspectives on an unfolding crisis

Novel coronavirus: From discovery to clinical diagnostics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges

The fight against the 2019-nCoV outbreak: an arduous march has just begun

Molecular epidemiology, evolution and phylogeny of SARS coronavirus

What we have learnt from SARS epidemics in China

Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

The molecular biology of SARS coronavirus

Preparedness and proactive infection control measures against the emerging novel coronavirus in China

Inhibitors of SARS-3CLpro: virtual screening, biological evaluation, and molecular dynamics simulation studies

An Overview of Severe Acute Respiratory Syndrome-Coronavirus

Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy

Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors

New insights into the antiviral effects of chloroquine

Chloroquine and hydroxychloroquine as available weapons to fight COVID-19

Inhibition of feline (FIPV) and human (SARS) coronavirus by semisynthetic derivatives of glycopeptide antibiotics

Cycloaddition-Iodination-Suzuki Reaction

Synthesis and antibacterial activity of 4-benzoyl-1-methyl-5-phenyl-1H-pyrazole-3-carboxylic acid and derivatives

Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors

Synthesis, modification and docking studies of 5-sulfonyl isatin derivatives as SARS-CoV 3C-like protease inhibitors

Isatin compounds as noncovalent SARS coronavirus 3C-like protease inhibitors

Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings

Individual and common inhibitors of coronavirus and picornavirus main proteases

A new lead for nonpeptidic active-site-directed inhibitors of the severe acute respiratory syndrome coronavirus main protease discovered by a combination of screening and docking methods

Biflavonoids from Torreya nucifera displaying SARS-CoV 3CLpro inhibition

Sabadinine: a potential nonpeptide anti-severe acute-respiratory-syndrome agent identified using structure-aided design

Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases

Inhibition of SARS-CoV 3C-like protease activity by theaflavin-3,3'-digallate (TF3). Evid.-Based Complementary Altern

Identification of phenanthroindolizines and phenanthroquinolizidines as novel potent anti-coronaviral agents for porcine enteropathogenic coronavirus transmissible gastroenteritis virus and human severe acute respiratory syndrome coronavirus

Emodin inhibits current through SARS-associated coronavirus 3a protein

Procyanidins and butanol extract of Cinnamomi Cortex inhibit SARS-CoV infection

Inhibition of severe acute respiratory syndrome-associated coronavirus (SARSCoV) by calpain inhibitors and β-D-N4-hydroxycytidine

6-Bis-arylmethyloxy-5-hydroxychromones with antiviral activity against both hepatitis C virus (HCV) and SARS-associated coronavirus (SCV)

Inhibition of SARS-coronavirus infection in vitro by S-nitroso-N-acetylpenicillamine, a nitric oxide donor compound

Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic

Identification of potential drug candidates to combat COVID-19: a structural study using the main protease (mpro) of SARS-CoV-2

COVID-19 epidemic: disease characteristics in children

Another decade, another coronavirus

The different clinical characteristics of corona virus disease cases between children and their families in China-the character of children with COVID-19

COVID-19 pandemic: perspectives on an unfolding crisis

Novel coronavirus: From discovery to clinical diagnostics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges

The fight against the 2019-nCoV outbreak: an arduous march has just begun

Middle East respiratory syndrome coronavirus (MERSCoV): A review. Germs

Molecular epidemiology, evolution and phylogeny of SARS coronavirus

What we have learnt from SARS epidemics in China

Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

Can we contain the COVID-19 outbreak with the same measures as for SARS?

The molecular biology of SARS coronavirus

Ninth Report of the International Committee on Taxonomy of Viruses

Coronavirus nonstructural protein 1: Common and distinct functions in the regulation of host and viral gene expression

Severe acute respiratory syndrome coronavirus phylogeny: toward consensus

Severe community-acquired pneumonia

Towards our understanding of SARS-CoV, an emerging and devastating but quickly conquered virus

The possibility of COVID-19 transmission from eye to nose

Novel human coronavirus (SARS-CoV-2): a lesson from animal coronaviruses

Learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV

Laboratory testing of SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures

New insights on the role of paired membrane structures in coronavirus replication

ACE2 receptor expression and severe acute respiratory syndrome coronavirus infection depend on differentiation of human airway epithelia

Coronaviruses: an overview of their replication and pathogenesis

The art of war: battles between virus and host

Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus

Measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in Wuhan

Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein

Coronavirus transcription: a perspective

Host factors in coronavirus replication

Evaluating the 3C-like protease activity of SARS-Coronavirus: recommendations for standardized assays for drug discovery

Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes

Sensitized detection of inhibitory fragments and iterative development of non-peptidic protease inhibitors by dynamic ligation screening

Structure-based design, synthesis, and evaluation of peptide-mimetic SARS 3CL protease inhibitors

Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors

How prepared are we to control severe acute respiratory syndrome in future

Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro

Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study

Novel wuhan (2019-nCoV) coronavirus

The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak

Insight into COVID-2019 for pediatricians

Ultrarapid diagnosis, microscope imaging, genome sequencing, and culture isolation of SARS-CoV-2

Battling 21st-century scourges with a 14th-century toolbox

Molecular strategies to inhibit the replication of RNA viruses

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

Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs

Characterization of SARS main protease and inhibitor assay using a fluorogenic substrate

Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus

The role of antimalarial agents in the treatment of SLE and lupus nephritis

Preparedness and proactive infection control measures against the emerging novel coronavirus in China

Inhibitors of SARS-3CLpro: virtual screening, biological evaluation, and molecular dynamics simulation studies

An Overview of Severe Acute Respiratory Syndrome-Coronavirus

Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy

Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors

New insights into the antiviral effects of chloroquine

Chloroquine and hydroxychloroquine as available weapons to fight COVID-19

Inhibition of feline (FIPV) and human (SARS) coronavirus by semisynthetic derivatives of glycopeptide antibiotics

Chloroquine is a potent inhibitor of SARS coronavirus infection and spread

Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro

Ribavirin in the treatment of severe acute respiratory syndrome (SARS)

Efficacy and safety of inhaled corticosteroids: new developments

Arbidol (Umifenovir): a broad-spectrum antiviral drug that inhibits medically important arthropod-borne flaviviruses

Treatment of SARS with human interferons

Evaluation of immunomodulators, interferons and known in vitro SARS-coV inhibitors for inhibition of SARS-coV replication in BALB/c mice

Adverse Events Associated with High-Dose Ribavirin: Evidence from the Toronto Outbreak of Severe Acute Respiratory Syndrome

Ribavirin and interferon therapy in patients infected with the Middle East respiratory syndrome coronavirus: an observational study

The use of corticosteroid as treatment in SARS was associated with adverse outcomes: a retrospective cohort study

Systematic review of treatment effects

Small molecules targeting severe acute respiratory syndrome human coronavirus

Potent and selective inhibition of SARS coronavirus replication by aurintricarboxylic acid

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

Screening of an FDA-approved compound library identifies four small-molecule inhibitors of Middle East respiratory syndrome coronavirus replication in cell culture

New developments for the design, synthesis and biological evaluation of potent SARS-CoV 3CLpro inhibitors

A comparative study of warheads for design of cysteine protease inhibitors

Synthesis and biological evaluation of nucleoside analogues having 6-chloropurine as anti-SARS-CoV agents

Synthesis and antiviral activity of 6-chloropurine arabinoside and its 2'-deoxy-2'-fluoro derivative

High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase

Design, synthesis and antiviral efficacy of a series of potent chloropyridyl ester-derived SARS-CoV 3CLpro inhibitors

Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase

Design, synthesis, and evaluation of inhibitors for severe acute respiratory syndrome 3C-like protease based on phthalhydrazide ketones or heteroaromatic esters

SARS-CoV 3C-like protease inhibitors of some newly synthesized substituted pyrazoles and substituted pyrimidines based on 1-(3-aminophenyl)-3-(1H-indol-3-yl) prop-2-en-1-one

Acidic Catalytic System for Synthesis of Pyrazole and its Biaryls Derivatives with Antimicrobial Activities through Cycloaddition-Iodination-Suzuki Reaction

Synthesis and antibacterial activity of 4-benzoyl-1-methyl-5-phenyl-1H-pyrazole-3-carboxylic acid and derivatives

Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors

Synthesis, modification and docking studies of 5-sulfonyl isatin derivatives as SARS-CoV 3C-like protease inhibitors

Isatin compounds as noncovalent SARS coronavirus 3C-like protease inhibitors

Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings

Identification of novel small-molecule inhibitors of severe acute respiratory syndrome-associated coronavirus by chemical genetics

Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors

Synthesis, docking studies, and evaluation of pyrimidines as inhibitors of SARS-CoV 3CL protease

Synthesis and evaluation of pyrazolone compounds as SARS-coronavirus 3C-like protease inhibitors Bioorg

Discovery, Synthesis, And Structure-Based Optimization of a Series of N-(tert-Butyl)-2-(N-arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CL Protease

Discovery of N-(benzo [1,2,3] triazol-1-yl)-N-(benzyl) acetamido) phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding

Synthesis of stilbene derivatives with inhibition of SARS coronavirus replication

Stable benzotriazole esters as mechanism-based inactivators of the severe acute respiratory syndrome 3CL protease

Synthesis, biological evaluation and molecular modeling of a novel series of fused 1,2,3-triazoles as potential anti-coronavirus agents

Discovery of potent anilide inhibitors against the severe acute respiratory syndrome 3CL protease

Inhibition of severe acute respiratory syndrome coronavirus replication by niclosamide

Synthesis and evaluation of benzoquinolinone derivatives as sars-cov 3CL protease inhibitors

Individual and common inhibitors of coronavirus and picornavirus main proteases

A new lead for nonpeptidic active-site-directed inhibitors of the severe acute respiratory syndrome coronavirus main protease discovered by a combination of screening and docking methods

Biflavonoids from Torreya nucifera displaying SARS-CoV 3CLpro inhibition

Sabadinine: a potential nonpeptide anti-severe acute-respiratory-syndrome agent identified using structure-aided design

Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases

Inhibition of SARS-CoV 3C-like protease activity by theaflavin-3,3'-digallate (TF3). Evid.-Based Complementary Altern

Identification of phenanthroindolizines and phenanthroquinolizidines as novel potent anti-coronaviral agents for porcine enteropathogenic coronavirus transmissible gastroenteritis virus and human severe acute respiratory syndrome coronavirus

Emodin inhibits current through SARS-associated coronavirus 3a protein

Procyanidins and butanol extract of Cinnamomi Cortex inhibit SARS-CoV infection

Inhibition of severe acute respiratory syndrome-associated coronavirus (SARSCoV) by calpain inhibitors and β-D-N4-hydroxycytidine

2, 6-Bis-arylmethyloxy-5-hydroxychromones with antiviral activity against both hepatitis C virus (HCV) and SARS-associated coronavirus (SCV)