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Biernacki K, Ciupak O, Daśko M, Rachon J, Flis D, Budka J, Inkielewicz-Stępniak I, Czaja A, Rak J, Demkowicz S. Development of potent and effective SARS-CoV-2 main protease inhibitors based on maleimide analogs for the potential treatment of COVID-19. J Enzyme Inhib Med Chem 2024; 39:2290910. [PMID: 38093611 PMCID: PMC10732195 DOI: 10.1080/14756366.2023.2290910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
In the present work, we report a new series of potent SARS-CoV-2 Main Protease (Mpro) inhibitors based on maleimide derivatives. The inhibitory activities were tested in an enzymatic assay using recombinant Mpro (3CL Protease from coronavirus SARS-CoV-2). Within the set of new Mpro inhibitors, 6e demonstrated the highest activity in the enzymatic assay with an IC50 value of 8.52 ± 0.44 µM. The IC50 value for Nirmatrelvir (PF-07321332, used as a reference) was 0.84 ± 0.37 µM. The cytotoxic properties were determined in the MTT assay using MRC-5 and HEK-293 cell lines. In the course of the investigation, we found that the newly obtained maleimide derivatives are not substantially cytotoxic (IC50 values for most compounds were above 200 µM).
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Affiliation(s)
- Karol Biernacki
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Olga Ciupak
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Mateusz Daśko
- Department of Inorganic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Janusz Rachon
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Damian Flis
- Department of Pharmaceutical Pathophysiology, Medical University of Gdansk, Gdańsk, Poland
| | - Justyna Budka
- Department of Pharmaceutical Pathophysiology, Medical University of Gdansk, Gdańsk, Poland
| | | | - Anna Czaja
- Department of Physical Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Janusz Rak
- Department of Physical Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Sebastian Demkowicz
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
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Nemčovičová I, Lopušná K, Štibrániová I, Benedetti F, Berti F, Felluga F, Drioli S, Vidali M, Katrlík J, Pažitná L, Holazová A, Blahutová J, Lenhartová S, Sláviková M, Klempa B, Ondrejovič M, Chmelová D, Legerská B, Miertuš S, Klacsová M, Uhríková D, Kerti L, Frecer V. Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. J Enzyme Inhib Med Chem 2024; 39:2301772. [PMID: 38221792 PMCID: PMC10791089 DOI: 10.1080/14756366.2024.2301772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024] Open
Abstract
The viral genome of the SARS-CoV-2 coronavirus, the aetiologic agent of COVID-19, encodes structural, non-structural, and accessory proteins. Most of these components undergo rapid genetic variations, though to a lesser extent the essential viral proteases. Consequently, the protease and/or deubiquitinase activities of the cysteine proteases Mpro and PLpro became attractive targets for the design of antiviral agents. Here, we develop and evaluate new bis(benzylidene)cyclohexanones (BBC) and identify potential antiviral compounds. Three compounds were found to be effective in reducing the SARS-CoV-2 load, with EC50 values in the low micromolar concentration range. However, these compounds also exhibited inhibitory activity IC50 against PLpro at approximately 10-fold higher micromolar concentrations. Although originally developed as PLpro inhibitors, the comparison between IC50 and EC50 of BBC indicates that the mechanism of their in vitro antiviral activity is probably not directly related to inhibition of viral cysteine proteases. In conclusion, our study has identified new potential noncytotoxic antiviral compounds suitable for in vivo testing and further improvement.
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Affiliation(s)
- Ivana Nemčovičová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Lopušná
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Iveta Štibrániová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Fabio Benedetti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Fulvia Felluga
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Sara Drioli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Mattia Vidali
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Holazová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Blahutová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Simona Lenhartová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Ondrejovič
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Daniela Chmelová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Barbora Legerská
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Stanislav Miertuš
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Lukáš Kerti
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Vladimír Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
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van Vliet VJE, De Silva A, Mark BL, Kikkert M. Viral deubiquitinating proteases and the promising strategies of their inhibition. Virus Res 2024; 344:199368. [PMID: 38588924 PMCID: PMC11025011 DOI: 10.1016/j.virusres.2024.199368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Several viruses are now known to code for deubiquitinating proteases in their genomes. Ubiquitination is an essential post-translational modification of cellular substrates involved in many processes in the cell, including in innate immune signalling. This post-translational modification is regulated by the ubiquitin conjugation machinery, as well as various host deubiquitinating enzymes. The conjugation of ubiquitin chains to several innate immune related factors is often needed to induce downstream signalling, shaping the antiviral response. Viral deubiquitinating proteins, besides often having a primary function in the viral replication cycle by cleaving the viral polyprotein, are also able to cleave ubiquitin chains from such host substrates, in that way exerting a function in innate immune evasion. The presence of viral deubiquitinating enzymes has been firmly established for numerous animal-infecting viruses, such as some well-researched and clinically important nidoviruses, and their presence has now been confirmed in several plant viruses as well. Viral proteases in general have long been highlighted as promising drug targets, with a current focus on small molecule inhibitors. In this review, we will discuss the range of viral deubiquitinating proteases known to date, summarise the various avenues explored to inhibit such proteases and discuss novel strategies and models intended to inhibit and study these specific viral enzymes.
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Affiliation(s)
- Vera J E van Vliet
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands; The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands.
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El Bakri Y, Ahmad B, Saravanan K, Ahmad I, Bakhite EA, Younis O, Al-Waleedy SAH, Ibrahim OF, Nafady A, Mague JT, Mohamed SK. Insight into crystal structures and identification of potential styrylthieno[2,3- b]pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach. J Biomol Struct Dyn 2024; 42:4325-4343. [PMID: 37318002 DOI: 10.1080/07391102.2023.2220799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Basharat Ahmad
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Etify A Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Osama Younis
- Chemistry Department, Faculty of Science, the New Valley University, El-Kharja, Egypt
| | | | - Omaima F Ibrahim
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Ayman Nafady
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, England
- Chemistry Department, Faculty of Science, Minia University, El-Minia, Egypt
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5
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Khatua K, Alugubelli YR, Yang KS, Vulupala VR, Blankenship LR, Coleman D, Atla S, Chaki SP, Geng ZZ, Ma XR, Xiao J, Chen PH, Cho CCD, Sharma S, Vatansever EC, Ma Y, Yu G, Neuman BW, Xu S, Liu WR. Azapeptides with unique covalent warheads as SARS-CoV-2 main protease inhibitors. Antiviral Res 2024; 225:105874. [PMID: 38555023 DOI: 10.1016/j.antiviral.2024.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
The main protease (MPro) of SARS-CoV-2, the causative agent of COVID-19, is a pivotal nonstructural protein critical for viral replication and pathogenesis. Its protease function relies on three active site pockets for substrate recognition and a catalytic cysteine for enzymatic activity. To develop potential SARS-CoV-2 antivirals, we successfully synthesized a diverse range of azapeptide inhibitors with various covalent warheads to target MPro's catalytic cysteine. Our characterization identified potent MPro inhibitors, including MPI89 that features an aza-2,2-dichloroacetyl warhead with a remarkable EC50 value of 10 nM against SARS-CoV-2 infection in ACE2+ A549 cells and a selective index of 875. MPI89 is also remarkably selective and shows no potency against SARS-CoV-2 papain-like protease and several human proteases. Crystallography analyses demonstrated that these inhibitors covalently engaged the catalytic cysteine and used the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 stands as one of the most potent MPro inhibitors, suggesting the potential for further exploration of azapeptides and the aza-2,2-dichloroacetyl warhead for developing effective therapeutics against COVID-19.
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Affiliation(s)
- Kaustav Khatua
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Yugendar R Alugubelli
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Kai S Yang
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Veerabhadra R Vulupala
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Lauren R Blankenship
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Demonta Coleman
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Sandeep Atla
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Sankar P Chaki
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhi Zachary Geng
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Xinyu R Ma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Jing Xiao
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Peng-Hsun Chen
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Chia-Chuan D Cho
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Shivangi Sharma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Erol C Vatansever
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Yuying Ma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Ge Yu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Benjamin W Neuman
- Department of Biology, Texas A&M University, College Station, TX 77843, USA; Texas A&M Global Health Research Complex, Texas A&M University, College Station, TX 77843, USA; Health Science Centre, Department of Molecular Pathogenesis and Immunology, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA; Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA.
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA; Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
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Rasul HO, Thomas NV, Ghafour DD, Aziz BK, Salgado M G, Mendoza-Huizar LH, Candia LG. Searching possible SARS-CoV-2 main protease inhibitors in constituents from herbal medicines using in silico studies. J Biomol Struct Dyn 2024; 42:4234-4248. [PMID: 37349945 DOI: 10.1080/07391102.2023.2220040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and efficient strategy in the battle against new epidemics because the process of developing new drugs is time-consuming. This research aimed to identify which herbal remedies had the highest affinity for the receptor and assess a variety of them for potential targets to suppress the SARS-CoV-2 Mpro. The use of AutoDock Vina for structure-based virtual screening was done first due to the importance of protein interactions in the development of drugs. Molecular docking was used in the comparative study to assess 89 different chemicals from medicinal herbs. To anticipate their effectiveness against the primary protease of SARS-CoV-2, more analysis was done on the ADMET profile, drug-likeness, and Lipinski's rule of five. The next step involved three replicas of 100 ns-long molecular dynamics simulations on the potential candidates, which were preceded by calculations of the binding free energy of MM-GBSA. The outcomes showed that Achyrodimer A, Cinchonain Ib, Symphonone F, and Lupeol acetate all performed well and had the highest 6LU7 binding affinities. Using RMSD, RMSF, and protein-ligand interactions, the stability of the protein-ligand complex was assessed. The studies indicate that bioactive substances obtained from herbal medicines may function as a COVID-19 therapeutic agent, necessitating additional wet lab research to confirm their therapeutic potential, efficacy, and pharmacological capacity against the condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hezha O Rasul
- Department of Pharmaceutical Chemistry, College of Science, Charmo University, Chamchamal, Sulaimani, Iraq
| | - Noel Vinay Thomas
- Department of BioMedical Science, College of Science, Komar University of Science and Technology, Sulaimani, Iraq
| | - Dlzar D Ghafour
- Department of Medical Laboratory Science, College of Science, Komar University of Science and Technology, Sulaimani, Iraq
- Department of Chemistry, College of Science, University of Sulaimani, Sulaimani, Iraq
| | - Bakhtyar K Aziz
- Department of Nanoscience and Applied Chemistry, College of Science, Charmo University, Chamchamal, Sulaimani, Iraq
| | | | - L H Mendoza-Huizar
- Academic Area of Chemistry, Mineral de la Reforma, Autonomous University of Hidalgo State, Hidalgo, México
| | - Lorena Gerli Candia
- Departamento de Química Ambiental, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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Pereira F, Bedda L, Tammam MA, Alabdullah AK, Arafa R, El-Demerdash A. Investigating the antiviral therapeutic potentialities of marine polycyclic lamellarin pyrrole alkaloids as promising inhibitors for SARS-CoV-2 and Zika main proteases (Mpro). J Biomol Struct Dyn 2024; 42:3983-4001. [PMID: 37232419 DOI: 10.1080/07391102.2023.2217513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
The new coronavirus variant (SARS-CoV-2) and Zika virus are two world-wide health pandemics. Along history, natural products-based drugs have always crucially recognized as a main source of valuable medications. Considering the SARS-CoV-2 and Zika main proteases (Mpro) as the re-production key element of the viral cycle and its main target, herein we report an intensive computer-aided virtual screening for a focused list of 39 marine lamellarins pyrrole alkaloids, against SARS-CoV-2 and Zika main proteases (Mpro) using a set of combined modern computational methodologies including molecular docking (MDock), molecule dynamic simulations (MDS) and structure-activity relationships (SARs) as well. Indeed, the molecular docking studies had revealed four promising marine alkaloids including [lamellarin H (14)/K (17)] and [lamellarin S (26)/Z (39)], according to their notable ligand-protein energy scores and relevant binding affinities with the SARS-CoV-2 and Zika (Mpro) pocket residues, respectively. Consequentially, these four chemical hits were further examined thermodynamically though investigating their MD simulations at 100 ns, where they showed prominent stability within the accommodated (Mpro) pockets. Moreover, in-deep SARs studies suggested the crucial roles of the rigid fused polycyclic ring system, particularly aromatic A- and F- rings, position of the phenolic -OH and δ-lactone functionalities as essential structural and pharmacophoric features. Finally, these four promising lamellarins alkaloids were investigated for their in-silico ADME using the SWISS ADME platform, where they displayed appropriated drug-likeness properties. Such motivating outcomes are greatly recommending further in vitro/vivo examinations regarding those lamellarins pyrrole alkaloids (LPAs).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Florbela Pereira
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Loay Bedda
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed A Tammam
- Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | | | - Reem Arafa
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Amr El-Demerdash
- Division of Organic Chemistry, Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
- Department of Biochemistry and Metabolism, the John Innes Centre, Norwich Research Park, Norwich, UK
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8
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Zhang J, Zhao L, Bai Y, Li S, Zhang M, Wei B, Wang X, Xue Y, Li L, Ma G, Tang Y, Wang X. An ascidian Polycarpa aurata-derived pan-inhibitor against coronaviruses targeting M pro. Bioorg Med Chem Lett 2024; 103:129706. [PMID: 38508325 DOI: 10.1016/j.bmcl.2024.129706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
Coronaviruses (CoVs) are responsible for a wide range of illnesses in both animals and human. The main protease (Mpro) of CoVs is an attractive drug target, owing its critical and highly conserved role in viral replication. Here, we developed and refined an enzymatic technique to identify putative Mpro inhibitors from 189 marine chemicals and 46 terrestrial natural products. The IC50 values of Polycarpine (1a), a marine natural substance we studied and synthesized, are 30.0 ± 2.5 nM for SARS-CoV-2 Mpro and 0.12 ± 0.05 μM for PEDV Mpro. Our research further demonstrated that pretreatment with Polycarpine (1a) inhibited the betacoronavirus SARS-CoV-2 and alphacoronavirus PEDV multiplication in Vero-E6 cells. As a result, Polycarpine (1a), a pan-inhibitor of Mpro, will function as an effective and promising antiviral option to combat CoVs infection and as a foundation for further therapeutic research.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Lili Zhao
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
| | - Yuxin Bai
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China
| | - Shanshan Li
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Meifang Zhang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Bo Wei
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xianyang Wang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yan Xue
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao 266000, China
| | - Li Li
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China
| | - Guiliang Ma
- Department of General Surgery, Qingdao Municipal Hospital, No. 5, Donghaizhong Road, Qingdao 266071, China.
| | - Yu Tang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
| | - Xin Wang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
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9
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Gu Z, Yan Y, Liu H, Wu D, Yao H, Lin K, Li X. Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network. J Chem Inf Model 2024; 64:3047-3058. [PMID: 38520328 DOI: 10.1021/acs.jcim.3c01900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Covalent drugs exhibit advantages in that noncovalent drugs cannot match, and covalent docking is an important method for screening covalent lead compounds. However, it is difficult for covalent docking to screen covalent compounds on a large scale because covalent docking requires determination of the covalent reaction type of the compound. Here, we propose to use deep learning of a lateral interactions spiking neural network to construct a covalent lead compound screening model to quickly screen covalent lead compounds. We used the 3CL protease (3CL Pro) of SARS-CoV-2 as the screen target and constructed two classification models based on LISNN to predict the covalent binding and inhibitory activity of compounds. The two classification models were trained on the covalent complex data set targeting cysteine (Cys) and the compound inhibitory activity data set targeting 3CL Pro, respected, with good prediction accuracy (ACC > 0.9). We then screened the screening compound library with 6 covalent binding screening models and 12 inhibitory activity screening models. We tested the inhibitory activity of the 32 compounds, and the best compound inhibited SARS-CoV-2 3CL Pro with an IC50 value of 369.5 nM. Further assay implied that dithiothreitol can affect the inhibitory activity of the compound to 3CL Pro, indicating that the compound may covalently bind 3CL Pro. The selectivity test showed that the compound had good target selectivity to 3CL Pro over cathepsin L. These correlation assays can prove the rationality of the covalent lead compound screening model. Finally, covalent docking was performed to demonstrate the binding conformation of the compound with 3CL Pro. The source code can be obtained from the GitHub repository (https://github.com/guzh970630/Screen_Covalent_Compound_by_LISNN).
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Affiliation(s)
- Zhihao Gu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong Yan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hanwen Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Di Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hequan Yao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kejiang Lin
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xuanyi Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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10
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Huang YJ, Cheng TL, Wang YT, Chen CS, Leu YL, Chang CS, Ho CH, Chao SW, Li CT, Chuang CH. Exploring the therapeutic potential of DV-B-120 as an inhibitor of dengue virus infection. J Virol 2024; 98:e0125823. [PMID: 38546211 PMCID: PMC11019862 DOI: 10.1128/jvi.01258-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Dengue fever, an infectious disease prevalent in subtropical and tropical regions, currently lacks effective small-molecule drugs as treatment. In this study, we used a fluorescence peptide cleavage assay to screen seven compounds to assess their inhibition of the dengue virus (DENV) NS2B-NS3 protease. DV-B-120 demonstrated superior inhibition of NS2B-NS3 protease activity and lower toxicity compared to ARDP0006. The selectivity index of DV-B-120 was higher than that of ARDP0006. In vivo assessments of the antiviral efficacy of DV-B-120 against DENV replication demonstrated delayed mortality of suckling mice treated with the compound, with 60-80% protection against life-threatening effects, compared to the outcomes of DENV-infected mice treated with saline. The lower clinical scores of DENV-infected mice treated with DV-B-120 indicated a reduction in acute-progressive illness symptoms, underscoring the potential therapeutic impact of DV-B-120. Investigations of DV-B-120's ability to restore the antiviral type I IFN response in the brain tissue of DENV-infected ICR suckling mice demonstrated its capacity to stimulate IFN and antiviral IFN-stimulated gene expression. DV-B-120 not only significantly delayed DENV-2-induced mortality and illness symptoms but also reduced viral numbers in the brain, ultimately restoring the innate antiviral response. These findings strongly suggest that DV-B-120 holds promise as a therapeutic agent against DENV infection and highlight its potential contribution in addressing the current lack of effective treatments for this infectious disease.IMPORTANCEThe prevalence of dengue virus (DENV) infection in tropical and subtropical regions is escalating due to factors like climate change and mosquito vector expansion. With over 300 million annual infections and potentially fatal outcomes, the urgent need for effective treatments is evident. While the approved Dengvaxia vaccine has variable efficacy, there are currently no antiviral drugs for DENV. This study explores seven compounds targeting the NS2B-NS3 protease, a crucial protein in DENV replication. These compounds exhibit inhibitory effects on DENV-2 NS2B-NS3, holding promise for disrupting viral replication and preventing severe manifestations. However, further research, including animal testing, is imperative to assess therapeutic efficacy and potential toxicity. Developing safe and potent treatments for DENV infection is critical in addressing the rising global health threat posed by this virus.
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Affiliation(s)
- Yi-Jung Huang
- Department of Biochemistry, School of Post Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tian-Lu Cheng
- Department of Biochemistry, School of Post Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Tseng Wang
- Department of Biochemistry, School of Post Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Shu Chen
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Ling Leu
- Department of Pharmacy, Chia Nan University of Pharmacy & Science, Tainan, Taiwan
| | - Chih-Shiang Chang
- School of Pharmacy, China Medical University, Taichung, Taiwan
- Drug Development Center, China Medical University, Taichung, Taiwan
| | - Cheng-Han Ho
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shi-Wei Chao
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Tse Li
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hung Chuang
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
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11
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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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12
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Shellenberger BM, Basile ON, Cassel J, Olsen MR, Salvino JM, Montaner LJ, Tietjen I, Henry GE. Synthesis, SARS-CoV-2 main protease inhibition, molecular docking and in silico ADME studies of furanochromene-quinoline hydrazone derivatives. Bioorg Med Chem Lett 2024; 102:129679. [PMID: 38423371 DOI: 10.1016/j.bmcl.2024.129679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Seven furanochromene-quinoline derivatives containing a hydrazone linker were synthesized by condensing a furanochromene hydrazide with quinoline 2-, 3-, 4-, 5-, 6-, and 8-carbaldehydes, including 8-hydroxyquinoline-2-carbaldehye. Structure-activity correlations were investigated to determine the influence of the location of the hydrazone linker on the quinoline unit on SARS-CoV-2 Mpro enzyme inhibition. The 3-, 5-, 6- and 8-substituted derivatives showed moderate inhibition of SARS-CoV-2 Mpro with IC50 values ranging from 16 to 44 μM. Additionally, all of the derivatives showed strong interaction with the SARS-CoV-2 Mpro substrate binding pocket, with docking energy scores ranging from -8.0 to -8.5 kcal/mol. These values are comparable to that of N3 peptide (-8.1 kcal/mol) and more favorable than GC-373 (-7.6 kcal/mol) and ML-188 (-7.5 kcal/mol), all of which are known SARS-CoV-2 Mpro inhibitors. Furthermore, in silico absorption, distribution, metabolism, and excretion (ADME) profiles indicate that the derivatives have good drug-likeness properties. Overall, this study highlights the potential of the furanochromene-quinoline hydrazone scaffold as a SARS-CoV-2 Mpro inhibitor.
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Affiliation(s)
- Blake M Shellenberger
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Olivia N Basile
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Joel Cassel
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Morgan R Olsen
- Department of Chemistry, Bucknell University, One Dent Drive, Lewisburg, PA 17837, USA
| | | | | | - Ian Tietjen
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Geneive E Henry
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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13
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Visser N, Herreman LCM, Vandooren J, Pereira RVS, Opdenakker G, Spelbrink REJ, Wilbrink MH, Bremer E, Gosens R, Nawijn MC, van der Ende-Metselaar HH, Smit JM, Laus MC, Laman JD. Novel high-yield potato protease inhibitor panels block a wide array of proteases involved in viral infection and crucial tissue damage. J Mol Med (Berl) 2024; 102:521-536. [PMID: 38381158 DOI: 10.1007/s00109-024-02423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Viruses critically rely on various proteases to ensure host cell entry and replication. In response to viral infection, the host will induce acute tissue inflammation pulled by granulocytes. Upon hyperactivation, neutrophil granulocytes may cause undue tissue damage through proteolytic degradation of the extracellular matrix. Here, we assess the potential of protease inhibitors (PI) derived from potatoes in inhibiting viral infection and reducing tissue damage. The original full spectrum of potato PI was developed into five fractions by means of chromatography and hydrolysis. Individual fractions showed varying inhibitory efficacy towards a panel of proteases including trypsin, chymotrypsin, ACE2, elastase, and cathepsins B and L. The fractions did not interfere with SARS-CoV-2 infection of Vero E6 cells in vitro. Importantly, two of the fractions fully inhibited elastin-degrading activity of complete primary human neutrophil degranulate. These data warrant further development of potato PI fractions for biomedical purposes, including tissue damage crucial to SARS-CoV-2 pathogenesis. KEY MESSAGES: Protease inhibitor fractions from potato differentially inhibit a series of human proteases involved in viral replication and in tissue damage by overshoot inflammation. Protease inhibition of cell surface receptors such as ACE2 does not prevent virus infection of Vero cells in vitro. Protease inhibitors derived from potato can fully inhibit elastin-degrading primary human neutrophil proteases. Protease inhibitor fractions can be produced at high scale (hundreds of thousands of kilograms, i.e., tons) allowing economically feasible application in lower and higher income countries.
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Affiliation(s)
- Nienke Visser
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | | | - Jennifer Vandooren
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | - Rafaela Vaz Sousa Pereira
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | | | | | - Edwin Bremer
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute, University of Groningen, 9713 GZ, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Heidi H van der Ende-Metselaar
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Marc C Laus
- Avebe Innovation Center Groningen, 9747 AW, Groningen, The Netherlands
| | - Jon D Laman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands.
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14
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Pu LY, Li Z, Huang F, Li L, Ma Y, Ma M, Hu S, Wu Z. Efficient synthesis of novel colchicine-magnolol hybrids and evaluation of their inhibitory activity on key proteases of 2019-nCoV replication and acute lung injury. Nat Prod Res 2024; 38:1238-1247. [PMID: 36302171 DOI: 10.1080/14786419.2022.2138870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/03/2022] [Accepted: 10/14/2022] [Indexed: 10/31/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV), is a life-threatening infectious condition. Acute lung injury is a common complication in patients with COVID-19. 3-chymotrypsin-like protease (3CLpro) of 2019-nCoV and neutrophil elastase are critical targets of COVID-19 and acute lung injury, respectively. Colchicine and magnolol are reported to exert inhibitory effects on inflammatory response, the severe comorbidity in both COVID-19 and acute lung injury. We thus designed and synthesized a series of novel colchicine-magnolol hybrids based on a two-step synthetic sequence. It was found that these novel hybrids provided unexpected inhibition on 3CLpro and neutrophil elastase, a bioactivity that colchicine and magnolol did not possess. These findings not only provide perquisites for further in vitro and in vivo investigation to confirm the therapeutic potentiality of novel colchicine-magnolol hybrids, but also suggest that the concurrent inhibition of 3CLpro and neutrophil elastase may enable novel colchicine-magnolol hybrids as effective multi-target drug compounds.
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Affiliation(s)
| | - Zhiyue Li
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Feijuan Huang
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Limin Li
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Yucui Ma
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Min Ma
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Shengquan Hu
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Zhengzhi Wu
- Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Geriatrics, Shenzhen, China
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15
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Li H, Sun M, Lei F, Liu J, Chen X, Li Y, Wang Y, Lu J, Yu D, Gao Y, Xu J, Chen H, Li M, Yi Z, He X, Chen L. Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection. Antiviral Res 2024; 224:105841. [PMID: 38408645 DOI: 10.1016/j.antiviral.2024.105841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been ongoing for more than three years and urgently needs to be addressed. Traditional Chinese medicine (TCM) prescriptions have played an important role in the clinical treatment of patients with COVID-19 in China. However, it is difficult to uncover the potential molecular mechanisms of the active ingredients in these TCM prescriptions. In this paper, we developed a new approach by integrating the experimental assay, virtual screening, and the experimental verification, exploring the rapid discovery of active ingredients from TCM prescriptions. To achieve this goal, 4 TCM prescriptions in clinical use for different indications were selected to find the antiviral active ingredients in TCMs. The 3-chymotrypsin-like protease (3CLpro), an important target for fighting COVID-19, was utilized to determine the inhibitory activity of the TCM prescriptions and single herb. It was found that 10 single herbs had better inhibitory activity than other herbs by using a fluorescence resonance energy transfer (FRET) - based enzymatic assay of SARS-CoV-2 3CLpro. The ingredients contained in 10 herbs were thus virtually screened and the predicted active ingredients were experimentally validated. Thus, such a research strategy firstly removed many single herbs with no inhibitory activity against SARS-CoV-2 3CLpro at the very beginning by FRET-based assay, making our subsequent virtual screening more effective. Finally, 4 active components were found to have stronger inhibitory effects on SARS-CoV-2 3CLpro, and their inhibitory mechanism was subsequently investigated. Among of them, methyl rosmarinate as an allosteric inhibitor of SARS-CoV-2 3CLpro was confirmed and its ability to inhibit viral replication was demonstrated by the SARS-CoV-2 replicon system. To validate the binding mode via docking, the mutation experiment, circular dichroism (CD), enzymatic inhibition and surface plasmon resonance (SPR) assay were performed, demonstrating that methyl rosmarinate bound to the allosteric site of SARS-CoV-2 3CLpro. In conclusion, this paper provides the new ideas for the rapid discovery of active ingredients in TCM prescriptions based on a specific target, and methyl rosmarinate has the potential to be developed as an antiviral therapeutic candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Meng Sun
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fuzhi Lei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China; Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; DP Technology, Beijing, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yueqiu Gao
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Man Li
- Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Longhua Hospital Shanghai University of Traditional Chinese Medicine, 725 South Wanping Road, Shanghai, 200032, China.
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16
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Abdel-Sattar E, Kutkat O, El-Shiekh RA, El-Ashrey MK, El Kerdawy AM. In Silico and In Vitro Screening of Some Pregnane Glycosides Isolated from Certain Caralluma Species as SARS-COV-2 Main Protease Inhibitors. Chem Biodivers 2024; 21:e202301786. [PMID: 38466126 DOI: 10.1002/cbdv.202301786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
SARS-CoV-2 caused pandemic represented a major risk for the worldwide human health, animal health and economy, forcing extraordinary efforts to discover drugs for its prevention and cure. Considering the extensive interest in the pregnane glycosides because of their diverse structures and excellent biological activities, we investigated them as antiviral agents against SARS-COV-2. We selected 21 pregnane glycosides previously isolated from the genus Caralluma from Asclepiadaceae family to be tested through virtual screening molecular docking simulations for their potential inhibition of SARS-CoV-2 Mpro. Almost all target compounds showed a more or equally negative docking energy score relative to the co-crystallized inhibitor X77 (S=-12.53 kcal/mol) with docking score range of (-12.55 to -19.76 kcal/mol) and so with a potent predicted binding affinity to the target enzyme. The activity of the most promising candidates was validated by in vitro testing. Arabincoside C showed the highest activity (IC50=35.42 μg/ml) and the highest selectivity index (SI=9.9) followed by Russelioside B (IC50=50.80 μg/ml), and Arabincoside B (IC50=53.31 μg/ml).
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Affiliation(s)
- Essam Abdel-Sattar
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Omnia Kutkat
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, 12622, Giza, Egypt
- Department of microbiology, Faculty of pharmacy, Ahram Canadian University, 6 th of October, Giza, 12566, Egypt
| | - Riham A El-Shiekh
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Mohamed K El-Ashrey
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University (KSIU), 46612, South Sinai, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, LN6 7DL, Lincoln, Lincolnshire, United Kingdom
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17
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Purohit P, Barik D, Agasti S, Panda M, Meher BR. Evaluation of the inhibitory potency of anti-dengue phytocompounds against DENV-2 NS2B-NS3 protease: virtual screening, ADMET profiling and molecular dynamics simulation investigations. J Biomol Struct Dyn 2024; 42:2990-3009. [PMID: 37194462 DOI: 10.1080/07391102.2023.2212798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023]
Abstract
Dengue fever has been a worldwide concern, with 50-100 million new infections each year mainly due to five different serotypes of the Dengue virus (DENV). Designing a perfect anti-dengue agent that can inhibit all the serotypes by distinguishing antigenic differences is quite difficult. Previous anti-dengue researches have included chemical compounds screening against DENV enzymes. The ongoing analysis is meant for investigation of the plant-based compounds as antagonistic to DENV-2 focusing on the specific NS2B-NS3Pro target, a trypsin like serine protease that cuts the DENV polyprotein into separate proteins crucial for viral reproduction. Initially, a virtual library of more than 130 phytocompounds was prepared from previously published reports of plants with anti-dengue properties, which were then virtually screened and shortlisted against the WT, H51N and S135A mutant of DENV-2 NS2B-NS3Pro. The three top-most compounds were viewed as Gallocatechin (GAL), Flavokawain-C (FLV), and Isorhamnetin (ISO) showing docking scores of -5.8, -5.7, -5.7 kcal/mol for WT, -7.5, -6.8, -7.6 kcal/mol for the H51N, and -6.9, -6.5, -6.1 kcal/mol for the S135A mutant protease, respectively. 100 ns long MD simulations and MM-GBSA based free energy calculations were performed on the NS2B-NS3Pro complexes to witness the relative binding affinity of the compounds and favourable molecular interactions network. A comprehensive analysis of the study reveals some promising outcomes with ISO as the topmost compound with favourable pharmacokinetic properties for the WT and mutants (H51N and S135A) as well, suggesting as a novel anti-NS2B-NS3Pro agent with better adapting characters in both the mutants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Debashis Barik
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Sidhartha Agasti
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
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18
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Roney M, Singh G, Huq AKMM, Forid MS, Ishak WMBW, Rullah K, Aluwi MFFM, Tajuddin SN. Identification of Pyrazole Derivatives of Usnic Acid as Novel Inhibitor of SARS-CoV-2 Main Protease Through Virtual Screening Approaches. Mol Biotechnol 2024; 66:696-706. [PMID: 36752937 PMCID: PMC9907211 DOI: 10.1007/s12033-023-00667-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
The infection produced by the SARS-CoV-2 virus remains a significant health crisis worldwide. The lack of specific medications for COVID-19 necessitates a concerted effort to find the much-desired therapies for this condition. The main protease (Mpro) of SARS-CoV-2 is a promising target, vital for virus replication and transcription. In this study, fifty pyrazole derivatives were tested for their pharmacokinetics and drugability, resulting in eight hit compounds. Subsequent molecular docking simulations on SARS-CoV-2 main protease afforded two lead compounds with strong affinity at the active site. Additionally, the molecular dynamics (MD) simulations of lead compounds (17 and 39), along with binding free energy calculations, were accomplished to validate the stability of the docked complexes and the binding poses achieved in docking experiments. Based on these findings, compound 17 and 39, with their favorable projected pharmacokinetics and pharmacological characteristics, are the proposed potential antiviral candidates which require further investigation to be used as anti-SARS-CoV-2 medication.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi, Uttar Pradesh, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
- School of Medicine, Department of Pharmacy, University of Asia Pacific, 74/A, Green Road, Dhaka, 1205, Bangladesh.
| | - Md Shaekh Forid
- Faculty of Chemical and Processing Engineering Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Wan Maznah Binti Wan Ishak
- Faculty of Chemical and Processing Engineering Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Kamal Rullah
- Kulliyyah of Pharmacy, International Islamic University Malaysia (IIUM), Jalan Sultan Ahmad Shah, 25200, Kuantan, Pahang, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Saiful Nizam Tajuddin
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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19
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Carney DW, Leffler AE, Bell JA, Chandrasinghe AS, Cheng C, Chang E, Dornford A, Dougan DR, Frye LL, Grimes ME, Knehans T, Knight JL, Komandla M, Lane W, Li H, Newman SR, Phimister K, Saikatendu KS, Silverstein H, Vafaei S. Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity. Bioorg Med Chem 2024; 103:117577. [PMID: 38518735 DOI: 10.1016/j.bmc.2023.117577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 03/24/2024]
Abstract
Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.
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Affiliation(s)
- Daniel W Carney
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States.
| | - Abba E Leffler
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States.
| | - Jeffrey A Bell
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States
| | | | - Cecilia Cheng
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Adam Dornford
- Schrödinger, Inc, 1 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Douglas R Dougan
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Leah L Frye
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Mary E Grimes
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Tim Knehans
- Schrödinger GmbH, Glücksteinallee 25, 68163 Mannheim, Germany
| | | | - Mallareddy Komandla
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Weston Lane
- Treeline Biosciences, 500 Arsenal Way, Watertown, MA 02472, United States
| | - Hubert Li
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Sophia R Newman
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Katalin Phimister
- Schrödinger Technologies Limited, 1st Floor West, Davidson House, Forbury Square, Reading RG1 3EU, United Kingdom
| | - Kumar S Saikatendu
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Hercules Silverstein
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
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20
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Wang F, Liu D, Gao D, Yuan J, Zhao J, Yuan S, Cen Y, Lin GQ, Zhao J, Tian P. Discovery of natural catechol derivatives as covalent SARS-CoV-2 3CL pro inhibitors. Int J Biol Macromol 2024; 264:130377. [PMID: 38395279 DOI: 10.1016/j.ijbiomac.2024.130377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a threat to public health, and extensive research by scientists worldwide has also prompted the development of antiviral therapies. The 3C-like protease (3CLpro) is critical for SARS-CoV-2 replication and acts as an effective target for drug development. To date, numerous of natural products have been reported to exhibit inhibitory effects on 3CLpro, which encourages us to identify other novel inhibitors and elucidate their mechanism of action. In this study, we first screened an in-house compound library of 101 natural products using FRET assay, and found that oleuropein showed good inhibitory activity against SARS CoV-2 3CLpro with an IC50 value of 4.18 μM. Further studies revealed that the catechol core is essential for activity and can covalently bind to SARS-CoV-2 3CLpro. Among other 45 catechol derivatives, wedelolactone, capsazepine and brazilin showed better SARS-CoV-2 3CLpro inhibitory activities with IC50 values of 1.35 μM, 1.95 μM and 1.18 μM, respectively. These catechol derivatives were verified to be irreversible covalent inhibitors by time-dependent experiments, enzymatic kinetic studies, dilution and dialysis assays. It also exhibited good selectivity towards different cysteine proteases (SARS-CoV-2 PLpro, cathepsin B and cathepsin L). Subsequently, the binding affinity between brazilin and SARS-CoV-2 3CLpro was determined by SPR assay with KD value of 0.80 μM. Molecular dynamic (MD) simulations study showed the binding mode of brazilin in the target protein. In particular, brazilin displayed good anti-SARS-CoV-2 activity in A549-hACE2-TMPRSS2 cells with EC50 values of 7.85 ± 0.20 μM and 5.24 ± 0.21 μM for full time and post-infection treatments, respectively. This study provides a promising lead compound for the development of novel anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Feng Wang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jinwei Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Shuai Yuan
- Health and Quarantine Laboratory, Guangzhou Customs District Technology Center, Guangzhou 510700, China
| | - Yixin Cen
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong 510320, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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21
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Stewart J, Shawon J, Ali MA, Williams B, Shahinuzzaman ADA, Rupa SA, Al-Adhami T, Jia R, Bourque C, Faddis R, Stone K, Sufian MA, Islam R, McShan AC, Rahman KM, Halim MA. Antiviral peptides inhibiting the main protease of SARS-CoV-2 investigated by computational screening and in vitro protease assay. J Pept Sci 2024; 30:e3553. [PMID: 38031661 DOI: 10.1002/psc.3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in viral replication and transcription and received great attention as a vital target for drug/peptide development. Therapeutic agents such as small-molecule drugs or peptides that interact with the Cys-His present in the catalytic site of Mpro are an efficient way to inhibit the protease. Although several emergency-approved vaccines showed good efficacy and drastically dropped the infection rate, evolving variants are still infecting and killing millions of people globally. While a small-molecule drug (Paxlovid) received emergency approval, small-molecule drugs have low target specificity and higher toxicity. Besides small-molecule drugs, peptide therapeutics are thus gaining increasing popularity as they are easy to synthesize and highly selective and have limited side effects. In this study, we investigated the therapeutic value of 67 peptides targeting Mpro using molecular docking. Subsequently, molecular dynamics (MD) simulations were implemented on eight protein-peptide complexes to obtain molecular-level information on the interaction between these peptides and the Mpro active site, which revealed that temporin L, indolicidin, and lymphocytic choriomeningitis virus (LCMV) GP1 are the best candidates in terms of stability, interaction, and structural compactness. These peptides were synthesized using the solid-phase peptide synthesis protocol, purified by reversed-phase high-performance liquid chromatography (RP-HPLC), and authenticated by mass spectrometry (MS). The in vitro fluorometric Mpro activity assay was used to validate the computational results, where temporin L and indolicidin were observed to be very active against SARS-CoV-2 Mpro with IC50 values of 38.80 and 87.23 μM, respectively. A liquid chromatography-MS (LC-MS) assay was developed, and the IC50 value of temporin L was measured at 23.8 μM. The solution-state nuclear magnetic resonance (NMR) structure of temporin L was determined in the absence of sodium dodecyl sulfate (SDS) micelles and was compared to previous temporin structures. This combined investigation provides critical insights and assists us to further develop peptide inhibitors of SARS-CoV-2 Mpro through structural guided investigation.
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Affiliation(s)
- James Stewart
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Jakaria Shawon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Blaise Williams
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - A D A Shahinuzzaman
- Pharmaceutical Sciences Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Taha Al-Adhami
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ruoqing Jia
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cole Bourque
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Ryan Faddis
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Kaylee Stone
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Md Abu Sufian
- School of Pharmacy, Temple University, Philadelphia, PA, USA
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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22
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Phillips MJA, Huston WM, McDonagh AM, Rawling T. 4-Chloroisocoumarins as Chlamydial Protease Inhibitors and Anti-Chlamydial Agents. Molecules 2024; 29:1519. [PMID: 38611800 PMCID: PMC11013143 DOI: 10.3390/molecules29071519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
4-Chloroisocoumarin compounds have broad inhibitory properties against serine proteases. Here, we show that selected 3-alkoxy-4-chloroisocoumarins preferentially inhibit the activity of the conserved serine protease High-temperature requirement A of Chlamydia trachomatis. The synthesis of a new series of isocoumarin-based scaffolds has been developed, and their anti-chlamydial properties were investigated. The structure of the alkoxy substituent was found to influence the potency of the compounds against High-temperature requirement A, and modifications to the C-7 position of the 3-alkoxy-4-chloroisocoumarin structure attenuate anti-chlamydial properties.
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Affiliation(s)
- Matthew J. A. Phillips
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Wilhelmina M. Huston
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Andrew M. McDonagh
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Tristan Rawling
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia;
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23
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Ruiz-Moreno AJ, Cedillo-González R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Velázquez MA. Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 M pro Inhibitors from Large Chemical Libraries. J Chem Inf Model 2024; 64:1984-1995. [PMID: 38472094 DOI: 10.1021/acs.jcim.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome and is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development, and multiple Mpro crystals complexed with competitive inhibitors have been reported. In this study, we aimed to develop an Mpro consensus pharmacophore as a tool to expand the search for inhibitors. We generated a consensus model by aligning and summarizing pharmacophoric points from 152 bioactive conformers of SARS-CoV-2 Mpro inhibitors. Validation against a library of conformers from a subset of ligands showed that our model retrieved poses that reproduced the crystal-binding mode in 77% of the cases. Using models derived from a consensus pharmacophore, we screened >340 million compounds. Pharmacophore-matching and chemoinformatics analyses identified new potential Mpro inhibitors. The candidate compounds were chemically dissimilar to the reference set, and among them, demonstrating the relevance of our model. We evaluated the effect of 16 candidates on Mpro enzymatic activity finding that seven have inhibitory activity. Three compounds (1, 4, and 5) had IC50 values in the midmicromolar range. The Mpro consensus pharmacophore reported herein can be used to identify compounds with improved activity and novel chemical scaffolds against Mpro. The method developed for its generation is provided as an open-access code (https://github.com/AngelRuizMoreno/ConcensusPharmacophore) and can be applied to other pharmacological targets.
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Affiliation(s)
- Angel J Ruiz-Moreno
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Raziel Cedillo-González
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Graduate Program in Biochemical Sciences, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Cordova-Bahena
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnología, Mexico City 03940, Mexico
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - José L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco A Velasco-Velázquez
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
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24
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Gheidari D, Mehrdad M, Bayat M. Synthesis, molecular docking analysis, molecular dynamic simulation, ADMET, DFT, and drug likeness studies: Novel Indeno[1,2-b]pyrrol-4(1H)-one as SARS-CoV-2 main protease inhibitors. PLoS One 2024; 19:e0299301. [PMID: 38517870 PMCID: PMC10959350 DOI: 10.1371/journal.pone.0299301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/07/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic began in 2019 as a result of the advent of a novel coronavirus, SARS-CoV-2. At present, there are a limited number of approved antiviral agents for the treatment of COVID-19. Remdesivir, Molnupiravir, and Paxlovid have been approved by the FDA to treat COVID-19 infections. Research has shown that the main protease enzyme (Mpro) of SARS-CoV-2 plays a crucial role in the enzymatic processing of viral polyproteins. This makes Mpro an interesting therapeutic target for combating infections caused by emerging coronaviruses. METHODS The pharmacological effects of pyrroles and their derivatives have a wide range of applications. In our study, we focused on synthesizing nine novel derivatives of 2-arylamino-dihydro-indeno[1,2-b] pyrrol-4(1H)-one, with a particular emphasis on their antiviral properties. Using in silico studies involving molecular docking and DFT analyses in the gas phase using the B3LYP/6-31++G(d,p) basis set, we studied these compounds with respect to their interactions with the Mpro of SARS-CoV-2. The results of the docking analysis revealed that the synthesized compounds exhibited favorable inhibitory effects. Notably, compound 5f demonstrated the highest effectiveness against the target protein. Furthermore, the pharmacokinetic and drug-like properties of the synthesized derivatives of 2-arylamino-dihydroindeno[1,2-b] pyrrol-4(1H)-one indicated their potential as promising candidates for further development as inhibitors targeting SARS-CoV-2. However, it is imperative to determine the in vitro efficacy of these compounds through comprehensive biochemical and structural analyses.
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Affiliation(s)
- Davood Gheidari
- Faculty of Science, Department of Chemistry, University of Guilan, Rasht, Iran
| | - Morteza Mehrdad
- Faculty of Science, Department of Chemistry, University of Guilan, Rasht, Iran
| | - Mohammad Bayat
- Faculty of Science, Department of Chemistry, Imam Khomeini International University, Qazvin, Iran
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25
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Amblard F, LeCher JC, De R, Zhou S, Liu P, Goh SL, Tao S, Patel D, Downs-Bowen J, Zandi K, Zhang H, Chaudhry G, McBrayer T, Muczynski M, Al-Homoudi A, Engel J, Lan S, Sarafianos SG, Kovari LC, Schinazi RF. Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease. Eur J Med Chem 2024; 268:116263. [PMID: 38432056 DOI: 10.1016/j.ejmech.2024.116263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and related variants, are responsible for the devastating coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 main protease (Mpro) plays a central role in the replication of the virus and represents an attractive drug target. Herein, we report the discovery of novel SARS-CoV-2 Mpro covalent inhibitors, including highly effective compound NIP-22c which displays high potency against several key variants and clinically relevant nirmatrelvir Mpro E166V mutants.
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Affiliation(s)
- Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| | - Julia C LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shaoman Zhou
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Peng Liu
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Jessica Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Gitika Chaudhry
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Michael Muczynski
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Abdullah Al-Homoudi
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Joseph Engel
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shuiyun Lan
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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26
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Shurtleff VW, Layton ME, Parish CA, Perkins JJ, Schreier JD, Wang Y, Adam GC, Alvarez N, Bahmanjah S, Bahnck-Teets CM, Boyce CW, Burlein C, Cabalu TD, Campbell BT, Carroll SS, Chang W, de Lera Ruiz M, Dolgov E, Fay JF, Fox NG, Goh SL, Hartingh TJ, Hurzy DM, Kelly MJ, Klein DJ, Klingler FM, Krishnamurthy H, Kudalkar S, Mayhood TW, McKenna PM, Murray EM, Nahas D, Nawrat CC, Park S, Qian D, Roecker AJ, Sharma V, Shipe WD, Su J, Taggart RV, Truong Q, Wu Y, Zhou X, Zhuang N, Perlin DS, Olsen DB, Howe JA, McCauley JA. Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic. J Med Chem 2024; 67:3935-3958. [PMID: 38365209 DOI: 10.1021/acs.jmedchem.3c02248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.
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Affiliation(s)
| | - Mark E Layton
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Craig A Parish
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - James J Perkins
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John D Schreier
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yunyi Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Gregory C Adam
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | | | | | - Tamara D Cabalu
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Brian T Campbell
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Steven S Carroll
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Wonsuk Chang
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Enriko Dolgov
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - John F Fay
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nicholas G Fox
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shih Lin Goh
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Danielle M Hurzy
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Michael J Kelly
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J Klein
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | | | - Shalley Kudalkar
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Philip M McKenna
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Edward M Murray
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Debbie Nahas
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | - Vijeta Sharma
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - William D Shipe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jing Su
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Robert V Taggart
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Quang Truong
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yin Wu
- Viva Biotech Ltd., Shanghai 201318, China
| | - Xiaoyan Zhou
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - David B Olsen
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A Howe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A McCauley
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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Lee D, Jung HG, Park D, Bang J, Cheong DY, Jang JW, Kim Y, Lee S, Lee SW, Lee G, Kim YH, Hong JH, Hwang KS, Lee JH, Yoon DS. Bioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2. Nat Commun 2024; 15:2108. [PMID: 38453923 PMCID: PMC10920794 DOI: 10.1038/s41467-024-46296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evoked a worldwide pandemic. As the emergence of variants has hampered the neutralization capacity of currently available vaccines, developing effective antiviral therapeutics against SARS-CoV-2 and its variants becomes a significant challenge. The main protease (Mpro) of SARS-CoV-2 has received increased attention as an attractive pharmaceutical target because of its pivotal role in viral replication and proliferation. Here, we generated a de novo Mpro-inhibitor screening platform to evaluate the efficacies of Mpro inhibitors based on Mpro cleavage site-embedded amyloid peptide (MCAP)-coated gold nanoparticles (MCAP-AuNPs). We fabricated MCAPs comprising an amyloid-forming sequence and Mpro-cleavage sequence, mimicking in vivo viral replication process mediated by Mpro. By measuring the proteolytic activity of Mpro and the inhibitory efficacies of various drugs, we confirmed that the MCAP-AuNP-based platform was suitable for rapid screening potential of Mpro inhibitors. These results demonstrated that our MCAP-AuNP-based platform has great potential for discovering Mpro inhibitors and may accelerate the development of therapeutics against COVID-19.
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Affiliation(s)
- Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Hyo Gi Jung
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Dongsung Park
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Junho Bang
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea
| | - Jae Won Jang
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Yonghwan Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Seungmin Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90064, USA
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea
| | - Yeon Ho Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea
| | - Ji Hye Hong
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea.
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea.
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea.
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea.
- Astrion Inc, Seoul, 02841, South Korea.
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28
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Zhang R, Zhou J, Yan H, Liu X, Shang C, Chen Y. Manidipine is not a potential inhibitor against SARS-CoV-2 main protease. Antimicrob Agents Chemother 2024; 68:e0129723. [PMID: 38294235 PMCID: PMC10916385 DOI: 10.1128/aac.01297-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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29
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Ghosh AK, Yadav M, Iddum S, Ghazi S, Lendy EK, Jayashankar U, Beechboard SN, Takamatsu Y, Hattori SI, Aamano M, Higashi-Kuwata N, Mitsuya H, Mesecar AD. Exploration of P1 and P4 modifications of nirmatrelvir: Design, synthesis, biological evaluation, and X-ray structural studies of SARS-CoV-2 Mpro inhibitors. Eur J Med Chem 2024; 267:116132. [PMID: 38335815 PMCID: PMC10964431 DOI: 10.1016/j.ejmech.2024.116132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/12/2024]
Abstract
We report the synthesis, biological evaluation, and X-ray structural studies of a series of SARS-CoV-2 Mpro inhibitors based upon the X-ray crystal structure of nirmatrelvir, an FDA approved drug that targets the main protease of SARS-CoV-2. The studies involved examination of various P4 moieties, P1 five- and six-membered lactam rings to improve potency. In particular, the six-membered P1 lactam ring analogs exhibited high SARS-CoV-2 Mpro inhibitory activity. Several compounds effectively blocked SARS-CoV-2 replication in VeroE6 cells. One of these compounds maintained good antiviral activity against variants of concern including Delta and Omicron variants. A high-resolution X-ray crystal structure of an inhibitor bound to SARS-CoV-2 Mpro was determined to gain insight into the ligand-binding properties in the Mpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Monika Yadav
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Satyanarayana Iddum
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Somayeh Ghazi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Emma K Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Uttara Jayashankar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Sydney N Beechboard
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yuki Takamatsu
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Masayuki Aamano
- Department of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan; Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD, 20892, USA
| | - Andrew D Mesecar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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30
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Omar R, Abd El-Salam M, Elsbaey M, Hassan M. Fourteen immunomodulatory alkaloids and two prenylated phenylpropanoids with dual therapeutic approach for COVID-19: molecular docking and dynamics studies. J Biomol Struct Dyn 2024; 42:2298-2315. [PMID: 37116054 DOI: 10.1080/07391102.2023.2204973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
The pandemic outbreak of COVID-19 caused by the new severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a global health burden. To date, there is no highly effective antiviral therapy to eradicate the virus; as a result, researchers are racing to introduce new potential therapeutic agents. Alternatively, traditional immunity boosters and symptomatic treatment based on natural bioactive compounds are also an option. The 3-chymotrypsin-like protease (3CLpro) crystal structure, the main proteolytic enzyme of SARS-CoV-2, has been unraveled, allowing the development of effective protease inhibitors via in silico and biological studies. In COVID-19 infected patients, the loss of lung function, and mortality are reported to be linked to several inflammatory mediators and cytokines. In this context, the approach of introducing immunomodulatory agents may be considered a dual lifesaving strategy in combination with antiviral drugs. This study aims to provide immunomodulatory natural products exhibiting potential protease inhibitory activities. Selected groups of alkaloids of different classes and two prenylated phenylpropanoids from the Brazilian green propolis were in silico screened for their ability to inhibit COVID-19 3CLpro protease. Results showed that compounds exhibited binding energy scores with values ranging from -6.96 to -3.70 compared to the reference synthetic protease inhibitor O6K with a binding energy score of -7.57. O6K binding energy was found comparable with lead phytochemicals in our study, while their toxicity and drug-likeness criteria are better than that of O6K. The activities of these molecules are mainly ascribed to their ability to form hydrogen bonding with 3CLpro crucial amino acid residues of the catalytic site. In addition, the molecular dynamics simulations further showed that some of these compounds formed stable complexes as evidenced by the occupancy fraction measurements. The study suggested that the major immunomodulators 3β, 20α-diacetamido-5α-pregnane, (20S)-(benzamido)-3β-(N,N-dimethyamino)-pregnane, and baccharin are 3CLpro inhibitors. Biological screenings of these phytochemicals will be valuable to experimentally validate and consolidate the results of this study before a rigid conclusion is reached, which may pave the way for the development of efficient modulatory bioactive compounds with dual bioactions in COVID-19 intervention. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rowida Omar
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, Egypt
| | - Mohamed Abd El-Salam
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, Egypt
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Marwa Elsbaey
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Madiha Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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31
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Peled A, Sprecher E. Proteolytic and Antiproteolytic Activity in the Skin: Gluing the Pieces Together. J Invest Dermatol 2024; 144:466-473. [PMID: 37865898 DOI: 10.1016/j.jid.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 08/22/2023] [Indexed: 10/23/2023]
Abstract
Epidermal differentiation is ultimately aimed at the formation of a functional barrier capable of protecting the organism from the environment while preventing loss of biologically vital elements. Epidermal differentiation entails a delicately regulated process of cell-cell junction formation and dissolution to enable upward cell migration and desquamation. Over the past two decades, the deciphering of the genetic basis of a number of inherited conditions has delineated the pivotal role played in this process by a series of proteases and protease inhibitors, including serpins, cathepsins, and cystatins, suggesting novel avenues for therapeutic intervention in both rare and common disorders of cornification.
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Affiliation(s)
- Alon Peled
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eli Sprecher
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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32
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Zhang R, Yan H, Zhou J, Yan G, Liu X, Shang C, Chen Y. Improved fluorescence-based assay for rapid screening and evaluation of SARS-CoV-2 main protease inhibitors. J Med Virol 2024; 96:e29498. [PMID: 38436148 DOI: 10.1002/jmv.29498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health. In parallel with vaccines, efficacious antivirals are urgently needed. SARS-CoV-2 main protease (Mpro) is an attractive drug target for antiviral development owing to its key roles in virus replication and host immune evasion. Due to the limitations of currently available methods, the development of novel high-throughput screening assays is of the highest importance for the discovery of Mpro inhibitors. In this study, we first developed an improved fluorescence-based assay for rapid screening of Mpro inhibitors from an anti-infection compound library using a versatile dimerization-dependent red fluorescent protein (ddRFP) biosensor. Utilizing this assay, we identified MG-101 as a competitive Mpro inhibitor in vitro. Moreover, our results revealed that ensitrelvir is a potent Mpro inhibitor, but baicalein, chloroquine, ebselen, echinatin, and silibinin are not. Therefore, this robust ddRFP assay provides a faithful avenue for rapid screening and evaluation of Mpro inhibitors to fight against COVID-19.
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Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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33
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Koharazawa R, Hayakawa M, Takeda K, Miyazaki K, Tode C, Hirota Y, Suhara Y. Exploring 2-methyl-substituted vitamin K 3 derivatives with potent inhibitory activity against the 3CL protease of SARS-CoV-2. Bioorg Med Chem Lett 2024; 100:129642. [PMID: 38310976 DOI: 10.1016/j.bmcl.2024.129642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
Since the outbreak of the pandemic, various anti-SARS-CoV-2 drugs have been developed. In particular, 3CL protease (3C-like protease, 3CLpro) is an attractive drug target because it is an essential enzyme for viral multiplication and is present only in viruses, not in humans. To date, 3CLpro inhibitors against SARS-CoV-2 such as nirmatrelvir and ensitrelvir have been launched as oral drugs in Japan, but there is still no potent drug against SARS-CoV-2, due to issues of in vivo absorption and stability. Recently, vitamin K3 was reported to show inhibitory activity against 3CLpro of SARS-CoV-2, and the mechanism of action was predicted to be the formation of a covalent bond between the thiol group of cysteine 145, the active center of 3CLpro, and the C-3 position of vitamin K3. Therefore, we synthesized derivatives in which the 2-methyl group of the vitamin K3 was systematically converted to other substituents and examined their inhibitory activity against 3CLpro of SARS-CoV-2. The results showed that the compounds with the sulfide structure showed an approximately 4-fold increase in activity over vitamin K3. These results indicated the possibility of creating new inhibitors based on vitamin K3 and its derivatives.
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Affiliation(s)
- Ryohto Koharazawa
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Mayu Hayakawa
- Laboratory of Biochemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kazuki Takeda
- Laboratory of Toxicology, School of Veterinary Medicine, Kitasato University, E23-35-1, Towada, Aomori 034-0021, Japan; Department of Computer Science, Tokyo Institute of Technology, 4259-J3-1818, Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-0026, Japan
| | - Kotone Miyazaki
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Tode
- Instrumental Analysis Center, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe 658-8558, Japan
| | - Yoshihisa Hirota
- Laboratory of Biochemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yoshitomo Suhara
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
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34
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Pillai U J, Cherian L, Taunk K, Iype E, Dutta M. Identification of antiviral phytochemicals from cranberry as potential inhibitors of SARS-CoV-2 main protease (M pro). Int J Biol Macromol 2024; 261:129655. [PMID: 38266830 DOI: 10.1016/j.ijbiomac.2024.129655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Cranberry phytochemicals are known to possess antiviral activities. In the current study, we explored the therapeutic potential of cranberry against SARS-CoV-2 by targeting its main protease (Mpro) enzyme. Firstly, phytochemicals of cranberry origin were identified from three independent databases. Subsequently, virtual screening, using molecular docking and molecular dynamics simulation approaches, led to the identification of three lead phytochemicals namely, cyanidin 3-O-galactoside, β-carotene and epicatechin. Furthermore, in vitro enzymatic assays revealed that cyanidin 3-O-galactoside had the highest inhibitory potential with IC50 of 9.98 μM compared to the other two phytochemicals. Cyanidin 3-O-galactoside belongs to the class of anthocyanins. Anthocyanins extracted from frozen cranberry also exhibited the highest inhibitory potential with IC50 of 23.58 μg/ml compared to the extracts of carotenoids and flavanols, the class for β-carotene and epicatechin, respectively. Finally, we confirm the presence of the phytochemicals in the cranberry extracts using targeted LC-MS/MS analysis. Our results, therefore, indicate that the identified cranberry-derived bioactive compounds as well as cranberry could be used for therapeutic interventions against SARS-CoV-2.
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Affiliation(s)
- Jisha Pillai U
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates
| | - Lucy Cherian
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates
| | - Khushman Taunk
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Eldhose Iype
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Mainak Dutta
- Department of Biotechnology, Birla Institute of Technology and Science (BITS) Pilani-Dubai Campus, Academic City, Dubai, United Arab Emirates.
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35
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Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (M pro) through pharmacophore modelling, covalent docking, and biological evaluation. J Mol Graph Model 2024; 127:108672. [PMID: 37992552 DOI: 10.1016/j.jmgm.2023.108672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
The main protease (Mpro) enzyme has an imperative function in disease progression and the life cycle of the SARS-CoV-2 virus. Although the orally active drug nirmatrelvir (co-administered with ritonavir as paxlovid) has been approved for emergency use as the frontline antiviral agent, there are a number of limitations that necessitate the discovery of new drug scaffolds, such as poor pharmacokinetics and susceptibility to proteolytic degradation due to its peptidomimetic nature. This study utilized a novel virtual screening workflow that combines pharmacophore modelling, multiple-receptor covalent docking, and biological evaluation in order to find new Mpro inhibitors. After filtering and analysing ∼66,000 ligands from three different electrophilic libraries, 29 compounds were shortlisted for experimental testing, and two of them exhibited ≥20% inhibition at 100 μM. Our top candidate, GF04, is a benzylpyrrolyl compound that exhibited the highest inhibition activity of 38.3%, with a relatively small size (<350 Da) and leadlike character. Interestingly, our approach also identified another hit, DR07, a pyrimidoindol with a non-peptide character, and a molecular weight of 438.9 Da, reporting an inhibition of 26.3%. The established approach detailed in this study, in conjunction with the discovered inhibitors, has the capacity to yield novel perspectives for devising covalent inhibitors targeting the COVID-19 Mpro enzyme and other comparable targets.
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Affiliation(s)
- Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates.
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36
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Gentile D, Chiummiento L, Santarsiere A, Funicello M, Lupattelli P, Rescifina A, Venuti A, Piperno A, Sciortino MT, Pennisi R. Targeting Viral and Cellular Cysteine Proteases for Treatment of New Variants of SARS-CoV-2. Viruses 2024; 16:338. [PMID: 38543704 PMCID: PMC10976049 DOI: 10.3390/v16030338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/21/2024] Open
Abstract
The continuous emergence of SARS-CoV-2 variants caused the persistence of the COVID-19 epidemic and challenged the effectiveness of the existing vaccines. The viral proteases are the most attractive targets for developing antiviral drugs. In this scenario, our study explores the use of HIV-1 protease inhibitors against SARS-CoV-2. An in silico screening of a library of HIV-1 proteases identified four anti-HIV compounds able to interact with the 3CLpro of SARS-CoV-2. Thus, in vitro studies were designed to evaluate their potential antiviral effectiveness against SARS-CoV-2. We employed pseudovirus technology to simulate, in a highly safe manner, the adsorption of the alpha (α-SARS-CoV-2) and omicron (ο-SARS-CoV-2) variants of SARS-CoV-2 and study the inhibitory mechanism of the selected compounds for cell-virus interaction. The results reported a mild activity against the viral proteases 3CLpro and PLpro, but efficient inhibitory effects on the internalization of both variants mediated by cathepsin B/L. Our findings provide insights into the feasibility of using drugs exhibiting antiviral effects for other viruses against the viral and host SARS-CoV-2 proteases required for entry.
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Affiliation(s)
- Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Lucia Chiummiento
- Department of Scienze, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (A.S.); (M.F.)
| | - Alessandro Santarsiere
- Department of Scienze, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (A.S.); (M.F.)
| | - Maria Funicello
- Department of Scienze, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (A.S.); (M.F.)
| | - Paolo Lupattelli
- Department of Chimica, Sapienza University of Roma, p. le Aldo Moro 5, 00185 Roma, Italy;
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V. le A. Doria, 95125 Catania, Italy;
| | - Assunta Venuti
- International Agency for Research on Cancer (IARC), World Health Organization, 69366 LYON CEDEX 07, France;
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (A.P.); (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (A.P.); (M.T.S.)
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (A.P.); (M.T.S.)
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37
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Dayan Elshan NGR, Wolff KC, Riva L, Woods AK, Grabovyi G, Wilson K, Pedroarena J, Ghorai S, Nazarian A, Weiss F, Liu Y, Mazumdar W, Song L, Okwor N, Malvin J, Bakowski MA, Beutler N, Kirkpatrick MG, Gebara-Lamb A, Huang E, Nguyen-Tran VTB, Chi V, Li S, Rogers TF, McNamara CW, Gupta AK, Rahimi A, Chen JJ, Joseph SB, Schultz PG, Chatterjee AK. Discovery of CMX990: A Potent SARS-CoV-2 3CL Protease Inhibitor Bearing a Novel Warhead. J Med Chem 2024; 67:2369-2378. [PMID: 38335279 PMCID: PMC10895651 DOI: 10.1021/acs.jmedchem.3c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
There remains a need to develop novel SARS-CoV-2 therapeutic options that improve upon existing therapies by an increased robustness of response, fewer safety liabilities, and global-ready accessibility. Functionally critical viral main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target due to its homology within the coronaviral family, and lack thereof toward human proteases. In this disclosure, we outline the advent of a novel SARS-CoV-2 3CLpro inhibitor, CMX990, bearing an unprecedented trifluoromethoxymethyl ketone warhead. Compared with the marketed drug nirmatrelvir (combination with ritonavir = Paxlovid), CMX990 has distinctly differentiated potency (∼5× more potent in primary cells) and human in vitro clearance (>4× better microsomal clearance and >10× better hepatocyte clearance), with good in vitro-to-in vivo correlation. Based on its compelling preclinical profile and projected once or twice a day dosing supporting unboosted oral therapy in humans, CMX990 advanced to a Phase 1 clinical trial as an oral drug candidate for SARS-CoV-2.
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Affiliation(s)
- N G R Dayan Elshan
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Karen C Wolff
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laura Riva
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ashley K Woods
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gennadii Grabovyi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Katy Wilson
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James Pedroarena
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sourav Ghorai
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Armen Nazarian
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Frank Weiss
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuyin Liu
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Wrickban Mazumdar
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lirui Song
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Neechi Okwor
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jacqueline Malvin
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Malina A Bakowski
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, 10466 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Melanie G Kirkpatrick
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Amal Gebara-Lamb
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Edward Huang
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vân T B Nguyen-Tran
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Victor Chi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shuangwei Li
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, 10466 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Case W McNamara
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anil Kumar Gupta
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alireza Rahimi
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jian Jeffrey Chen
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean B Joseph
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Arnab K Chatterjee
- Calibr at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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38
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Goettig P, Chen X, Harris JM. Correlation of Experimental and Calculated Inhibition Constants of Protease Inhibitor Complexes. Int J Mol Sci 2024; 25:2429. [PMID: 38397107 PMCID: PMC10889394 DOI: 10.3390/ijms25042429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Predicting the potency of inhibitors is key to in silico screening of promising synthetic or natural compounds. Here we describe a predictive workflow that provides calculated inhibitory values, which concord well with empirical data. Calculations of the free interaction energy ΔG with the YASARA plugin FoldX were used to derive inhibition constants Ki from PDB coordinates of protease-inhibitor complexes. At the same time, corresponding KD values were obtained from the PRODIGY server. These results correlated well with the experimental values, particularly for serine proteases. In addition, analyses were performed for inhibitory complexes of cysteine and aspartic proteases, as well as of metalloproteases, whereby the PRODIGY data appeared to be more consistent. Based on our analyses, we calculated theoretical Ki values for trypsin with sunflower trypsin inhibitor (SFTI-1) variants, which yielded the more rigid Pro14 variant, with probably higher potency than the wild-type inhibitor. Moreover, a hirudin variant with an Arg1 and Trp3 is a promising basis for novel thrombin inhibitors with high potency. Further examples from antibody interaction and a cancer-related effector-receptor system demonstrate that our approach is applicable to protein interaction studies beyond the protease field.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Xingchen Chen
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
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39
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Giri-Rachman EA, Effendy VV, Azmi MHS, Yamahoki N, Stephanie R, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Aditama R, Ningrum RA, Wardiana A, Fibriani A. The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential. ACS Synth Biol 2024; 13:509-520. [PMID: 38316139 PMCID: PMC10877612 DOI: 10.1021/acssynbio.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.
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Affiliation(s)
| | - Vergio V. Effendy
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Muhammad H. S. Azmi
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Nicholas Yamahoki
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Rebecca Stephanie
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Dian F. Agustiyanti
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Popi H. Wisnuwardhani
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Marissa Angelina
- Research
Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency
(BRIN), Serpong 15314, Indonesia
| | - Yana Rubiyana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Reza Aditama
- Biochemistry
Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Ratih A. Ningrum
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Andri Wardiana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Azzania Fibriani
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
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40
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Barton LS, Callahan JF, Cantizani J, Concha NO, Cotillo Torrejon I, Goodwin NC, Joshi-Pangu A, Kiesow TJ, McAtee JJ, Mellinger M, Nixon CJ, Padrón-Barthe L, Patterson JR, Pearson ND, Pouliot JJ, Rendina AR, Buitrago Santanilla A, Schneck JL, Sanz O, Thalji RK, Ward P, Williams SP, King BW. Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement. Bioorg Med Chem 2024; 100:117618. [PMID: 38309201 DOI: 10.1016/j.bmc.2024.117618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The virally encoded 3C-like protease (3CLpro) is a well-validated drug target for the inhibition of coronaviruses including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Most inhibitors of 3CLpro are peptidomimetic, with a γ-lactam in place of Gln at the P1 position of the pseudopeptide chain. An effort was pursued to identify a viable alternative to the γ-lactam P1 mimetic which would improve physicochemical properties while retaining affinity for the target. Discovery of a 2-tetrahydrofuran as a suitable P1 replacement that is a potent enzymatic inhibitor of 3CLpro in SARS-CoV-2 virus is described herein.
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Affiliation(s)
- Linda S Barton
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States.
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Juan Cantizani
- GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Nestor O Concha
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Nicole C Goodwin
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Amruta Joshi-Pangu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Terry J Kiesow
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Jeff J McAtee
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Mark Mellinger
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Christopher J Nixon
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Jaclyn R Patterson
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Neil D Pearson
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Jeffrey J Pouliot
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Alan R Rendina
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | | | - Jessica L Schneck
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Olalla Sanz
- GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Reema K Thalji
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Paris Ward
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Shawn P Williams
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
| | - Bryan W King
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, United States
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41
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Ciaglia T, Vestuto V, Di Sarno V, Musella S, Smaldone G, Di Matteo F, Napolitano V, Miranda MR, Pepe G, Basilicata MG, Novi S, Capolupo I, Bifulco G, Campiglia P, Gomez-Monterrey I, Snoeck R, Andrei G, Manfra M, Ostacolo C, Lauro G, Bertamino A. Peptidomimetics as potent dual SARS-CoV-2 cathepsin-L and main protease inhibitors: In silico design, synthesis and pharmacological characterization. Eur J Med Chem 2024; 266:116128. [PMID: 38232463 DOI: 10.1016/j.ejmech.2024.116128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
In this paper we present the design, synthesis, and biological evaluation of a new series of peptidomimetics acting as potent anti-SARS-CoV-2 agents. Starting from our previously described Main Protease (MPro) and Papain Like Protease (PLPro) dual inhibitor, CV11, here we disclose its high inhibitory activity against cathepsin L (CTSL) (IC50 = 19.80 ± 4.44 nM), an emerging target in SARS-CoV-2 infection machinery. An in silico design, inspired by the structure of CV11, led to the development of a library of peptidomimetics showing interesting activities against CTSL and Mpro, allowing us to trace the chemical requirements for the binding to both enzymes. The screening in Vero cells infected with 5 different SARS-CoV-2 variants of concerns, highlighted sub-micromolar activities for most of the synthesized compounds (13, 15, 16, 17 and 31) in agreement with the enzymatic inhibition assays results. The compounds showed lack of activity against several different RNA viruses except for the 229E and OC43 human coronavirus strains, also characterized by a cathepsin-L dependent release into the host cells. The most promising derivatives were also evaluated for their chemical and metabolic in-vitro stability, with derivatives 15 and 17 showing a suitable profile for further preclinical characterization.
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Affiliation(s)
- Tania Ciaglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Vincenzo Vestuto
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Veronica Di Sarno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Simona Musella
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gerardina Smaldone
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Valeria Napolitano
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Maria Rosaria Miranda
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giacomo Pepe
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | | | - Sara Novi
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Ilaria Capolupo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy; European Biomedical Research Institute (EBRIS), Via S. De Renzi 50, 84125, Salerno, Italy
| | - Isabel Gomez-Monterrey
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131, Naples, Italy
| | - Robert Snoeck
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, Department of Microbiology, Immunology, and Transplantation, KU Leuven, BE-3000, Leuven, Belgium
| | - Michele Manfra
- Department of Science, University of Basilicata, Via Dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Carmine Ostacolo
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
| | - Alessia Bertamino
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084, Fisciano, Salerno, Italy.
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Novakova Z, Tehrani ZA, Jurok R, Motlova L, Kutil Z, Pavlicek J, Shukla S, Choy CJ, Havlinova B, Baranova P, Berkman CE, Kuchar M, Cerny J, Barinka C. Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. J Chem Inf Model 2024; 64:1030-1042. [PMID: 38224368 PMCID: PMC10865363 DOI: 10.1021/acs.jcim.3c01542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates. Accompanying quantum mechanics calculations revealed that electroneutrality of the sulfamide function is a major factor contributing to the markedly lower potency of bisubstituted compounds by considerably lowering their interaction energy with the enzyme. Overall, while bisubstituted uncharged sulfamide functions can bolster favorable pharmacological properties of a given inhibitor, their use as ZBGs in metalloenzyme inhibitors might be less advantageous due to their suboptimal metal-ligand properties.
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Affiliation(s)
- Zora Novakova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Zahra Aliakbar Tehrani
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Radek Jurok
- Forensic
Laboratory of Biologically Active Substances, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Lucia Motlova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Zsofia Kutil
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Jiri Pavlicek
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Shivam Shukla
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Cindy J. Choy
- Department
of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Barbora Havlinova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Petra Baranova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Clifford E. Berkman
- Department
of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Martin Kuchar
- Forensic
Laboratory of Biologically Active Substances, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Jiri Cerny
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Cyril Barinka
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
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Khamto N, Utama K, Boontawee P, Janthong A, Tatieng S, Arthan S, Choommongkol V, Sangthong P, Yenjai C, Suree N, Meepowpan P. Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CL pro: Insights from the Computational and Experimental Investigations. J Chem Inf Model 2024; 64:874-891. [PMID: 38277124 DOI: 10.1021/acs.jcim.3c01477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The emergence of the COVID-19 situation has become a global issue due to the lack of effective antiviral drugs for treatment. Flavonoids are a class of plant secondary metabolites that have antiviral activity against SARS-CoV-2 through inhibition of the main protease (3CLpro). In this study, 22 flavonoids obtained from natural sources and semisynthetic approaches were investigated for their inhibitory activity against SARS-CoV-2 3CLpro, along with cytotoxicity on Vero cells. The protein-ligand interactions were examined using molecular dynamics simulation. Moreover, QSAR analysis was conducted to clarify the structural effects on bioactivity. Accordingly, the in vitro investigation demonstrated that four flavonoids, namely, tectochrysin (7), 6″,6″-dimethylchromeno-[2″,3″:7,8]-flavone (9), panduratin A (19), and genistein (20), showed higher protease inhibitory activity compared to the standard flavonoid baicalein. Finally, our finding suggests that genistein (20), an isoflavone discovered in Millettia brandisiana, has potential for further development as a SARS-CoV-2 3CLpro inhibitor.
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Affiliation(s)
- Nopawit Khamto
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Multidisciplinary and Interdisciplinary School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Kraikrit Utama
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Office of Research Administration, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Panida Boontawee
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Multidisciplinary and Interdisciplinary School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Atchara Janthong
- Program in Biotechnology, Multidisciplinary and Interdisciplinary School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Suriya Tatieng
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Supakorn Arthan
- Program of Chemistry, Faculty of Science and Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon47000, Thailand
| | - Vachira Choommongkol
- Department of Chemistry, Faculty of Science, Maejo University, 63 Nong Han, Chiang Mai 50290, Thailand
| | - Padchanee Sangthong
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, 123, Khon Kaen 40002, Thailand
| | - Nuttee Suree
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Puttinan Meepowpan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
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Bouzidi HS, Driouich JS, Klitting R, Bernadin O, Piorkowski G, Amaral R, Fraisse L, Mowbray CE, Scandale I, Escudié F, Chatelain E, de Lamballerie X, Nougairède A, Touret F. Generation and evaluation of protease inhibitor-resistant SARS-CoV-2 strains. Antiviral Res 2024; 222:105814. [PMID: 38272321 DOI: 10.1016/j.antiviral.2024.105814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Since the start of the SARS-CoV-2 pandemic, the search for antiviral therapies has been at the forefront of medical research. To date, the 3CLpro inhibitor nirmatrelvir (Paxlovid®) has shown the best results in clinical trials and the greatest robustness against variants. A second SARS-CoV-2 protease inhibitor, ensitrelvir (Xocova®), has been developed. Ensitrelvir, currently in Phase 3, was approved in Japan under the emergency regulatory approval procedure in November 2022, and is available since March 31, 2023. One of the limitations for the use of antiviral monotherapies is the emergence of resistance mutations. Here, we experimentally generated mutants resistant to nirmatrelvir and ensitrelvir in vitro following repeating passages of SARS-CoV-2 in the presence of both antivirals. For both molecules, we demonstrated a loss of sensitivity for resistance mutants in vitro. Using a Syrian golden hamster infection model, we showed that the ensitrelvir M49L mutation, in the multi-passage strain, confers a high level of in vivo resistance. Finally, we identified a recent increase in the prevalence of M49L-carrying sequences, which appears to be associated with multiple repeated emergence events in Japan and may be related to the use of Xocova® in the country since November 2022. These results highlight the strategic importance of genetic monitoring of circulating SARS-CoV-2 strains to ensure that treatments administered retain their full effectiveness.
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Affiliation(s)
- Hawa Sophia Bouzidi
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Jean-Sélim Driouich
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Raphaëlle Klitting
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Ornéllie Bernadin
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Rayane Amaral
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Laurent Fraisse
- Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | | | - Ivan Scandale
- Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | - Fanny Escudié
- Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | - Eric Chatelain
- Drugs for Neglected Diseases Initiative, Geneva, Switzerland
| | - Xavier de Lamballerie
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France
| | - Franck Touret
- Unité des Virus Émergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France.
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El-Saghier AM, Enaili SS, Abdou A, Kadry AM. An efficient eco-friendly, simple, and green synthesis of some new spiro-N-(4-sulfamoyl-phenyl)-1,3,4-thiadiazole-2-carboxamide derivatives as potential inhibitors of SARS-CoV-2 proteases: drug-likeness, pharmacophore, molecular docking, and DFT exploration. Mol Divers 2024; 28:249-270. [PMID: 37946070 PMCID: PMC10876818 DOI: 10.1007/s11030-023-10761-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION The coronavirus disease 2019 (COVID-19) pandemic has caused a global health crisis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious virus that can cause severe respiratory illness. There is no specific treatment for COVID-19, and the development of new drugs is urgently needed. PROBLEM STATEMENT The SARS-CoV-2 main protease (Mpro) enzyme is a critical viral enzyme that plays a vital role in viral replication. The inhibition of Mpro enzyme can be an effective strategy for developing new COVID-19 drugs. METHODOLOGY An efficient operationally simple and convenient green synthesis method had been done towards a series of novel spiro-N-(4-sulfamoylphenyl)-2-carboxamide derivatives, in ethanol at room temperature in green conditions, up to 90% yield. The molecular structures of the synthesized compounds were verified using spectroscopic methods.The title compounds were subjected to in silico analysis, including Lipinski's rule and ADMET prediction, in addition to pharmacophore modeling and molecular docking against the active site of SARS-CoV-2 target main protease (Mpro) enzyme (6LU7). Furthermore, both of the top-ranked compounds (5 and 6) and the standard Nirmatrelvir were subjected to DFT analysis. FINDINGS The synthesized compounds exhibited good binding affinity to SARS-CoV-2 Mpro enzyme, with binding energy scores ranging from - 7.33 kcal/mol (compound 6) and - 7.22kcal/mol (compound 5) to - 6.54 kcal/mol (compounds 8 and 9). The top-ranked compounds (5 and 6) had lower HOMO-LUMO energy difference (ΔE) than the standard drug Nirmatrelvir. This highlights the potential and relevance of charge transfer at the molecular level. RECOMMENDATION These findings suggest that the synthesized spiro-N-(4-sulfamoylphenyl)-2-carboxamide derivatives could be potential candidates for COVID-19 drug development. To confirm these drugs' antiviral efficacy in vivo, more research is required. With very little possibility of failure, this proven method could aid in the search for the SARS-CoV-2 pandemic's desperately needed medications.
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Affiliation(s)
- Ahmed M El-Saghier
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt.
| | - Souhaila S Enaili
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
- Chemistry Department, Faculty of Science, Al Zawiya University, Al Zawia, Libya
| | - Aly Abdou
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Asmaa M Kadry
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
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Zhang H, Zhou K, Peng F, Gao Z, Song G, Hu B, Chun S, Xiao J, Qian M, Wu J, Pan K, Gao F, Guo M, Peng C, Zou G, Wu JZ, Cai K, Li Y. Novel small-molecule inhibitors of SARS-CoV-2 main protease with nanomolar antiviral potency. J Infect 2024; 88:211-214. [PMID: 38191095 DOI: 10.1016/j.jinf.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/23/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Affiliation(s)
- Haoran Zhang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, China
| | - Kangping Zhou
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention (Hubei CDC), Wuhan 430079, China
| | - Fei Peng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, China
| | - Zhao Gao
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Guowei Song
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China.
| | - Bing Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention (Hubei CDC), Wuhan 430079, China
| | - Sophia Chun
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Junfeng Xiao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, China
| | - Mengfei Qian
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Jin Wu
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Kai Pan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention (Hubei CDC), Wuhan 430079, China
| | - Fan Gao
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Meng Guo
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention (Hubei CDC), Wuhan 430079, China
| | - Cheng Peng
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Gang Zou
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Jim Zhen Wu
- Suzhou Ark Biopharmaceutical Co. Ltd., 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention (Hubei CDC), Wuhan 430079, China.
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, China; Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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47
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Huang Q, Quan B, Chen Y, Zhao X, Zhou Y, Huang C, Qiao J, Wang Y, Li Y, Yang S, Lei J, Li L. Discovery of α-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups. Bioorg Chem 2024; 143:107001. [PMID: 38101266 DOI: 10.1016/j.bioorg.2023.107001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
Although the SARS-CoV-2 pandemic has ended, multiple sporadic cases still exist, posing a request for more antivirals. The main protease (Mpro) of SARS-CoV-2, a key enzyme for viral replication, is an attractive target for drug development. Here, we report the discovery of a new potent α-ketoamide-containing Mpro inhibitor, N-((R)-1-cyclohexyl-2-(((R)-3-methoxy-1-oxo-1-((1-(2-oxo-2-((thiazol-2-ylmethyl)amino)acetyl)cyclobutyl)amino)propan-2-yl)amino)-2-oxoethyl)-4,4-difluorocyclohexane-1-carboxamide (20j). This compound presented promising enzymatic inhibitory activity against SARS-CoV-2 Mpro with an IC50 value of 19.0 nM, and an excellent antiviral activity in cell-based assay with an EC50 value of 138.1 nM. This novel covalent inhibitor may be used as a lead compound for subsequent drug discovery against SARS-CoV-2.
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Affiliation(s)
- Qiao Huang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Baoxue Quan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yan Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiu Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanmei Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chong Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingxin Qiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yifei Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yueyue Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan 610212, China
| | - Jian Lei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China.
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48
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Gutti G, He Y, Coldren WH, Lalisse RF, Border SE, Hadad CM, McElroy CA, Ekici ÖD. In-silico guided design, screening, and molecular dynamic simulation studies for the identification of potential SARS-CoV-2 main protease inhibitors for the targeted treatment of COVID-19. J Biomol Struct Dyn 2024; 42:1733-1750. [PMID: 37114441 DOI: 10.1080/07391102.2023.2202247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
COVID-19, the disease responsible for the recent pandemic, is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) of SARS-CoV-2 is an essential proteolytic enzyme that plays a number of important roles in the replication of the virus in human host cells. Blocking the function of SARS-CoV-2 Mpro offers a promising and targeted, therapeutic option for the treatment of the COVID-19 infection. Such an inhibitory strategy is currently successful in treating COVID-19 under FDA's emergency use authorization, although with limited benefit to the immunocompromised along with an unfortunate number of side effects and drug-drug interactions. Current COVID vaccines protect against severe disease and death but are mostly ineffective toward long COVID which has been seen in 5-36% of patients. SARS-CoV-2 is a rapidly mutating virus and is here to stay endemically. Hence, alternate therapeutics to treat SARS-CoV-2 infections are still needed. Moreover, because of the high degree of conservation of Mpro among different coronaviruses, any newly developed antiviral agents should better prepare us for potential future epidemics or pandemics. In this paper, we first describe the design and computational docking of a library of novel 188 first-generation peptidomimetic protease inhibitors using various electrophilic warheads with aza-peptide epoxides, α-ketoesters, and β-diketones identified as the most effective. Second-generation designs, 192 compounds in total, focused on aza-peptide epoxides with drug-like properties, incorporating dipeptidyl backbones and heterocyclic ring motifs such as proline, indole, and pyrrole groups, yielding 8 hit candidates. These novel and specific inhibitors for SARS-CoV-2 Mpro can ultimately serve as valuable alternate and broad-spectrum antivirals against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gopichand Gutti
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Yiran He
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - William H Coldren
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Remy F Lalisse
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah E Border
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Craig A McElroy
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Özlem Doğan Ekici
- Department of Chemistry and Biochemistry, The Ohio State University, Newark, Ohio, USA
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49
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR QSAR Environ Res 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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50
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Wang R, Chen X, Li H, Chen X, Sun D, Yu D, Lu J, Xie Y, Zhang Q, Xu J, Zhang W, Chen H, Liu S, Chen L. Danshensu inhibits SARS-CoV-2 by targeting its main protease as a specific covalent inhibitor and discovery of bifunctional compounds eliciting antiviral and anti-inflammatory activity. Int J Biol Macromol 2024; 257:128623. [PMID: 38070810 DOI: 10.1016/j.ijbiomac.2023.128623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to human. Since there are still no effective treatment options against the new emerging variants of SARS-CoV-2, it is necessary to devote a continuous endeavor for more targeted drugs and the preparation for the next pandemic. Salvia miltiorrhiza and its active ingredients possess wide antiviral activities, including against SARS-CoV-2. Danshensu, as one of the most important active ingredients in Salvia miltiorrhiza, has been reported to inhibit the entry of SARS-CoV-2 into ACE2 (angiotensin-converting enzyme 2)-overexpressed HEK-293T cells and Vero-E6 cells. However, there is a paucity of information regarding its detailed target and mechanism against SARS-CoV-2. Here, we present Danshensu as a covalent inhibitor of 3-chymotrypsin-like protease (3CLpro) against SARS-CoV-2 by the time-dependent inhibition assay (TDI) and mass spectrometry analysis. Further molecular docking, site-directed mutagenesis, circular dichroism (CD) and fluorescence spectra revealed that Danshensu covalently binds to C145 of SARS-CoV-2 3CLpro, meanwhile forming the hydrogen bonds with S144, H163 and E166 in the S1 site. Structure-based optimization of Danshensu led to the discovery of the promising compounds with good inhibitory activity and microsomal stability in vitro. Due to Danshensu inhibiting lung inflammation in the mouse model, we found that Danshensu derivatives also showed better anti-inflammatory activity than Danshensu in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. Thus, our study provides not only the clue of the efficacy of Salvia miltiorrhiza against SARS-CoV-2, but also a detailed mechanistic insight into the covalent mode of action of Danshensu for design of covalent inhibitors against SARS-CoV-2 3CLpro, highlighting its potential as a bifunctional molecule with antivirus and anti-inflammation.
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Affiliation(s)
- Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xuwen Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Donghui Sun
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuanyuan Xie
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shunying Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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