1
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Li W, Chang X, Zhou H, Yu W, Wang R, Chang J. Investigating the Inhibition of Diindolylmethane Derivatives on SARS-CoV-2 Main Protease. J Mol Recognit 2024:e3101. [PMID: 39221493 DOI: 10.1002/jmr.3101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/08/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
The SARS-CoV-2 main protease (Mpro) is an essential enzyme that promotes viral transcription and replication. Mpro conserved nature in different variants and its nonoverlapping nature with human proteases make it an attractive target for therapeutic intervention against SARS-CoV-2. In this work, the interaction mechanism between Mpro and diindolylmethane derivatives was investigated by molecular docking, enzymatic inhibition assay, UV-vis, fluorescence spectroscopy, and circular dichroism spectroscopy. Results of IC50 values show that 1p (9.87 μM) was the strongest inhibitor for Mpro in this work, which significantly inhibited the activity of Mpro. The binding constant (4.07 × 105 Lmol-1), the quenching constant (5.41 × 105 Lmol-1), and thermodynamic parameters indicated that the quenching mode of 1p was static quenching, and the main driving forces between 1p and Mpro are hydrogen bond and van der Waals force. The influence of molecular structure on the binding is investigated. Chlorine atoms and methoxy groups are favorable for the diindolylmethane derivative inhibitors of Mpro. This work confirms the changes in the microenvironment of Mpro by 1p, and provides clues for the design of potential inhibitors.
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Affiliation(s)
- Wenjin Li
- College of Chemistry, Pingyuan Laboratory, Zhengzhou University, Zhengzhou, China
| | - Xiaoyu Chang
- College of Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Hang Zhou
- College of Chemistry, Pingyuan Laboratory, Zhengzhou University, Zhengzhou, China
| | - Wenquan Yu
- College of Chemistry, Pingyuan Laboratory, Zhengzhou University, Zhengzhou, China
| | - Ruiyong Wang
- College of Chemistry, Pingyuan Laboratory, Zhengzhou University, Zhengzhou, China
| | - Junbiao Chang
- College of Chemistry, Pingyuan Laboratory, Zhengzhou University, Zhengzhou, China
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2
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Al Adem K, Ferreira JC, Villanueva AJ, Fadl S, El-Sadaany F, Masmoudi I, Gidiya Y, Gurudza T, Cardoso THS, Saksena NK, Rabeh WM. 3-chymotrypsin-like protease in SARS-CoV-2. Biosci Rep 2024; 44:BSR20231395. [PMID: 39036877 DOI: 10.1042/bsr20231395] [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: 01/31/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024] Open
Abstract
Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.
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Affiliation(s)
- Kenana Al Adem
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Farah El-Sadaany
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Imen Masmoudi
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Yugmee Gidiya
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Tariro Gurudza
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Masdar City, Abu Dhabi, United Arab Emirates
| | - Nitin K Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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3
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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] [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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4
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Li J, Guan X, Zhang O, Sun K, Wang Y, Bagni D, Head-Gordon T. Leak Proof PDBBind: A Reorganized Dataset of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction. ARXIV 2024:arXiv:2308.09639v2. [PMID: 37645037 PMCID: PMC10462179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Many physics-based and machine-learned scoring functions (SFs) used to predict protein-ligand binding free energies have been trained on the PDBBind dataset. However, it is controversial as to whether new SFs are actually improving since the general, refined, and core datasets of PDBBind are cross-contaminated with proteins and ligands with high similarity, and hence they may not perform comparably well in binding prediction of new protein-ligand complexes. In this work we have carefully prepared a cleaned PDBBind data set of non-covalent binders that are split into training, validation, and test datasets to control for data leakage, defined as proteins and ligands with high sequence and structural similarity. The resulting leak-proof (LP)-PDBBind data is used to retrain four popular SFs: AutoDock Vina, Random Forest (RF)-Score, InteractionGraphNet (IGN), and DeepDTA, to better test their capabilities when applied to new protein-ligand complexes. In particular we have formulated a new independent data set, BDB2020+, by matching high quality binding free energies from BindingDB with co-crystalized ligand-protein complexes from the PDB that have been deposited since 2020. Based on all the benchmark results, the retrained models using LP-PDBBind consistently perform better, with IGN especially being recommended for scoring and ranking applications for new protein-ligand systems.
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Papini C, Ullah I, Ranjan AP, Zhang S, Wu Q, Spasov KA, Zhang C, Mothes W, Crawford JM, Lindenbach BD, Uchil PD, Kumar P, Jorgensen WL, Anderson KS. Proof-of-concept studies with a computationally designed M pro inhibitor as a synergistic combination regimen alternative to Paxlovid. Proc Natl Acad Sci U S A 2024; 121:e2320713121. [PMID: 38621119 PMCID: PMC11046628 DOI: 10.1073/pnas.2320713121] [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: 11/24/2023] [Accepted: 02/27/2024] [Indexed: 04/17/2024] Open
Abstract
As the SARS-CoV-2 virus continues to spread and mutate, it remains important to focus not only on preventing spread through vaccination but also on treating infection with direct-acting antivirals (DAA). The approval of Paxlovid, a SARS-CoV-2 main protease (Mpro) DAA, has been significant for treatment of patients. A limitation of this DAA, however, is that the antiviral component, nirmatrelvir, is rapidly metabolized and requires inclusion of a CYP450 3A4 metabolic inhibitor, ritonavir, to boost levels of the active drug. Serious drug-drug interactions can occur with Paxlovid for patients who are also taking other medications metabolized by CYP4503A4, particularly transplant or otherwise immunocompromised patients who are most at risk for SARS-CoV-2 infection and the development of severe symptoms. Developing an alternative antiviral with improved pharmacological properties is critical for treatment of these patients. By using a computational and structure-guided approach, we were able to optimize a 100 to 250 μM screening hit to a potent nanomolar inhibitor and lead compound, Mpro61. In this study, we further evaluate Mpro61 as a lead compound, starting with examination of its mode of binding to SARS-CoV-2 Mpro. In vitro pharmacological profiling established a lack of off-target effects, particularly CYP450 3A4 inhibition, as well as potential for synergy with the currently approved alternate antiviral, molnupiravir. Development and subsequent testing of a capsule formulation for oral dosing of Mpro61 in B6-K18-hACE2 mice demonstrated favorable pharmacological properties, efficacy, and synergy with molnupiravir, and complete recovery from subsequent challenge by SARS-CoV-2, establishing Mpro61 as a promising potential preclinical candidate.
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Affiliation(s)
- Christina Papini
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520-8066
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT06520-8066
| | - Amalendu P. Ranjan
- Department of Microbiology, Immunology and Genetics Graduate School for Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX76107
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | - Qihao Wu
- Department of Chemistry, Yale University, New Haven, CT06520-8107
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520-8066
| | - Chunhui Zhang
- Department of Chemistry, Yale University, New Haven, CT06520-8107
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | | | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT06520-8066
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT06520-8066
| | | | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520-8066
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT06520-8066
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6
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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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7
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Tian L, Qiang T, Yang X, Gao Y, Zhai X, Kang K, Du C, Lu Q, Gao H, Zhang D, Xie X, Liang C. Development of de-novo coronavirus 3-chymotrypsin-like protease (3CL pro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection. Eur J Med Chem 2024; 264:115979. [PMID: 38048696 DOI: 10.1016/j.ejmech.2023.115979] [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: 09/18/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Although no longer a public health emergency of international concern, COVID-19 remains a persistent and critical health concern. The development of effective antiviral drugs could serve as the ultimate piece of the puzzle to curbing this global crisis. 3-chymotrypsin-like protease (3CLpro), with its substrate specificity mirroring that of the main picornavirus 3C protease and conserved across various coronaviruses, emerges as an ideal candidate for broad-spectrum antiviral drug development. Moreover, it holds the potential as a reliable contingency option to combat emerging SARS-CoV-2 variants. In this light, the approved drugs, promising candidates, and de-novo small molecule therapeutics targeting 3CLpro since the COVID-19 outbreak in 2020 are discussed. Emphasizing the significance of diverse structural characteristics in inhibitors, be they peptidomimetic or nonpeptidic, with a shared mission to minimize the risk of cross-resistance. Moreover, the authors propose an innovative optimization strategy for 3CLpro reversible covalent PROTACs, optimizing pharmacodynamics and pharmacokinetics to better prepare for potential future viral outbreaks.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiuding Yang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yue Gao
- College of Pharmacy, Jinan University, Guangzhou, 511436, PR China
| | - Xiaopei Zhai
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Xi'an, 710032, PR China
| | - Kairui Kang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Cong Du
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qi Lu
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Gao
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Pioneer Biotech Co., Ltd., Xi'an, 710021, PR China
| | - Dezhu Zhang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Chengyuan Liang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
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8
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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9
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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10
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Jiang X, Li J, Viayna A, Luque FJ, Woodson M, Jing L, Gao S, Zhao F, Xie M, Toth K, Tavis J, Tollefson AE, Liu X, Zhan P. Identification of novel 1,2,3-triazole isatin derivatives as potent SARS-CoV-2 3CLpro inhibitors via click-chemistry-based rapid screening. RSC Med Chem 2023; 14:2068-2078. [PMID: 37859715 PMCID: PMC10583828 DOI: 10.1039/d3md00306j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/12/2023] [Indexed: 10/21/2023] Open
Abstract
SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) is considered an attractive target for the development of anti-COVID-19 agents due to its vital function. The N-substituted isatin derivative L-26 is a potential SARS-CoV-2 3CLpro inhibitor, but it has poor cell-based antiviral activity and high cytotoxicity. With L-26 as the lead compound, 58 isatin derivatives were prepared using click-chemistry-based miniaturized synthesis and their 3CLpro inhibitory activities were determined by a fluorescence resonance energy transfer-based enzymatic assay. Compounds D1N8 (IC50 = 0.44 ± 0.12 μM) and D1N52 (IC50 = 0.53 ± 0.21 μM) displayed excellent inhibitory potency against SARS-CoV-2 3CLpro, being equivalent to that of L-26 (IC50 = 0.30 ± 0.14 μM). In addition, the cytotoxicity of D1N8 (CC50 >20 μM) and D1N52 (CC50 >20 μM) decreased significantly compared with L-26 (CC50 <2.6 μM). Further molecular dynamics simulations revealed the potential binding interactions between D1N52 and SARS-CoV-2 3CLpro. These efforts lay a solid foundation for the research of novel anti-SARS-CoV-2 agents targeting 3CLpro.
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Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Antonio Viayna
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB) Av. Prat de la Riba 171 08921 Santa Coloma de Gramenet Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona (UB) Barcelona Spain
| | - F Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB) Av. Prat de la Riba 171 08921 Santa Coloma de Gramenet Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona (UB) Barcelona Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB) Barcelona Spain
| | - Molly Woodson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis Missouri 63104 USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation St. Louis Missouri 63104 USA
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Fabao Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Karoly Toth
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis Missouri 63104 USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation St. Louis Missouri 63104 USA
| | - John Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis Missouri 63104 USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation St. Louis Missouri 63104 USA
| | - Ann E Tollefson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis Missouri 63104 USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation St. Louis Missouri 63104 USA
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University 44 West Culture Road 250012 Jinan Shandong PR China
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11
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Jacobs L, van der Westhuyzen A, Pribut N, Dentmon ZW, Cui D, D’Erasmo MP, Bartsch PW, Liu K, Cox RM, Greenlund SF, Plemper RK, Mitchell D, Marlow J, Andrews MK, Krueger RE, Sticher ZM, Kolykhalov AA, Natchus MG, Zhou B, Pelly SC, Liotta DC. Design and Optimization of Novel Competitive, Non-peptidic, SARS-CoV-2 M pro Inhibitors. ACS Med Chem Lett 2023; 14:1434-1440. [PMID: 37849558 PMCID: PMC10577883 DOI: 10.1021/acsmedchemlett.3c00335] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
The SARS-CoV-2 main protease (Mpro) has been proven to be a highly effective target for therapeutic intervention, yet only one drug currently holds FDA approval status for this target. We were inspired by a series of publications emanating from the Jorgensen and Anderson groups describing the design of potent, non-peptidic, competitive SARS-CoV-2 Mpro inhibitors, and we saw an opportunity to make several design modifications to improve the overall pharmacokinetic profile of these compounds without losing potency. To this end, we created a focused virtual library using reaction-based enumeration tools in the Schrödinger suite. These compounds were docked into the Mpro active site and subsequently prioritized for synthesis based upon relative binding affinity values calculated by FEP+. Fourteen compounds were selected, synthesized, and evaluated both biochemically and in cell culture. Several of the synthesized compounds proved to be potent, competitive Mpro inhibitors with improved metabolic stability profiles.
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Affiliation(s)
- Leon Jacobs
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | - Nicole Pribut
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Zackery W. Dentmon
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Dan Cui
- COVID-19
Emergency Response, Centers for Disease
Control and Prevention, Atlanta, Georgia 30329, United States
| | - Michael P. D’Erasmo
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Perry W. Bartsch
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ken Liu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Robert M. Cox
- Center for
Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sujay F. Greenlund
- Center for
Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, United States
| | - Richard K. Plemper
- Center for
Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303, United States
| | - Deborah Mitchell
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Joshua Marlow
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Meghan K. Andrews
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Rebecca E. Krueger
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Zachary M. Sticher
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Alexander A. Kolykhalov
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Michael G. Natchus
- Emory
Institute for Drug Development, Emory University, Atlanta, Georgia 30322, United States
| | - Bin Zhou
- COVID-19
Emergency Response, Centers for Disease
Control and Prevention, Atlanta, Georgia 30329, United States
| | - Stephen C. Pelly
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Dennis C. Liotta
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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12
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Ghahremanpour MM, Saar A, Tirado-Rives J, Jorgensen WL. Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease. J Chem Inf Model 2023; 63:5309-5318. [PMID: 37561001 DOI: 10.1021/acs.jcim.3c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Accurate, routine calculation of absolute binding free energies (ABFEs) for protein-ligand complexes remains a key goal of computer-aided drug design since it can enable screening and optimization of drug candidates. For development and testing of related methods, it is important to have high-quality datasets. To this end, from our own experimental studies, we have selected a set of 16 inhibitors of the SARS-CoV-2 main protease (Mpro) with structural diversity and well-distributed BFEs covering a 5 kcal/mol range. There is also minimal structural uncertainty since X-ray crystal structures have been deposited for 12 of the compounds. For methods testing, we report ABFE results from 2 μs molecular dynamics (MD) simulations using free energy perturbation (FEP) theory. The correlation of experimental and computed results is encouraging, with a Pearson's r2 of 0.58 and a Kendall τ of 0.24. The results indicate that current FEP-based ABFE calculations can be used for identification of active compounds (hits). While their accuracy for lead optimization is not yet sufficient, this activity remains addressable in separate lead series by relative BFE calculations.
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Affiliation(s)
| | - Anastasia Saar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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13
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Fadlallah S, Julià C, García-Vallvé S, Pujadas G, Serratosa F. Drug Potency Prediction of SARS-CoV-2 Main Protease Inhibitors Based on a Graph Generative Model. Int J Mol Sci 2023; 24:ijms24108779. [PMID: 37240128 DOI: 10.3390/ijms24108779] [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: 04/20/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
The prediction of a ligand potency to inhibit SARS-CoV-2 main protease (M-pro) would be a highly helpful addition to a virtual screening process. The most potent compounds might then be the focus of further efforts to experimentally validate their potency and improve them. A computational method to predict drug potency, which is based on three main steps, is defined: (1) defining the drug and protein in only one 3D structure; (2) applying graph autoencoder techniques with the aim of generating a latent vector; and (3) using a classical fitting model to the latent vector to predict the potency of the drug. Experiments in a database of 160 drug-M-pro pairs, from which the pIC50 is known, show the ability of our method to predict their drug potency with high accuracy. Moreover, the time spent to compute the pIC50 of the whole database is only some seconds, using a current personal computer. Thus, it can be concluded that a computational tool that predicts, with high reliability, the pIC50 in a cheap and fast way is achieved. This tool, which can be used to prioritize which virtual screening hits, will be further examined in vitro.
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Affiliation(s)
- Sarah Fadlallah
- Research Group ASCLEPIUS: Smart Technology for Smart Healthcare, Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Carme Julià
- Research Group ASCLEPIUS: Smart Technology for Smart Healthcare, Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago García-Vallvé
- Research Group in Cheminformatics and Nutrition, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Gerard Pujadas
- Research Group in Cheminformatics and Nutrition, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Francesc Serratosa
- Research Group ASCLEPIUS: Smart Technology for Smart Healthcare, Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain
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14
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Hooper A, Macdonald JD, Reilly B, Maw J, Wirrick AP, Han SH, Lindsey AA, Rico EG, Romigh T, Goins CM, Wang NS, Stauffer S. SARS-CoV-2 3CL-protease inhibitors derived from ML300: investigation of P1 and replacements of the 1,2,3-benzotriazole. RESEARCH SQUARE 2023:rs.3.rs-2880312. [PMID: 37214977 PMCID: PMC10197776 DOI: 10.21203/rs.3.rs-2880312/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Starting from compound 5 (CCF0058981), a structure-based optimization of the P1 subsite was performed against the severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (3CLpro). Inhibitor 5 and the compounds disclosed bind to 3CLpro using a non-covalent mode of action that utilize a His163 H-bond interaction in the S1 subpocket. In an effort to examine more structurally diverse P1 groups a number of azoles and heterocycles were designed. Several azole ring systems and replacements, including C-linked azoles, with similar or enhanced potency relative to 5 were discovered (28, 29, and 30) with demonstrated IC50 values less than 100 nM. In addition, pyridyl and isoquinoline P1 groups were successful as P1 replacements leading to 3-methyl pyridyl 36 (IC50 = 85 nM) and isoquinoline 27 (IC50 = 26 nM). High resolution X-ray crystal structures of these inhibitors were utilized to confirm binding orientation and guide optimization. These findings have implications towards antiviral development and preparedness to combat SARS-like zoonotic coronavirus outbreaks.
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Affiliation(s)
| | | | | | - Joshua Maw
- Cleveland Clinic Lerner Research Institute
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15
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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: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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16
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Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement. Int J Mol Sci 2023; 24:ijms24043596. [PMID: 36835004 PMCID: PMC9968212 DOI: 10.3390/ijms24043596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In this work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of protein-ligand unbinding kinetics, to the refinement of docking results. TTMD evaluates the conservation of the native binding mode throughout a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints. The protocol was successfully applied to retrieve the native-like binding pose among a set of decoy poses of drug-like ligands generated on four different pharmaceutically relevant biological targets, including casein kinase 1δ, casein kinase 2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease.
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17
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Yamari I, Abchir O, Nour H, El Kouali M, Chtita S. Identification of new dihydrophenanthrene derivatives as promising anti-SARS-CoV-2 drugs through in silico investigations. MAIN GROUP CHEMISTRY 2023. [DOI: 10.3233/mgc-220127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To research, evaluate, and invent novel compounds that inhibit SARS-CoV-2 activity, a series of reported 39 substituted 9, 10-dihydrophenanthrene derivatives were subjected to a quantitative structure-activity relationship (QSAR) study. Gaussian 09 and ChemOffice programs were used to calculate the molecular descriptors employed to determine their impact on the studied activity. Then we reduced the number of descriptors by eliminating the redundant information using principal component analysis (PCA). The creation of molecular models was done by using multiple linear regression (MLR) according to the principles established by the Organization for Economic Co-operation and Development (OECD) and the validation by using external and internal validation, Y-randomization tests, and domain of applicability. Moreover, we evaluated the toxicity of developed compounds using ADMET and Molecular docking to determine their optimal position to form a stable complex. As a result, four molecules may be used to develop a novel drug that can inhibit SARS-CoV-2 without causing the side effect.
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Affiliation(s)
- Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Morocco
| | - Ossama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Morocco
| | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Morocco
| | - Mhammed El Kouali
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Morocco
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18
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Naidu SAG, Tripathi YB, Shree P, Clemens RA, Naidu AS. Phytonutrient Inhibitors of SARS-CoV-2/NSP5-Encoded Main Protease (M pro) Autocleavage Enzyme Critical for COVID-19 Pathogenesis. J Diet Suppl 2023; 20:284-311. [PMID: 34821532 DOI: 10.1080/19390211.2021.2006388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The genomic reshuffling, mutagenicity, and high transmission rate of the SARS-CoV-2 pathogen highlights an urgent need for effective antiviral interventions for COVID-19 control. Targeting the highly conserved viral genes and/or gene-encoded viral proteins such as main proteinase (Mpro), RNA-dependent RNA polymerase (RdRp) and helicases are plausible antiviral approaches to prevent replication and propagation of the SARS-CoV-2 infection. Coronaviruses (CoVs) are prone to extensive mutagenesis; however, any genetic alteration to its highly conserved Mpro enzyme is often detrimental to the viral pathogen. Therefore, inhibitors that target the Mpro enzyme could reduce the risk of mutation-mediated drug resistance and provide effective antiviral protection. Several existing antiviral drugs and dietary bioactives are currently repurposed to treat COVID-19. Dietary bioactives from three ayurvedic medicinal herbs, 18 β-glycyrrhetinic acid (ΔG = 8.86 kcal/mol), Solanocapsine (ΔG = 8.59 kcal/mol), and Vasicoline (ΔG = 7.34 kcal/mol), showed high-affinity binding to Mpro enzyme than the native N3 inhibitor (ΔG = 5.41 kcal/mol). Flavonoids strongly inhibited SARS-CoV-2 Mpro with comparable or higher potency than the antiviral drug, remdesivir. Several tannin hydrolysates avidly bound to the receptor-binding domain and catalytic dyad (His41 and Cys145) of SARS-CoV-2 Mpro through H-bonding forces. Quercetin binding to Mpro altered the thermostability of the viral protein through redox-based mechanism and inhibited the viral enzymatic activity. Interaction of quercetin-derivatives with the Mpro seem to be influenced by the 7-OH group and the acetoxylation of sugar moiety on the ligand molecule. Based on pharmacokinetic and ADMET profiles, several phytonutrients could serve as a promising redox nutraceutical for COVID-19 management.
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Affiliation(s)
- Sreus A G Naidu
- N-terminus Research Laboratory, Yorba Linda, California, USA
| | - Yamini B Tripathi
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priya Shree
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, California, USA
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19
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Ivanova YO, Voronina AI, Skvortsov VS. [The prediction of SARS-CoV-2 main protease inhibition with filtering by position of ligand]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:444-458. [PMID: 36573412 DOI: 10.18097/pbmc20226806444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The paper analyzes a set of equations that adequately predict the IC50 value for SARS-CoV-2 main protease inhibitors. The training set was obtained using filtering by criteria independent of prediction of target value. It included 76 compounds, and the test set included nine compounds. We used the values of energy contributions obtained in the calculation of the change of the free energy of complex by MMGBSA method and a number of characteristics of the physical and chemical properties of the inhibitors as independent variables. It is sufficient to use only seven independent variables without loss of prediction quality (Q² = 0.79; R²prediction = 0.89). The maximum error in this case does not exceed 0.92 lg(IC50) units with a full range of observed values from 1.26 to 4.95.
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Affiliation(s)
- Ya O Ivanova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Voronina
- Institute of Biomedical Chemistry, Moscow, Russia
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20
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Pavan M, Menin S, Bassani D, Sturlese M, Moro S. Qualitative Estimation of Protein-Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:5715-5728. [PMID: 36315402 PMCID: PMC9709921 DOI: 10.1021/acs.jcim.2c00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The prediction of ligand efficacy has long been linked to thermodynamic properties such as the equilibrium dissociation constant, which considers both the association and the dissociation rates of a defined protein-ligand complex. In the last 15 years, there has been a paradigm shift, with an increased interest in the determination of kinetic properties such as the drug-target residence time since they better correlate with ligand efficacy compared to other parameters. In this article, we present thermal titration molecular dynamics (TTMD), an alternative computational method that combines a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints for the qualitative estimation of protein-ligand-binding stability. The protocol has been applied to four different pharmaceutically relevant test cases, including protein kinase CK1δ, protein kinase CK2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease, on a variety of ligands with different sizes, structures, and experimentally determined affinity values. In all four cases, TTMD was successfully able to distinguish between high-affinity compounds (low nanomolar range) and low-affinity ones (micromolar), proving to be a useful screening tool for the prioritization of compounds in a drug discovery campaign.
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21
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Yin S, Mei S, Li Z, Xu Z, Wu Y, Chen X, Liu D, Niu MM, Li J. Non-covalent cyclic peptides simultaneously targeting Mpro and NRP1 are highly effective against Omicron BA.2.75. Front Pharmacol 2022; 13:1037993. [PMID: 36408220 PMCID: PMC9666779 DOI: 10.3389/fphar.2022.1037993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022] Open
Abstract
Available vaccine-based immunity may at high risk of being evaded due to substantial mutations in the variant Omicron. The main protease (Mpro) of SARS-CoV-2 and human neuropilin-1 (NRP1), two less mutable proteins, have been reported to be crucial for SARS-CoV-2 replication and entry into host cells, respectively. Their dual blockade may avoid vaccine failure caused by continuous mutations of the SARS-CoV-2 genome and exert synergistic antiviral efficacy. Herein, four cyclic peptides non-covalently targeting both Mpro and NRP1 were identified using virtual screening. Among them, MN-2 showed highly potent affinity to Mpro (Kd = 18.2 ± 1.9 nM) and NRP1 (Kd = 12.3 ± 1.2 nM), which was about 3,478-fold and 74-fold stronger than that of the positive inhibitors Peptide-21 and EG3287. Furthermore, MN-2 exhibited significant inhibitory activity against Mpro and remarkable anti-infective activity against the pseudotyped variant Omicron BA.2.75 without obvious cytotoxicity. These data demonstrated that MN-2, a novel non-covalent cyclic peptide, is a promising agent against Omicron BA.2.75.
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Affiliation(s)
- Shengnan Yin
- Department of Pharmacy, Taizhou Hospital Affiliated to Nanjing University of Chinese Medicine, Taizhou, China
| | - Shuang Mei
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Zhiqin Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Zhen Xu
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yuting Wu
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Xiujuan Chen
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Dongmei Liu
- Department of Pharmacy, Taizhou Hospital Affiliated to Nanjing University of Chinese Medicine, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Jindong Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
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22
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Gao S, Sylvester K, Song L, Claff T, Jing L, Woodson M, Weiße RH, Cheng Y, Schäkel L, Petry M, Gütschow M, Schiedel AC, Sträter N, Kang D, Xu S, Toth K, Tavis J, Tollefson AE, Müller CE, Liu X, Zhan P. Discovery and Crystallographic Studies of Trisubstituted Piperazine Derivatives as Non-Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity and Low Toxicity. J Med Chem 2022; 65:13343-13364. [PMID: 36107752 PMCID: PMC9491405 DOI: 10.1021/acs.jmedchem.2c01146] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Indexed: 01/08/2023]
Abstract
The continuous spread of SARS-CoV-2 calls for more direct-acting antiviral agents to combat the highly infectious variants. The main protease (Mpro) is an promising target for anti-SARS-CoV-2 drug design. Here, we report the discovery of potent non-covalent non-peptide Mpro inhibitors featuring a 1,2,4-trisubstituted piperazine scaffold. We systematically modified the non-covalent hit MCULE-5948770040 by structure-based rational design combined with multi-site binding and privileged structure assembly strategies. The optimized compound GC-14 inhibits Mpro with high potency (IC50 = 0.40 μM) and displays excellent antiviral activity (EC50 = 1.1 μM), being more potent than Remdesivir. Notably, GC-14 exhibits low cytotoxicity (CC50 > 100 μM) and excellent target selectivity for SARS-CoV-2 Mpro (IC50 > 50 μM for cathepsins B, F, K, L, and caspase 3). X-ray co-crystal structures prove that the inhibitors occupy multiple subpockets by critical non-covalent interactions. These studies may provide a basis for developing a more efficient and safer therapy for COVID-19.
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Affiliation(s)
- Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
- Shenzhen Research Institute of Shandong
University, A301 Virtual University Park in South District of Shenzhen,
Guangdong518057, P. R. China
| | - Katharina Sylvester
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Letian Song
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
| | - Tobias Claff
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
| | - Molly Woodson
- Department of Molecular Microbiology and Immunology,
Saint Louis University School of Medicine, St. Louis,
Missouri63103, United States
- Saint Louis University Institute for Drug
and Biotherapeutic Innovation, St. Louis, Missouri63103, United
States
| | - Renato H. Weiße
- Institute of Bioanalytical Chemistry, Center for
Biotechnology and Biomedicine, Leipzig University, Deutscher
Platz 5, Leipzig04103, Germany
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
| | - Laura Schäkel
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Marvin Petry
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Michael Gütschow
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Anke C. Schiedel
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for
Biotechnology and Biomedicine, Leipzig University, Deutscher
Platz 5, Leipzig04103, Germany
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
| | - Karoly Toth
- Department of Molecular Microbiology and Immunology,
Saint Louis University School of Medicine, St. Louis,
Missouri63103, United States
- Saint Louis University Institute for Drug
and Biotherapeutic Innovation, St. Louis, Missouri63103, United
States
| | - John Tavis
- Department of Molecular Microbiology and Immunology,
Saint Louis University School of Medicine, St. Louis,
Missouri63103, United States
- Saint Louis University Institute for Drug
and Biotherapeutic Innovation, St. Louis, Missouri63103, United
States
| | - Ann E. Tollefson
- Department of Molecular Microbiology and Immunology,
Saint Louis University School of Medicine, St. Louis,
Missouri63103, United States
- Saint Louis University Institute for Drug
and Biotherapeutic Innovation, St. Louis, Missouri63103, United
States
| | - Christa E. Müller
- PharmaCenter Bonn & Pharmaceutical Institute,
Department of Pharmaceutical & Medicinal Chemistry, University of
Bonn, An der Immenburg 4, Bonn53113, Germany
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of
Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences,
Shandong University, Ji’nan250012,
China
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23
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X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun 2022; 13:5196. [PMID: 36057636 PMCID: PMC9440467 DOI: 10.1038/s41467-022-32854-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/16/2022] [Indexed: 11/11/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes COVID-19, produces polyproteins 1a and 1ab that contain, respectively, 11 or 16 non-structural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for viral assembly and maturation. Using C-terminally substituted Mpro chimeras, we have determined X-ray crystallographic structures of Mpro in complex with 10 of its 11 viral cleavage sites, bound at full occupancy intermolecularly in trans, within the active site of either the native enzyme and/or a catalytic mutant (C145A). Capture of both acyl-enzyme intermediate and product-like complex forms of a P2(Leu) substrate in the native active site provides direct comparative characterization of these mechanistic steps as well as further informs the basis for enhanced product release of Mpro’s own unique C-terminal P2(Phe) cleavage site to prevent autoinhibition. We characterize the underlying noncovalent interactions governing binding and specificity for this diverse set of substrates, showing remarkable plasticity for subsites beyond the anchoring P1(Gln)-P2(Leu/Val/Phe), representing together a near complete analysis of a multiprocessing viral protease. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for antiviral therapeutic development. The SARS-CoV-2 protease Mpro is essential for viral replication. Here, the authors have determined the structures of Mpro in complex with 10 of the 11 viral cleavage sequences including a covalent acyl-enzyme intermediate, providing mechanistic and structural insights for antiviral development.
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24
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Hu Q, Xiong Y, Zhu G, Zhang Y, Zhang Y, Huang P, Ge G. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3-chymotrypsin-like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β-coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus-caused infectious diseases, including COVID-19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS-CoV-2 3CLpro inhibitors. To better understand the characteristics of SARS-CoV-2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non-peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti-coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS-CoV-2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti-coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang‐Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ya‐Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yi‐Wen Zhang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Ping Huang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Guang‐Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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25
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Daoui O, Elkhattabi S, Chtita S. Rational identification of small molecules derived from 9,10-dihydrophenanthrene as potential inhibitors of 3CL pro enzyme for COVID-19 therapy: a computer-aided drug design approach. Struct Chem 2022; 33:1667-1690. [PMID: 35818588 PMCID: PMC9261181 DOI: 10.1007/s11224-022-02004-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/23/2022] [Indexed: 01/11/2023]
Abstract
Small molecules such as 9,10-dihydrophenanthrene derivatives have remarkable activity toward inhibition of SARS-CoV-2 3CLpro and COVID-19 proliferation, which show a strong correlation between their structures and bioactivity. Therefore, these small compounds could be suitable for clinical pharmaceutical use against COVID-19. The objective of this study was to remodel the structures of 9,10-dihydrophenanthrene derivatives to achieve a powerful biological activity against 3CLpro and favorable pharmacokinetic properties for drug design and discovery. Therefore, by the use of bioinformatics techniques, we developed robust 3D-QSAR models that are capable of describing the structure-activity relationship for 46 molecules based on 9,10-dihydrophenanthrene derivatives using CoMFA/SE (R 2 = 0.97, Q 2 = 0.81, R 2 pred = 0.95, c R 2 p = 0.71) and CoMSIA/SEHDA (R 2 = 0.94, Q 2 = 0.76, R 2 pred = 0.91, c R 2 p = 0.65) techniques. Accordingly, 96 lead compounds were generated based on a template molecule that showed the highest observed activity in vitro (T40, pIC50 = 5.81) and predicted their activities and bioavailability in silico. The rational screening outputs of 3D-QSAR, Molecular docking, ADMET, and MM-GBSA led to the identification of 9 novel modeled molecules as potent noncovalent drugs against SARS-CoV-2-3CLpro. Finally, by molecular dynamics simulations, the stability and structural dynamics of 3CLpro free and complex (PDB code: 6LU7) were discussed in the presence of samples of 9,10-dihydrophenanthrene derivative in an aqueous environment. Overall, the retrosynthesis of the proposed drug compounds in this study and the evaluation of their bioactivity in vitro and in vivo may be interesting for designing and discovering a new drug effective against COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02004-z.
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Affiliation(s)
- Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, BP Box 72, Fez, Morocco
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, BP Box 72, Fez, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, B.P 7955 Casablanca, Morocco
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26
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Proia E, Ragno A, Antonini L, Sabatino M, Mladenovič M, Capobianco R, Ragno R. Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal. J Comput Aided Mol Des 2022; 36:483-505. [PMID: 35716228 PMCID: PMC9206107 DOI: 10.1007/s10822-022-00460-7] [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: 04/12/2022] [Accepted: 05/28/2022] [Indexed: 11/05/2022]
Abstract
The main protease (Mpro) of SARS-Cov-2 is the essential enzyme for maturation of functional proteins implicated in viral replication and transcription. The peculiarity of its specific cleavage site joint with its high degree of conservation among all coronaviruses promote it as an attractive target to develop broad-spectrum inhibitors, with high selectivity and tolerable safety profile. Herein is reported a combination of three-dimensional quantitative structure-activity relationships (3-D QSAR) and comparative molecular binding energy (COMBINE) analysis to build robust and predictive ligand-based and structure-based statistical models, respectively. Models were trained on experimental binding poses of co-crystallized Mpro-inhibitors and validated on available literature data. By means of deep optimization both models' goodness and robustness reached final statistical values of r2/q2 values of 0.97/0.79 and 0.93/0.79 for the 3-D QSAR and COMBINE approaches respectively, and an overall predictiveness values of 0.68 and 0.57 for the SDEPPRED and AAEP metrics after application to a test set of 60 compounds covered by the training set applicability domain. Despite the different nature (ligand-based and structure-based) of the employed methods, their outcome fully converged. Furthermore, joint ligand- and structure-based structure-activity relationships were found in good agreement with nirmatrelvir chemical features properties, a novel oral Mpro-inhibitor that has recently received U.S. FDA emergency use authorization (EUA) for the oral treatment of mild-to-moderate COVID-19 infected patients. The obtained results will guide future rational design and/or virtual screening campaigns with the aim of discovering new potential anti-coronavirus lead candidates, minimizing both time and financial resources. Moreover, as most of calculation were performed through the well-established web portal 3d-qsar.com the results confirm the portal as a useful tool for drug design.
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Affiliation(s)
- Eleonora Proia
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Alessio Ragno
- Department of Computer, Control and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Rome, Italy
| | - Lorenzo Antonini
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Manuela Sabatino
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Milan Mladenovič
- Department of Chemistry, Faculty of Science, Kragujevac Center for Computational Biochemistry, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000, Kragujevac, Serbia
| | - Roberto Capobianco
- Department of Computer, Control and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Rome, Italy
- Sony AI, Rome, Italy
| | - Rino Ragno
- Department of Drug Chemistry and Technology, Rome Center for Molecular Design, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
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27
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Munafò F, Donati E, Brindani N, Ottonello G, Armirotti A, De Vivo M. Quercetin and luteolin are single-digit micromolar inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase. Sci Rep 2022; 12:10571. [PMID: 35732785 PMCID: PMC9216299 DOI: 10.1038/s41598-022-14664-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/10/2022] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. Among the viral proteins, RNA-dependent RNA polymerase (RdRp) is responsible for viral genome replication and has emerged as one of the most promising targets for pharmacological intervention against SARS-CoV-2. To this end, we experimentally tested luteolin and quercetin for their ability to inhibit the RdRp enzyme. These two compounds are ancestors of flavonoid natural compounds known for a variety of basal pharmacological activities. Luteolin and quercetin returned a single-digit IC50 of 4.6 µM and 6.9 µM, respectively. Then, through dynamic docking simulations, we identified possible binding modes of these compounds to a recently published cryo-EM structure of RdRp. Collectively, these data indicate that these two compounds are a valid starting point for further optimization and development of a new class of RdRp inhibitors to treat SARS-CoV-2 and potentially other viral infections.
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Affiliation(s)
- Federico Munafò
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Nicoletta Brindani
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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28
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Dampalla CS, Rathnayake AD, Kankanamalage ACG, Kim Y, Perera KD, Nguyen HN, Miller MJ, Madden TK, Picard HR, Thurman HA, Kashipathy MM, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J Med Chem 2022; 65:7818-7832. [PMID: 35638577 PMCID: PMC9172056 DOI: 10.1021/acs.jmedchem.2c00224] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 12/22/2022]
Abstract
The worldwide impact of the ongoing COVID-19 pandemic on public health has made imperative the discovery and development of direct-acting antivirals aimed at targeting viral and/or host targets. SARS-CoV-2 3C-like protease (3CLpro) has emerged as a validated target for the discovery of SARS-CoV-2 therapeutics because of the pivotal role it plays in viral replication. We describe herein the structure-guided design of highly potent inhibitors of SARS-CoV-2 3CLpro that incorporate in their structure novel spirocyclic design elements aimed at optimizing potency by accessing new chemical space. Inhibitors of both SARS-CoV-2 3CLpro and MERS-CoV 3CLpro that exhibit nM potency and high safety indices have been identified. The mechanism of action of the inhibitors and the structural determinants associated with binding were established using high-resolution cocrystal structures.
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Affiliation(s)
- Chamandi S. Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Athri D. Rathnayake
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Matthew J. Miller
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Trent K. Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hunter R. Picard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hayden A. Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
| | | | - Lijun Liu
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, USA
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29
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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30
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Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Nat Commun 2022; 13:2268. [PMID: 35477935 PMCID: PMC9046211 DOI: 10.1038/s41467-022-29915-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022] Open
Abstract
Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals. Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency.
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31
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Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc Natl Acad Sci U S A 2022; 119:e2117142119. [PMID: 35380892 PMCID: PMC9172370 DOI: 10.1073/pnas.2117142119] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is a deadly rampaging infectious disease with over 480 million cases worldwide. Unfortunately, effective therapies remain very limited. Novel antiviral agents are urgently needed to combat this global healthcare crisis. Here, we elucidate the structural basis for replicase polyprotein cleavage and substrate specificity of SARS-CoV-2 main protease (Mpro). Through analyzing a series of high-resolution structures of SARS-CoV-2 Mpro throughout the proteolytic process, we demonstrate the molecular mechanism of Mpro in proteolytic processing that confers substrate specificity. Substrate selectivity is revealed using structures of the H41A mutant in complex with six individual native cleavage substrates. Our study underscores the mechanistic function of Mpro in the viral life cycle, which provides structural insights to develop effective inhibitors against this essential target of SARS-CoV-2. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key enzyme, which extensively digests CoV replicase polyproteins essential for viral replication and transcription, making it an attractive target for antiviral drug development. However, the molecular mechanism of how Mpro of SARS-CoV-2 digests replicase polyproteins, releasing the nonstructural proteins (nsps), and its substrate specificity remain largely unknown. Here, we determine the high-resolution structures of SARS-CoV-2 Mpro in its resting state, precleavage state, and postcleavage state, constituting a full cycle of substrate cleavage. The structures show the delicate conformational changes that occur during polyprotein processing. Further, we solve the structures of the SARS-CoV-2 Mpro mutant (H41A) in complex with six native cleavage substrates from replicase polyproteins, and demonstrate that SARS-CoV-2 Mpro can recognize sequences as long as 10 residues but only have special selectivity for four subsites. These structural data provide a basis to develop potent new inhibitors against SARS-CoV-2.
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32
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Zhou T, Wu Z, Das S, Eslami H, Müller-Plathe F. How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative Particle Dynamics Simulation Study. J Chem Theory Comput 2022; 18:2597-2615. [PMID: 35286098 PMCID: PMC8938819 DOI: 10.1021/acs.jctc.1c01120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Indexed: 01/03/2023]
Abstract
We have developed dissipative particle dynamics models for pure dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and dimyristoylphosphatidylcholine (DMPC) as well as their binary and ternary mixed membranes, as coronavirus model membranes. The stabilities of pure and mixed membranes, surrounded by aqueous solutions containing up to 70 mol % ethanol (alcoholic disinfectants), have been investigated at room temperature. We found that aqueous solutions containing 5-10 mol % ethanol already have a significant weakening effect on the pure and mixed membranes. The magnitude of the effect depends on the membrane composition and the ethanol concentration. Ethanol permeabilizes the membrane, causing its lateral swelling and thickness shrinking and reducing the orientational order of the hydrocarbon tail of the bilayer. The free energy barrier for the permeation of ethanol in the bilayers is considerably reduced by the ethanol uptake. The rupture-critical ethanol concentrations causing the membrane failure are 20.7, 27.5, and 31.7 mol % in the aqueous phase surrounding pure DMPC, DOPC, and DPPC membranes, respectively. Characterizing the failure of lipid membranes by a machine-learning neural network framework, we found that all mixed binary and/or ternary membranes disrupt when immersed in an aqueous solution containing a rupture-critical ethanol concentration, ranging from 20.7 to 31.7 mol %, depending on the composition of the membrane; the DPPC-rich membranes are more intact, while the DMPC-rich membranes are least intact. Due to the tight packing of long, saturated hydrocarbon tails in DPPC, increasing the DPPC content of the mixed membrane increases its stability against the disinfectant. At high DPPC concentrations, where the DOPC and DMPC molecules are confined between the DPPC lipids, the ordered hydrocarbon tails of DPPC also induce order in the DOPC and DMPC molecules and, hence, stabilize the membrane more. Our simulations on pure and mixed membranes of a diversity of compositions reveal that a maximum ethanol concentration of 32 mol % (55 wt %) in the alcohol-based disinfectants is enough to disintegrate any membrane composed of these three lipids.
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Affiliation(s)
- Tianhang Zhou
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Shubhadip Das
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Hossein Eslami
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
- College of Sciences, Persian Gulf
University, Boushehr 75168, Iran
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt,
Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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33
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Antonopoulou I, Sapountzaki E, Rova U, Christakopoulos P. Inhibition of the main protease of SARS-CoV-2 (M pro) by repurposing/designing drug-like substances and utilizing nature's toolbox of bioactive compounds. Comput Struct Biotechnol J 2022; 20:1306-1344. [PMID: 35308802 PMCID: PMC8920478 DOI: 10.1016/j.csbj.2022.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in a long pandemic, with numerous cases and victims worldwide and enormous consequences on social and economic life. Although vaccinations have proceeded and provide a valuable shield against the virus, the approved drugs are limited and it is crucial that further ways to combat infection are developed, that can also act against potential mutations. The main protease (Mpro) of the virus is an appealing target for the development of inhibitors, due to its importance in the viral life cycle and its high conservation among different coronaviruses. Several compounds have shown inhibitory potential against Mpro, both in silico and in vitro, with few of them also having entered clinical trials. These candidates include: known drugs that have been repurposed, molecules specifically designed based on the natural substrate of the protease or on structural moieties that have shown high binding affinity to the protease active site, as well as naturally derived compounds, either isolated or in plant extracts. The aim of this work is to collectively present the results of research regarding Mpro inhibitors to date, focusing on the function of the compounds founded by in silico simulations and further explored by in vitro and in vivo assays. Creating an extended portfolio of promising compounds that may block viral replication by inhibiting Mpro and by understanding involved structure-activity relationships, could provide a basis for the development of effective solutions against SARS-CoV-2 and future related outbreaks.
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Affiliation(s)
| | | | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
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Fornasier E, Macchia ML, Giachin G, Sosic A, Pavan M, Sturlese M, Salata C, Moro S, Gatto B, Bellanda M, Battistutta R. A new inactive conformation of SARS-CoV-2 main protease. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:363-378. [PMID: 35234150 PMCID: PMC8900819 DOI: 10.1107/s2059798322000948] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/27/2022] [Indexed: 11/26/2022]
Abstract
The SARS‐CoV‐2 main protease (Mpro) has a pivotal role in mediating viral genome replication and transcription of the coronavirus, making it a promising target for drugs against the COVID‐19 pandemic. Here, a crystal structure is presented in which Mpro adopts an inactive state that has never been observed before, called new‐inactive. It is shown that the oxyanion loop, which is involved in substrate recognition and enzymatic activity, adopts a new catalytically incompetent conformation and that many of the key interactions of the active conformation of the enzyme around the active site are lost. Solvation/desolvation energetic contributions play an important role in the transition from the inactive to the active state, with Phe140 moving from an exposed to a buried environment and Asn142 moving from a buried environment to an exposed environment. In new‐inactive Mpro a new cavity is present near the S2′ subsite, and the N‐terminal and C‐terminal tails, as well as the dimeric interface, are perturbed, with partial destabilization of the dimeric assembly. This novel conformation is relevant both for comprehension of the mechanism of action of Mpro within the catalytic cycle and for the successful structure‐based drug design of antiviral drugs.
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35
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Kneller D, Li H, Phillips G, Weiss K, Zhang Q, Arnould M, Jonsson C, Surendranathan S, Parvathareddy J, Blakeley M, Coates L, Louis J, Bonnesen P, Kovalevsky A. Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease: room-temperature X-ray and neutron crystallography, binding thermodynamics, and antiviral activity. RESEARCH SQUARE 2022:rs.3.rs-1318037. [PMID: 35169792 PMCID: PMC8845512 DOI: 10.21203/rs.3.rs-1318037/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The COVID-19 pandemic continues to disrupt everyday life, with constantly emerging SARS-CoV-2 variants threatening to render current vaccines ineffective. Small-molecule antivirals can provide an important therapeutic treatment option that is subject to challenges caused by the virus variants. The viral main protease (M pro ) is critical for the virus replication and thus is considered an attractive drug target for specific protease inhibitors. We performed the design and characterization of three reversible covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2, whose structures were derived from those of hepatitis C protease inhibitors boceprevir and narlaprevir. A joint X-ray/neutron structure of the M pro /BBH-1 complex demonstrated that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion, similar to that proposed for the M pro -catalyzed peptide bond hydrolysis. Protonation states of the ionizable residues in the M pro active site adapt to the inhibitor, which appears to be an intrinsic property of M pro . Structural comparisons of the hybrid inhibitors with PF-07321332 revealed unconventional interactions of PF-07321332 with M pro which may explain its more favorable enthalpy of binding and consequently higher potency. BBH-1, BBH-2 and NBH-2 demonstrated comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.
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36
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Zhang JW, Xiong Y, Wang F, Zhang FM, Yang X, Lin GQ, Tian P, Ge G, Gao D. Discovery of 9,10-dihydrophenanthrene derivatives as SARS-CoV-2 3CL pro inhibitors for treating COVID-19. Eur J Med Chem 2022; 228:114030. [PMID: 34883292 PMCID: PMC8634693 DOI: 10.1016/j.ejmech.2021.114030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/23/2022]
Abstract
The epidemic coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread worldwide and efficacious therapeutics are urgently needed. 3-Chymotrypsin-like cysteine protease (3CLpro) is an indispensable protein in viral replication and represents an attractive drug target for fighting COVID-19. Herein, we report the discovery of 9,10-dihydrophenanthrene derivatives as non-peptidomimetic and non-covalent inhibitors of the SARS-CoV-2 3CLpro. The structure-activity relationships of 9,10-dihydrophenanthrenes as SARS-CoV-2 3CLpro inhibitors have carefully been investigated and discussed in this study. Among all tested 9,10-dihydrophenanthrene derivatives, C1 and C2 display the most potent SARS-CoV-2 3CLpro inhibition activity, with IC50 values of 1.55 ± 0.21 μM and 1.81 ± 0.17 μM, respectively. Further enzyme kinetics assays show that these two compounds dose-dependently inhibit SARS-CoV-2 3CLprovia a mixed-inhibition manner. Molecular docking simulations reveal the binding modes of C1 in the dimer interface and substrate-binding pocket of the target. In addition, C1 shows outstanding metabolic stability in the gastrointestinal tract, human plasma, and human liver microsome, suggesting that this agent has the potential to be developed as an orally administrated SARS-CoV-2 3CLpro inhibitor.
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Affiliation(s)
- Jian-Wei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Feng Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Fu-Mao Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiaodi Yang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guo-Qiang Lin
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ping Tian
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Dingding Gao
- Shanghai Frontiers Science Center of TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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37
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Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J Chem Inf Model 2022; 62:116-128. [PMID: 34793155 PMCID: PMC8610012 DOI: 10.1021/acs.jcim.1c00851] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.
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Affiliation(s)
- Austin Clyde
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Heng Ma
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Yadu Babuji
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ben Blaiszik
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Alexander Brace
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Thomas Brettin
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Kyle Chard
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ryan Chard
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ian Foster
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Darin Hauner
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Vlimos Kertesz
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hyungro Lee
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Zhuozhao Li
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andre Merzky
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Li Tan
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Mikhail Titov
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Anda Trifan
- University of Illinois at
Urbana-Champaign, Champaign, Illinois 61820, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Matteo Turilli
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hubertus Van Dam
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Srinivas C. Chennubhotla
- Department of Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Shantenu Jha
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andrey Kovalevsky
- Second Target Station, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Arvind Ramanathan
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Martha S. Head
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Rick Stevens
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
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38
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Martí S, Arafet K, Lodola A, Mulholland AJ, Świderek K, Moliner V. Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M pro Explored by QM/MM Simulations. ACS Catal 2022; 12:698-708. [PMID: 35036042 PMCID: PMC8751016 DOI: 10.1021/acscatal.1c04661] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/17/2021] [Indexed: 12/18/2022]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 main protease (Mpro), a cysteine hydrolase essential for the life cycle of the virus. The free energy landscape for the mechanism of the inhibition process is explored by QM/MM umbrella sampling and free energy perturbation simulations at the M06-2X/MM level of theory for two proposed peptidyl covalent inhibitors that share the same recognition motif but feature distinct cysteine-targeting warheads. Regardless of the intrinsic reactivity of the modeled inhibitors, namely a Michael acceptor and a hydroxymethyl ketone activated carbonyl, our results confirm that the inhibitory process takes place by means of a two-step mechanism, in which the formation of an ion pair C145/H41 dyad precedes the protein-inhibitor covalent bond formation. The nature of this second step is strongly dependent on the functional groups in the warhead: while the nucleophilic attack of the C145 sulfur atom on the Cα of the double bond of the Michael acceptor takes place concertedly with the proton transfer from H41 to Cβ, in the compound with an activated carbonyl, the sulfur attacks the carbonyl carbon concomitant with a proton transfer from H41 to the carbonyl oxygen via the hydroxyl group. An analysis of the free energy profiles, structures along the reaction path, and interactions between the inhibitors and the different pockets of the active site on the protein shows a measurable effect of the warhead on the kinetics and thermodynamics of the process. These results and QM/MM methods can be used as a guide to select warheads to design efficient irreversible and reversible inhibitors of SARS-CoV-2 Mpro.
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Affiliation(s)
- Sergio Martí
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Kemel Arafet
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, I-43124 Parma, Italy
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Katarzyna Świderek
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
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39
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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
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Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
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40
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Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson CB, Head MS, Coates L, Louis JM, Bonnesen PV, Kovalevsky A. Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J Med Chem 2021; 64:17366-17383. [PMID: 34705466 PMCID: PMC8565456 DOI: 10.1021/acs.jmedchem.1c01475] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Hui Li
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Audrey Labbé
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Mark A. Arnould
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Austin Clyde
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Computer Science, University of Chicago, Chicago, IL 60615, USA
| | - Heng Ma
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60615
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Martha S. Head
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Peter V. Bonnesen
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
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41
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Yan F, Gao F. An overview of potential inhibitors targeting non-structural proteins 3 (PL pro and Mac1) and 5 (3CL pro/M pro) of SARS-CoV-2. Comput Struct Biotechnol J 2021; 19:4868-4883. [PMID: 34457214 PMCID: PMC8382591 DOI: 10.1016/j.csbj.2021.08.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/02/2021] [Accepted: 08/21/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to develop effective treatments for coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid spread of SARS-CoV-2 has resulted in a global pandemic that has not only affected the daily lives of individuals but also had a significant impact on the global economy and public health. Although extensive research has been conducted to identify inhibitors targeting SARS-CoV-2, there are still no effective treatment strategies to combat COVID-19. SARS-CoV-2 comprises two important proteolytic enzymes, namely, the papain-like proteinase, located within non-structural protein 3 (nsp3), and nsp5, both of which cleave large replicase polypeptides into multiple fragments that are required for viral replication. Moreover, a domain within nsp3, known as the macrodomain (Mac1), also plays an important role in viral replication. Inhibition of their functions should be able to significantly interfere with the replication cycle of the virus, and therefore these key proteins may serve as potential therapeutic targets. The functions of the above viral targets and their corresponding inhibitors have been summarized in the current review. This review provides comprehensive updates of nsp3 and nsp5 inhibitor development and would help advance the discovery of novel anti-viral therapeutics against SARS-CoV-2.
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Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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