1
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Zabiegala A, Kim Y, Chang KO. Host susceptibilities and entry processes of SARS-CoV-2 Omicron variants using pseudotyped viruses carrying spike protein. BMC Vet Res 2025; 21:377. [PMID: 40426227 PMCID: PMC12108000 DOI: 10.1186/s12917-025-04822-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025] Open
Abstract
The zoonotic potential has been well studied for SARS-CoV-2 and its earlier variants, but the information for Omicron variants and SARS-CoV is lacking. In this study, we generated lentivirus-based pseudoviruses carrying spike protein (S) of SARS-CoV-2, parental and Omicron variants including BA.1.1, BA.4/5, XBB.1 and JN.1 to assess the entry into cells expressing human or animal ACE2 including dogs, cats and white-tailed deer. Using these pseudoviruses, along with pseudoviruses carrying S of MERS-CoV and SARS-CoV, we assessed the protease processing of these various S through western blotting, entry/inhibition assays, and fusion assays. The results showed that overall, pseudotyped viruses carrying each S of SARS-CoV-2 Omicron strains efficiently entered cells expressing human or animal ACE2 comparably (BA.1.1 and JN.1) or better (BA.4/5 and XBB.1) than those with parental strain. In addition, the entries of pseudotyped viruses carrying S of SARS-CoV were also efficient the cells expressing human or animal ACE2. The presence of TMPRSS2 significantly increased the entry of all tested pseudoviruses including those with S of MERS-CoV, SARS-CoV and SARS-CoV-2, with BA.1.1, JN1, and XBB.1 Omicron having the largest fold increase. When cathepsin inhibitors were examined to assess their inhibitory effects on entry of parental and Omicron variants, they were significantly less effective in the entry of Omicron variants compared to parent strain, suggesting Omicron strains do not depend on the endosomal route compared to parental strain.
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Affiliation(s)
- Alexandria Zabiegala
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS, 66506, USA.
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2
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Luong QXT, Hoang PT, Ho PT, Ayun RQ, Lee TK, Lee S. Potential Broad-Spectrum Antiviral Agents: A Key Arsenal Against Newly Emerging and Reemerging Respiratory RNA Viruses. Int J Mol Sci 2025; 26:1481. [PMID: 40003946 PMCID: PMC11855616 DOI: 10.3390/ijms26041481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 12/05/2024] [Accepted: 12/16/2024] [Indexed: 02/27/2025] Open
Abstract
Respiratory viral infections present significant global health challenges, causing substantial morbidity and mortality, particularly among highly susceptible components of the population. The emergence of pandemics and epidemics, such as those caused by influenza viruses and coronaviruses, emphasizes the urgent need for effective antiviral therapeutics. In this review, we explore the potential of broad-spectrum antiviral agents targeting respiratory RNA viruses, including influenza viruses, coronaviruses, respiratory syncytial virus, human metapneumovirus, human parainfluenza viruses, and rhinoviruses. Various broad-spectrum direct-acting and host-targeting antivirals are discussed, including monoclonal antibodies targeting conserved regions of viral surface proteins, molecules interfering with host cell receptors or viral replication machinery, viral protease inhibitors, siRNA therapies, ribonuclease, and 3D8 scFv. Advancements in host-targeting approaches to reduce resistance and RNA-based therapeutics offer significant potential for combating respiratory viral threats. Despite challenges, broad-spectrum antiviral agents represent a crucial strategy, particularly when specific viral pathogens are unidentified or rapid intervention is essential, such as during pandemics or outbreaks.
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Affiliation(s)
- Quynh Xuan Thi Luong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (Q.X.T.L.); (P.T.H.); (P.T.H.); (R.Q.A.)
| | - Phuong Thi Hoang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (Q.X.T.L.); (P.T.H.); (P.T.H.); (R.Q.A.)
| | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (Q.X.T.L.); (P.T.H.); (P.T.H.); (R.Q.A.)
| | - Ramadhani Qurrota Ayun
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (Q.X.T.L.); (P.T.H.); (P.T.H.); (R.Q.A.)
| | - Taek Kyun Lee
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (Q.X.T.L.); (P.T.H.); (P.T.H.); (R.Q.A.)
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3
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Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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4
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Dampalla CS, Kim Y, Zabiegala A, Howard DJ, Nguyen HN, Madden TK, Thurman HA, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J Med Chem 2024; 67:11937-11956. [PMID: 38953866 DOI: 10.1021/acs.jmedchem.4c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Zoonotic coronaviruses are known to produce severe infections in humans and have been the cause of significant morbidity and mortality worldwide. SARS-CoV-2 was the largest and latest contributor of fatal cases, even though MERS-CoV has the highest case-fatality ratio among zoonotic coronaviruses. These infections pose a high risk to public health worldwide warranting efforts for the expeditious discovery of antivirals. Hence, we hereby describe a novel series of inhibitors of coronavirus 3CLpro embodying an N-substituted 2-pyrrolidone scaffold envisaged to exploit favorable interactions with the S3-S4 subsites and connected to an invariant Leu-Gln P2-P1 recognition element. Several inhibitors showed nanomolar antiviral activity in enzyme and cell-based assays, with no significant cytotoxicity. High-resolution crystal structures of inhibitors bound to the 3CLpro were determined to probe and identify the molecular determinants associated with binding, to inform the structure-guided optimization of the inhibitors, and to confirm the mechanism of action of the inhibitors.
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Affiliation(s)
- Chamandi S Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Alexandria Zabiegala
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Dennis J Howard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Trent K Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Hayden A Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
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5
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Kim Y, Pool E, Kim E, Dampalla CS, Nguyen HN, Johnson DK, Lovell S, Groutas WC, Chang KO. Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus. Microbiol Spectr 2024; 12:e0337223. [PMID: 38466127 PMCID: PMC10986521 DOI: 10.1128/spectrum.03372-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/18/2024] [Indexed: 03/12/2024] Open
Abstract
Foot-and-mouth disease (FMD) is one of the most devastating diseases of livestock which can cause significant economic losses, especially when introduced to FMD-free countries. FMD virus (FMDV) belongs to the family Picornaviridae and is antigenically heterogeneous with seven established serotypes. The prevailing preventive and control strategies are limited to restriction of animal movement and elimination of infected or exposed animals, which can be potentially combined with vaccination. However, FMD vaccination has limitations including delayed protection and lack of cross-protection against different serotypes. Recently, antiviral drug use for FMD outbreaks has increasingly been recognized as a potential tool to augment the existing early response strategies, but limited research has been reported on potential antiviral compounds for FMDV. FMDV 3C protease (3Cpro) cleaves the viral-encoded polyprotein into mature and functional proteins during viral replication. The essential role of viral 3Cpro in viral replication and the high conservation of 3Cpro among different FMDV serotypes make it an excellent target for antiviral drug development. We have previously reported multiple series of inhibitors against picornavirus 3Cpro or 3C-like proteases (3CLpros) encoded by coronaviruses or caliciviruses. In this study, we conducted structure-activity relationship studies for our in-house focused compound library containing 3Cpro or 3CLpro inhibitors against FMDV 3Cpro using enzyme and cell-based assays. Herein, we report the discovery of aldehyde and α-ketoamide inhibitors of FMDV 3Cpro with high potency. These data inform future preclinical studies that are related to the advancement of these compounds further along the drug development pathway.IMPORTANCEFood-and-mouth disease (FMD) virus (FMDV) causes devastating disease in cloven-hoofed animals with a significant economic impact. Emergency response to FMD outbreaks to limit FMD spread is critical, and the use of antivirals may overcome the limitations of existing control measures by providing immediate protection for susceptible animals. FMDV encodes 3C protease (3Cpro), which is essential for virus replication and an attractive target for antiviral drug discovery. Here, we report a structure-activity relationship study on multiple series of protease inhibitors and identified potent inhibitors of FMDV 3Cpro. Our results suggest that these compounds have the potential for further development as FMD antivirals.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Emma Pool
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Eunji Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - David K. Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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6
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Li P, Kim Y, Dampalla CS, Nhat Nguyen H, Meyerholz DK, Johnson DK, Lovell S, Groutas WC, Perlman S, Chang KO. Potent 3CLpro inhibitors effective against SARS-CoV-2 and MERS-CoV in animal models by therapeutic treatment. mBio 2024; 15:e0287823. [PMID: 38126789 PMCID: PMC10865860 DOI: 10.1128/mbio.02878-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic betacoronaviruses that continue to have a significant impact on public health. Timely development and introduction of vaccines and antivirals against SARS-CoV-2 into the clinic have substantially mitigated the burden of COVID-19. However, a limited or lacking therapeutic arsenal for SARS-CoV-2 and MERS-CoV infections, respectively, calls for an expanded and diversified portfolio of antivirals against these coronavirus infections. In this report, we examined the efficacy of two potent 3CLpro inhibitors, 5d and 11d, in fatal animal models of SARS-CoV-2 and MERS-CoV to demonstrate their broad-spectrum activity against both viral infections. These compounds significantly increased the survival of mice in both models when treatment started 1 day post infection compared to no treatment which led to 100% fatality. Especially, the treatment with compound 11d resulted in 80% and 90% survival in SARS-CoV-2 and MERS-CoV-infected mice, respectively. Amelioration of lung viral load and histopathological changes in treated mice correlated well with improved survival in both infection models. Furthermore, compound 11d exhibited significant antiviral activities in K18-hACE2 mice infected with SARS-CoV-2 Omicron subvariant XBB.1.16. The results suggest that these are promising candidates for further development as broad-spectrum direct-acting antivirals against highly virulent human coronaviruses.IMPORTANCEHuman coronaviruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) continue to have a significant impact on public health. A limited or lacking therapeutic arsenal for SARS-CoV-2 and MERS-CoV infections calls for an expanded and diversified portfolio of antivirals against these coronavirus infections. We have previously reported a series of small-molecule 3C-like protease (3CLpro) inhibitors against human coronaviruses. In this report, we demonstrated the in vivo efficacy of 3CLpro inhibitors for their broad-spectrum activity against both SARS-CoV-2 and MERS-CoV infections using the fatal animal models. The results suggest that these are promising candidates for further development as broad-spectrum direct-acting antivirals against highly virulent human coronaviruses.
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Affiliation(s)
- Pengfei Li
- Department of Microbiology and Immunology, The University of Iowa, lowa, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | | | - David K. Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, lowa, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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7
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Flury P, Breidenbach J, Krüger N, Voget R, Schäkel L, Si Y, Krasniqi V, Calistri S, Olfert M, Sylvester K, Rocha C, Ditzinger R, Rasch A, Pöhlmann S, Kronenberger T, Poso A, Rox K, Laufer SA, Müller CE, Gütschow M, Pillaiyar T. Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity. ACS Pharmacol Transl Sci 2024; 7:493-514. [PMID: 38357286 PMCID: PMC10863444 DOI: 10.1021/acsptsci.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024]
Abstract
Cathepsins (Cats) are proteases that mediate the successful entry of SARS-CoV-2 into host cells. We designed and synthesized a tailored series of 21 peptidomimetics and evaluated their inhibitory activity against human cathepsins L, B, and S. Structural diversity was realized by combinations of different C-terminal warhead functions and N-terminal capping groups, while a central Leu-Phe fragment was maintained. Several compounds were identified as promising cathepsin L and S inhibitors with Ki values in the low nanomolar to subnanomolar range, for example, the peptide aldehydes 9a and 9b (9a, 2.67 nM, CatL; 0.455 nM, CatS; 9b, 1.76 nM, CatL; 0.512 nM, CatS). The compounds' inhibitory activity against the main protease of SARS-CoV-2 (Mpro) was additionally investigated. Based on the results at CatL, CatS, and Mpro, selected inhibitors were subjected to investigations of their antiviral activity in cell-based assays. In particular, the peptide nitrile 11e exhibited promising antiviral activity with an EC50 value of 38.4 nM in Calu-3 cells without showing cytotoxicity. High metabolic stability and favorable pharmacokinetic properties make 11e suitable for further preclinical development.
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Affiliation(s)
- Philipp Flury
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Julian Breidenbach
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Rabea Voget
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Laura Schäkel
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Yaoyao Si
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Vesa Krasniqi
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Sara Calistri
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Matthias Olfert
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Katharina Sylvester
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Raphael Ditzinger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Alexander Rasch
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Thales Kronenberger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
- Excellence
Cluster “Controlling Microbes to Fight Infections” (CMFI), Tübingen 72076, Germany
| | - Antti Poso
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), Braunschweig 38124, Germany
- Partner
Site Hannover-Braunschweig, German Center
for Infection Research (DZIF), Braunschweig 38124, Germany
| | - Stefan A. Laufer
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Michael Gütschow
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Thanigaimalai Pillaiyar
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
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8
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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Duan Y, Wang H, Yuan Z, Yang H. Structural biology of SARS-CoV-2 M pro and drug discovery. Curr Opin Struct Biol 2023; 82:102667. [PMID: 37544112 DOI: 10.1016/j.sbi.2023.102667] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/10/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Since its outbreak in late 2019, the COVID-19 pandemic has drawn enormous attention worldwide as a consequence of being the most disastrous infectious disease in the past century. As one of the most immediately druggable targets of SARS-CoV-2, the main protease (Mpro) has been studied thoroughly. In this review, we provide a comprehensive summary of recent advances in structural studies of Mpro, which provide new knowledge about Mpro in terms of its biological function, structural characteristics, substrate specificity, and autocleavage process. We examine the remarkable strides made in targeting Mpro for drug discovery during the pandemic. We summarize insights into the current understanding of the structural features of Mpro and the discovery of existing Mpro-targeting drugs, illuminating pathways for the future development of anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Institute of Infectious Disease and Biosecurity, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China.
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Dampalla CS, Miller MJ, Kim Y, Zabiegala A, Nguyen HN, Madden TK, Thurman HA, Machen AJ, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur J Med Chem 2023; 254:115376. [PMID: 37080108 PMCID: PMC10105399 DOI: 10.1016/j.ejmech.2023.115376] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/08/2023] [Accepted: 04/11/2023] [Indexed: 04/22/2023]
Abstract
The high morbidity and mortality associated with SARS-CoV-2 infection, the etiological agent of COVID-19, has had a major impact on global public health. Significant progress has been made in the development of an array of vaccines and biologics, however, the emergence of SARS-CoV-2 variants and breakthrough infections are an ongoing major concern. Furthermore, there is an existing paucity of small-molecule host and virus-directed therapeutics and prophylactics that can be used to counter the spread of SARS-CoV-2, and any emerging and re-emerging coronaviruses. We describe herein our efforts to address this urgent need by focusing on the structure-guided design of potent broad-spectrum inhibitors of SARS-CoV-2 3C-like protease (3CLpro or Main protease), an enzyme essential for viral replication. The inhibitors exploit the directional effects associated with the presence of a gem-dimethyl group that allow the inhibitors to optimally interact with the S4 subsite of the enzyme. Several compounds were found to potently inhibit SARS-CoV-2 and MERS-CoV 3CL proteases in biochemical and cell-based assays. Specifically, the EC50 values of aldehyde 1c and its corresponding bisulfite adduct 1d against SARS-CoV-2 were found to be 12 and 10 nM, respectively, and their CC50 values were >50 μM. Furthermore, deuteration of these compounds yielded compounds 2c/2d with EC50 values 11 and 12 nM, respectively. Replacement of the aldehyde warhead with a nitrile (CN) or an α-ketoamide warhead or its corresponding bisulfite adduct yielded compounds 1g, 1eand1f with EC50 values 60, 50 and 70 nM, respectively. High-resolution cocrystal structures have identified the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and, furthermore, have illuminated the mechanism of action of the inhibitors. Overall, the high Safety Index (SI) (SI=CC50/EC50) displayed by these compounds suggests that they are well-suited to conducting further preclinical studies.
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Affiliation(s)
- Chamandi S Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Matthew J Miller
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Alexandria Zabiegala
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Trent K Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Hayden A Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA
| | - Alexandra J Machen
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | | | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - William C Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, 67260, USA.
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