1
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Zhang W, Xiao L, Li D, Hu Y, Yu W. New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs. J Med Chem 2024; 67:11522-11542. [PMID: 38967785 DOI: 10.1021/acs.jmedchem.4c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths, posing a serious threat to public health and safety. Rapid mutations of SARS-CoV-2 and complex interactions among multiple targets during infection pose a risk of expiry for small molecule inhibitors. This suggests that the traditional concept of "one bug, one drug" could be ineffective in dealing with the coronavirus. The dual-target drug strategy is expected to be the key to ending coronavirus infections. However, the lack of design method and improper combination of dual-targets poses obstacle to the discovery of new dual-target drugs. In this Perspective, we summarized the profiles concerning drug design methods, structure-activity relationships, and pharmacological parameters of dual-target drugs for the treatment of COVID-19. Importantly, we underscored how target combination and rational drug design illuminate the development of dual-target drugs for SARS-CoV-2.
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Affiliation(s)
- Wenyi Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lecheng Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Hu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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2
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Anton DB, de Lima JC, Dahmer BR, Camini AM, Goettert MI, Timmers LFSM. Taming the storm: potential anti-inflammatory compounds targeting SARS-CoV-2 MPro. Inflammopharmacology 2024:10.1007/s10787-024-01525-9. [PMID: 39048773 DOI: 10.1007/s10787-024-01525-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
In severe COVID-19 cases, an exacerbated inflammatory response triggers a cytokine storm that can worsen the prognosis. Compounds with both antiviral and anti-inflammatory activities show promise as candidates for COVID-19 therapy, as they potentially act against the SARS-CoV-2 infection regardless of the disease stage. One of the most attractive drug targets among coronaviruses is the main protease (MPro). This enzyme is crucial for cleaving polyproteins into non-structural proteins required for viral replication. The aim of this review was to identify SARS-CoV-2 MPro inhibitors with both antiviral and anti-inflammatory properties. The interactions of the compounds within the SARS-CoV-2 MPro binding site were analyzed through molecular docking when data from crystallographic structures were unavailable. 18 compounds were selected and classified into five different superclasses. Five of them exhibit high potency against MPro: GC-376, baicalein, naringenin, heparin, and carmofur, with IC50 values below 0.2 μM. The MPro inhibitors selected have the potential to alleviate lung edema and decrease cytokine release. These molecules mainly target three critical inflammatory pathways: NF-κB, JAK/STAT, and MAPK, all previously associated with COVID-19 pathogenesis. The structures of the compounds occupy the S1/S2 substrate binding subsite of the MPro. They interact with residues from the catalytic dyad (His41 and Cys145) and/or with the oxyanion hole (Gly143, Ser144, and Cys145), which are pivotal for substrate recognition. The MPro SARS-CoV-2 inhibitors with potential anti-inflammatory activities present here could be optimized for maximum efficacy and safety and be explored as potential treatment of both mild and severe COVID-19.
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Affiliation(s)
- Débora Bublitz Anton
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, CEP 95914-014, Brazil
| | - Jeferson Camargo de Lima
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, CEP 95914-014, Brazil
| | - Bruno Rampanelli Dahmer
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, CEP 95914-014, Brazil
| | - Ana Micaela Camini
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, CEP 95914-014, Brazil
| | - Marcia Inês Goettert
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
| | - Luis Fernando Saraiva Macedo Timmers
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, CEP 95914-014, Brazil.
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado, CEP 95914-014, Brazil.
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3
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Rauch S, Costacurta F, Schöppe H, Peng JY, Bante D, Erisoez EE, Sprenger B, He X, Moghadasi SA, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Wang D, Naschberger A, Dunzendorfer-Matt T, Kaserer T, von Laer D, Heilmann E. Highly specific SARS-CoV-2 main protease (M pro) mutations against the clinical antiviral ensitrelvir selected in a safe, VSV-based system. Antiviral Res 2024:105969. [PMID: 39053514 DOI: 10.1016/j.antiviral.2024.105969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 07/04/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
In the SARS-CoV-2 pandemic, the so far two most effective approved antivirals are the protease inhibitors nirmatrelvir, in combination with ritonavir (Paxlovid) and ensitrelvir (Xocova). However, antivirals and indeed all antimicrobial drugs are sooner or later challenged by resistance mutations. Studying such mutations is essential for treatment decisions and pandemic preparedness. At the same time, generating resistant viruses to assess mutants is controversial, especially with pathogens of pandemic potential like SARS-CoV-2. To circumvent gain-of-function research with non-attenuated SARS-CoV-2, a previously developed safe system based on a chimeric vesicular stomatitis virus dependent on the SARS-CoV-2 main protease (VSV-Mpro) was used to select mutations against ensitrelvir. Ensitrelvir is clinically especially relevant due to its single-substance formulation, avoiding drug-drug interactions by the co-formulated CYP3A4 inhibitor ritonavir in Paxlovid. By treating VSV-Mpro with ensitrelvir, several highly-specific resistant mutants against this inhibitor were selected, while being still fully or largely susceptible to nirmatrelvir. We then confirmed several ensitrelvir-specific mutants in gold standard enzymatic assays and SARS-CoV-2 replicons. These findings indicate that the two inhibitors can have distinct viral resistance profiles, which could determine treatment decisions.
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Affiliation(s)
- Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Ju-Yi Peng
- Department of Infectious Disease and Vaccines Research, Merck & Co., Inc., Rahway, NJ, USA
| | - David Bante
- Institute of Molecular Biochemistry, Biocentre, Medical University of Innsbruck, Austria
| | - Ela Emilie Erisoez
- Institute of Molecular Biochemistry, Biocentre, Medical University of Innsbruck, Austria
| | - Bernhard Sprenger
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020, Austria
| | - Xi He
- Department of Infectious Disease and Vaccines Research, Merck & Co., Inc., Rahway, NJ, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Dai Wang
- Department of Infectious Disease and Vaccines Research, Merck & Co., Inc., Rahway, NJ, USA
| | - Andreas Naschberger
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | | | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria; Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
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4
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Krismer L, Schöppe H, Rauch S, Bante D, Sprenger B, Naschberger A, Costacurta F, Fürst A, Sauerwein A, Rupp B, Kaserer T, von Laer D, Heilmann E. Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir. NPJ VIRUSES 2024; 2:23. [PMID: 38933182 PMCID: PMC11196219 DOI: 10.1038/s44298-024-00028-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/14/2024] [Indexed: 06/28/2024]
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia in 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring the ability to efficiently spread among humans and become pandemic. Its high mortality rate of up to 35% and the absence of effective targeted therapies call for the development of antiviral drugs for this pathogen. Since the beginning of the SARS-CoV-2 pandemic, extensive research has focused on identifying protease inhibitors for the treatment of SARS-CoV-2. Our intention was therefore to assess whether these protease inhibitors are viable options for combating MERS-CoV. To that end, we used previously established protease assays to quantify inhibition of SARS-CoV-2, MERS-CoV and other main proteases. Nirmatrelvir inhibited several of these proteases, whereas ensitrelvir was less broadly active. To simulate nirmatrelvir's clinical use against MERS-CoV and subsequent resistance development, we applied a safe, surrogate virus-based system. Using the surrogate virus, we previously selected hallmark mutations of SARS-CoV-2-Mpro, such as T21I, M49L, S144A, E166A/K/V and L167F. In the current study, we selected a pool of MERS-CoV-Mpro mutants, characterized the resistance and modelled the steric effect of catalytic site mutants S142G, S142R, S147Y and A171S.
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Affiliation(s)
- Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Sprenger
- Institute of Biochemistry, University of Innsbruck, CMBI – Center for Molecular Biosciences Innsbruck, Innsbruck, 6020 Austria
| | - Andreas Naschberger
- Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | | | - Anna Fürst
- Institute of Molecular Immunology, Technical University of Munich, Munich, 81675 Germany
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, 6020 Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020 Austria
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5
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Kenward C, Vuckovic M, Paetzel M, Strynadka NCJ. Kinetic comparison of all eleven viral polyprotein cleavage site processing events by SARS-CoV-2 main protease using a linked protein FRET platform. J Biol Chem 2024; 300:107367. [PMID: 38750796 PMCID: PMC11209022 DOI: 10.1016/j.jbc.2024.107367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
The main protease (Mpro) remains an essential therapeutic target for COVID-19 post infection intervention given its critical role in processing the majority of viral proteins encoded by the genome of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2). Upon viral entry, the +ssRNA genome is translated into two long polyproteins (pp1a or the frameshift-dependent pp1ab) containing all the nonstructural proteins (nsps) required by the virus for immune modulation, replication, and ultimately, virion assembly. Included among these nsps is the cysteine protease Mpro (nsp5) which self-excises from the polyprotein, dimerizes, then sequentially cleaves 11 of the 15 cut-site junctions found between each nsp within the polyprotein. Many structures of Mpro (often bound to various small molecule inhibitors or peptides) have been detailed recently, including structures of Mpro bound to each of the polyprotein cleavage sequences, showing that Mpro can accommodate a wide range of targets within its active site. However, to date, kinetic characterization of the interaction of Mpro with each of its native cleavage sequences remains incomplete. Here, we present a robust and cost-effective FRET based system that benefits from a more consistent presentation of the substrate that is also closer in organization to the native polyprotein environment compared to previously reported FRET systems that use chemically modified peptides. Using this system, we were able to show that while each site maintains a similar Michaelis constant, the catalytic efficiency of Mpro varies greatly between cut-site sequences, suggesting a clear preference for the order of nsp processing.
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Affiliation(s)
- Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada.
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6
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Moreira Costa MA, de Sousa NF, Mansur Pontes CL, Scotti MT, de Assis FF, Braga AL, Sandjo LP. Inhibitory effects against SARSCoV-2 main protease (M pro) of biflavonoids and benzophenones from the fruit of Platonia insignis. Fitoterapia 2024; 173:105784. [PMID: 38128621 DOI: 10.1016/j.fitote.2023.105784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
The SARS-CoV-2 mutation and the limitation of the approved drug against COVID-19 are still a challenge in many country healthcare systems and need to be affronted despite the set of vaccines to prevent this viral infection. To contribute to the identification of new antiviral agents, the present study focused on natural products from an edible fruit with potential inhibitory effects against the SARS-CoV-2 main protease (Mpro). First, LC-ESIMS analysis of Platonia insignis fruits was performed and showed the presence of biflavonoids and benzophenones in the seed and pulp, respectively. Then, maceration and chromatographic purification led to the identification of two triglycerides (1 and 2) alongside chamaejasmine (3) and volkensiflavone (4) from the seed and isogarcinol (5) and cycloxanthochymol (6), from the pulp. Compounds 1-6 after evaluating their inhibitory against Mpro, displayed from no to significant activity. Compound 5 was the most potent with an IC50 value of 0.72 μM and was more active than the positive control, Ebselen (IC50 of 3.4 μM). It displayed weak and no cytotoxicity against THP-1 (CC50 of 116.2 μM) and Vero cell lines, respectively. Other active compounds showed no cytotoxicity against THP-1. and Vero cell lines. Molecular docking studies revealed interactions in the catalytic pocket between compound 5 and amino acid residues that composed the catalytic dyads (His 41 and Cyst 145).
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Affiliation(s)
- Monalisa A Moreira Costa
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Natália F de Sousa
- Department of Chemistry, Center for Exact and Natural Sciences, Universidade Federal de Paraíba, Campus I, João Pessoa, PB, Brazil
| | - Carime L Mansur Pontes
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Marcus T Scotti
- Department of Chemistry, Center for Exact and Natural Sciences, Universidade Federal de Paraíba, Campus I, João Pessoa, PB, Brazil
| | - Francisco F de Assis
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Antonio L Braga
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Louis P Sandjo
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil.
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7
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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] [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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8
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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9
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Mao L, Shaabani N, Zhang X, Jin C, Xu W, Argent C, Kushnareva Y, Powers C, Stegman K, Liu J, Xie H, Xu C, Bao Y, Xu L, Zhang Y, Yang H, Qian S, Hu Y, Shao J, Zhang C, Li T, Li Y, Liu N, Lin Z, Wang S, Wang C, Shen W, Lin Y, Shu D, Zhu Z, Kotoi O, Kerwin L, Han Q, Chumakova L, Teijaro J, Royal M, Brunswick M, Allen R, Ji H, Lu H, Xu X. Olgotrelvir, a dual inhibitor of SARS-CoV-2 M pro and cathepsin L, as a standalone antiviral oral intervention candidate for COVID-19. MED 2024; 5:42-61.e23. [PMID: 38181791 DOI: 10.1016/j.medj.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/18/2023] [Accepted: 12/03/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Oral antiviral drugs with improved antiviral potency and safety are needed to address current challenges in clinical practice for treatment of COVID-19, including the risks of rebound, drug-drug interactions, and emerging resistance. METHODS Olgotrelvir (STI-1558) is designed as a next-generation antiviral targeting the SARS-CoV-2 main protease (Mpro), an essential enzyme for SARS-CoV-2 replication, and human cathepsin L (CTSL), a key enzyme for SARS-CoV-2 entry into host cells. FINDINGS Olgotrelvir is a highly bioavailable oral prodrug that is converted in plasma to its active form, AC1115. The dual mechanism of action of olgotrelvir and AC1115 was confirmed by enzyme activity inhibition assays and co-crystal structures of AC1115 with SARS-CoV-2 Mpro and human CTSL. AC1115 displayed antiviral activity by inhibiting replication of all tested SARS-CoV-2 variants in cell culture systems. Olgotrelvir also inhibited viral entry into cells using SARS-CoV-2 Spike-mediated pseudotypes by inhibition of host CTSL. In the K18-hACE2 transgenic mouse model of SARS-CoV-2-mediated disease, olgotrelvir significantly reduced the virus load in the lungs, prevented body weight loss, and reduced cytokine release and lung pathologies. Olgotrelvir demonstrated potent activity against the nirmatrelvir-resistant Mpro E166 mutants. Olgotrelvir showed enhanced oral bioavailability in animal models and in humans with significant plasma exposure without ritonavir. In phase I studies (ClinicalTrials.gov: NCT05364840 and NCT05523739), olgotrelvir demonstrated a favorable safety profile and antiviral activity. CONCLUSIONS Olgotrelvir is an oral inhibitor targeting Mpro and CTSL with high antiviral activity and plasma exposure and is a standalone treatment candidate for COVID-19. FUNDING Funded by Sorrento Therapeutics.
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Affiliation(s)
- Long Mao
- ACEA Therapeutics, Inc., San Diego, CA 92121, USA
| | | | - Xiaoying Zhang
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Can Jin
- ACEA Therapeutics, Inc., San Diego, CA 92121, USA
| | - Wanhong Xu
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | | | | | - Colin Powers
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | - Karen Stegman
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | - Jia Liu
- ACEA Therapeutics, Inc., San Diego, CA 92121, USA
| | - Hui Xie
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | - Changxu Xu
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Yimei Bao
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Lijun Xu
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Yuren Zhang
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Haigang Yang
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Shengdian Qian
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Yong Hu
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Jianping Shao
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Can Zhang
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Tingting Li
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Yi Li
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Na Liu
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Zhenhao Lin
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Shanbo Wang
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Chao Wang
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Wei Shen
- ACEA Pharmaceutical Co., Ltd., Hangzhou, Zhejiang, P.R. China
| | - Yuanlong Lin
- Shenzhen Third People's Hospital, SUSTech, Shenzhen, P.R. China
| | - Dan Shu
- Shenzhen Third People's Hospital, SUSTech, Shenzhen, P.R. China
| | - Zhenhong Zhu
- ACEA Therapeutics, Inc., San Diego, CA 92121, USA
| | - Olivia Kotoi
- ACEA Therapeutics, Inc., San Diego, CA 92121, USA
| | - Lisa Kerwin
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | - Qing Han
- Structure Based Design, Inc., San Diego, CA 92121, USA
| | | | - John Teijaro
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mike Royal
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | | | - Robert Allen
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | - Henry Ji
- Sorrento Therapeutics, Inc., San Diego, CA 92121, USA
| | - Hongzhou Lu
- Shenzhen Third People's Hospital, SUSTech, Shenzhen, P.R. China.
| | - Xiao Xu
- ACEA Therapeutics, Inc., San Diego, CA 92121, USA.
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10
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Wu A, Shi K, Wang J, Zhang R, Wang Y. Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors. Eur J Med Chem 2024; 263:115923. [PMID: 37981443 DOI: 10.1016/j.ejmech.2023.115923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.
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Affiliation(s)
- Aijia Wu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kunyu Shi
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Ruofei Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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11
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Vijay Gone N, Ghalib Enayathullah M, Thomas J, Rathee P, Prabhakar R, Kumar Bokara K, Sanjayan GJ. Discovery of SARS-CoV-2 Inhibitors Featuring Novel Histidine α-Nitrile Motif. Chem Biodivers 2023; 20:e202300957. [PMID: 37888938 DOI: 10.1002/cbdv.202300957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 10/28/2023]
Abstract
As COVID-19 infection caused severe public health concerns recently, the development of novel antivirals has become the need of the hour. Main protease (Mpro ) has been an attractive target for antiviral drugs since it plays a vital role in polyprotein processing and virus maturation. Herein we report the discovery of a novel class of inhibitors against the SARS-CoV-2, bearing histidine α-nitrile motif embedded on a simple dipeptide framework. In-vitro and in-silico studies revealed that the histidine α-nitrile motif envisioned to target the Mpro contributes to the inhibitory activity. Among a series of dipeptides synthesized featuring this novel structural motif, some dipeptides displayed strong viral reduction (EC50 =0.48 μM) with a high selectivity index, SI>454.54. These compounds also exhibit strong binding energies in the range of -28.7 to -34.2 Kcal/mol. The simple dipeptide structural framework, amenable to quick structural variations, coupled with ease of synthesis from readily available commercial starting materials are the major attractive features of this novel class of SARS-CoV-2 inhibitors. The histidine α-nitrile dipeptides raise the hope of discovering potent drug candidates based on this motif to fight the dreaded SARS-CoV-2.
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Affiliation(s)
- Nilu Vijay Gone
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohammed Ghalib Enayathullah
- Annexe-II, Medical Biotechnology Complex, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Jessie Thomas
- Annexe-II, Medical Biotechnology Complex, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Kiran Kumar Bokara
- Annexe-II, Medical Biotechnology Complex, CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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12
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Vickos U, Camasta M, Grandi N, Scognamiglio S, Schindler T, Belizaire MRD, Lango-Yaya E, Koyaweda GW, Senzongo O, Pounguinza S, Estimé KKJF, N’yetobouko S, Gadia CLB, Feiganazoui DA, Le Faou A, Orsini M, Perno CF, Zinzula L, Rafaï CD. COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome. Viruses 2023; 15:2309. [PMID: 38140550 PMCID: PMC10748234 DOI: 10.3390/v15122309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.
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Affiliation(s)
- Ulrich Vickos
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
- Department of Medicine, Infectious and Tropical Diseases, Sino-Central African Amitié Hospital, Bangui 94045, Central African Republic
| | - Marianna Camasta
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Sante Scognamiglio
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland;
- Department of Medical Parasitology and Infection Biology, University of Basel, 4051 Basel, Switzerland
| | | | - Ernest Lango-Yaya
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Giscard Wilfried Koyaweda
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Oscar Senzongo
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Simon Pounguinza
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Kaleb Kandou Jephté Francis Estimé
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Stephanie N’yetobouko
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Christelle Luce Bobossi Gadia
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Dominos-Alfred Feiganazoui
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Alain Le Faou
- EA 3452 CITHEFOR, Campus Brabois Santé, 54500 Vandœuvre-lès-Nancy, France;
- Faculty of Medicine, Maieutic and Health Sciences, University of Lorraine, Pole Brabois Santé, 54500 Nancy, France
| | - Massimiliano Orsini
- General and Experimental Microbiology, Laboratory of Microbial Ecology and Genomics of Microorganisms, Experimental Zooprophylactic Institute of the Venezie (IZSVe), 35020 Legnaro, Italy;
| | - Carlo Federico Perno
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
| | - Luca Zinzula
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Clotaire Donatien Rafaï
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
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13
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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14
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Dai R, Gao H, Su R. Computer-aided drug design for virtual-screening and active-predicting of main protease (M pro) inhibitors against SARS-CoV-2. Front Pharmacol 2023; 14:1288363. [PMID: 38026989 PMCID: PMC10661973 DOI: 10.3389/fphar.2023.1288363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: SARS-CoV-2 is a novel coronavirus with highly contagious and has posed a significant threat to global public health. The main protease (Mpro) is a promising target for antiviral drugs against SARS-CoV-2. Methods: In this study, we have used pharmacophore-based drug design technology to identify potential compounds from drug databases as Mpro inhibitors. Results: The procedure involves pharmacophore modeling, validation, and pharmacophore-based virtual screening, which identifies 257 compounds with promising inhibitory activity. Discussion: Molecular docking and non-bonding interactions between the targeted protein Mpro and compounds showed that ENA482732 was the best compound. These results provided a theoretical foundation for future studies of Mpro inhibitors against SARS-CoV-2.
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Affiliation(s)
| | - Hongwei Gao
- School of Life Science, Ludong University, Yantai, Shandong, China
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15
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Costacurta F, Dodaro A, Bante D, Schöppe H, Sprenger B, Moghadasi SA, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (M pro) inhibitor-resistant mutants selected in a VSV-based system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558628. [PMID: 37808638 PMCID: PMC10557589 DOI: 10.1101/2023.09.22.558628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available PIs (nirmatrelvir and ensitrelvir) with cell-based and biochemical assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease-inhibitor-resistance mechanisms and show the relevance of specific mutations in the clinic, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Bernhard Sprenger
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, United States
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, United States
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, Innsbruck, 6020, Tyrol, Austria
| | - Rainer Schneider
- Department of Biochemistry, University of Innsbruck, Innsbruck, 6020, Austria
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, 6020, Tyrol, Austria
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16
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Zhao S, Jiang M, Qing H, Ni J. Cathepsins and SARS-CoV-2 infection: From pathogenic factors to potential therapeutic targets. Br J Pharmacol 2023; 180:2455-2481. [PMID: 37403614 DOI: 10.1111/bph.16187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/04/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection. The COVID-19 pandemic began in March 2020 and has wrought havoc on health and economic systems worldwide. Efficacious treatment for COVID-19 is lacking: Only preventive measures as well as symptomatic and supportive care are available. Preclinical and clinical studies have indicated that lysosomal cathepsins might contribute to the pathogenesis and disease outcome of COVID-19. Here, we discuss cutting-edge evidence on the pathological roles of cathepsins in SARS-CoV-2 infection, host immune dysregulations, and the possible underlying mechanisms. Cathepsins are attractive drug targets because of their defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Accordingly, the potential modulatory strategies of cathepsin activity are discussed. These insights could shed light on the development of cathepsin-based interventions for COVID-19.
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Affiliation(s)
- Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Muzhou Jiang
- Department of Periodontics, Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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17
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Tran N, Dasari S, Barwell SAE, McLeod MJ, Kalyaanamoorthy S, Holyoak T, Ganesan A. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun 2023; 14:5625. [PMID: 37699927 PMCID: PMC10497556 DOI: 10.1038/s41467-023-40023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 07/04/2023] [Indexed: 09/14/2023] Open
Abstract
The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.
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Affiliation(s)
- Norman Tran
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sathish Dasari
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Sarah A E Barwell
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | | | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Todd Holyoak
- Department of Biology, Faculty of Science, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| | - Aravindhan Ganesan
- ArGan's Lab, School of Pharmacy, Faculty of Science, University of Waterloo, 10A Victoria Street South, Kitchener, ON, N2G 1C5, Canada.
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18
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Citarella A, Dimasi A, Moi D, Passarella D, Scala A, Piperno A, Micale N. Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives. Biomolecules 2023; 13:1339. [PMID: 37759739 PMCID: PMC10647625 DOI: 10.3390/biom13091339] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The main protease (Mpro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of Mpro produces a detrimental effect on the course of the infection, making this target one of the most attractive for the treatment of COVID-19. The current success of the SARS-CoV-2 Mpro inhibitor Nirmatrelvir, the first oral drug for the treatment of severe forms of COVID-19, has further focused the attention of researchers on this important viral target, making the search for new Mpro inhibitors a thriving and exciting field for the development of antiviral drugs active against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- Andrea Citarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Alessandro Dimasi
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Davide Moi
- Department of Chemical and Geological Sciences, University of Cagliari, S.P. 8 CA, 09042 Cagliari, Italy;
| | - Daniele Passarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
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19
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Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons LM, Lorenzo‐Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García‐Sastre A, Shoichet BK, Craik CS. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci 2023; 32:e4712. [PMID: 37354015 PMCID: PMC10364469 DOI: 10.1002/pro.4712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023]
Abstract
Antiviral therapeutics to treat SARS-CoV-2 are needed to diminish the morbidity of the ongoing COVID-19 pandemic. A well-precedented drug target is the main viral protease (MPro ), which is targeted by an approved drug and by several investigational drugs. Emerging viral resistance has made new inhibitor chemotypes more pressing. Adopting a structure-based approach, we docked 1.2 billion non-covalent lead-like molecules and a new library of 6.5 million electrophiles against the enzyme structure. From these, 29 non-covalent and 11 covalent inhibitors were identified in 37 series, the most potent having an IC50 of 29 and 20 μM, respectively. Several series were optimized, resulting in low micromolar inhibitors. Subsequent crystallography confirmed the docking predicted binding modes and may template further optimization. While the new chemotypes may aid further optimization of MPro inhibitors for SARS-CoV-2, the modest success rate also reveals weaknesses in our approach for challenging targets like MPro versus other targets where it has been more successful, and versus other structure-based techniques against MPro itself.
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Affiliation(s)
- Elissa A. Fink
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in BiophysicsUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Conner Bardine
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in Chemistry and Chemical BiologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Stefan Gahbauer
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isha Singh
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Tyler C. Detomasi
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Kris White
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Shuo Gu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Xiaobo Wan
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Chen
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Beatrice Ary
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isabella Glenn
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Joseph O'Connell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Henry O'Donnell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Jiankun Lyu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Seth Vigneron
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Nicholas J. Young
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Ivan S. Kondratov
- Enamine Ltd.KyïvUkraine
- V.P. Kukhar Institute of Bioorganic Chemistry and PetrochemistryNational Academy of Sciences of UkraineKyïvUkraine
| | - Arghavan Alisoltani
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Lacy M. Simons
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Ramon Lorenzo‐Redondo
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Egon A. Ozer
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Yurii S. Moroz
- National Taras Shevchenko University of KyïvKyïvUkraine
- Chemspace LLCKyïvUkraine
| | - Jack Taunton
- Department of Cellular and Molecular PharmacologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adam R. Renslo
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - John J. Irwin
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adolfo García‐Sastre
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Medicine, Division of Infectious DiseasesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Brian K. Shoichet
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
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20
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Biolatti M, Blangetti M, Baggieri M, Marchi A, Gioacchini S, Bajetto G, Arnodo D, Bucci P, Fioravanti R, Kojouri M, Bersani M, D'Arrigo G, Siragusa L, Ghinato S, De Andrea M, Gugliesi F, Albano C, Pasquero S, Visentin I, D'Ugo E, Esposito F, Malune P, Tramontano E, Prandi C, Spyrakis F, Magurano F, Dell'Oste V. Strigolactones as Broad-Spectrum Antivirals against β-Coronaviruses through Targeting the Main Protease M pro. ACS Infect Dis 2023; 9:1310-1318. [PMID: 37358826 DOI: 10.1021/acsinfecdis.3c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The current SARS-CoV-2 pandemic and the likelihood that new coronavirus strains will emerge in the immediate future point out the urgent need to identify new pan-coronavirus inhibitors. Strigolactones (SLs) are a class of plant hormones with multifaceted activities whose roles in plant-related fields have been extensively explored. Recently, we proved that SLs also exert antiviral activity toward herpesviruses, such as human cytomegalovirus (HCMV). Here we show that the synthetic SLs TH-EGO and EDOT-EGO impair β-coronavirus replication including SARS-CoV-2 and the common cold human coronavirus HCoV-OC43. Interestingly, in silico simulations suggest the binding of SLs in the SARS-CoV-2 main protease (Mpro) active site, and this was further confirmed by an in vitro activity assay. Overall, our results highlight the potential efficacy of SLs as broad-spectrum antivirals against β-coronaviruses, which may provide the rationale for repurposing this class of hormones for the treatment of COVID-19 patients.
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Affiliation(s)
- Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Marco Blangetti
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Marchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Silvia Gioacchini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Greta Bajetto
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, 28100 Novara, Italy
| | - Davide Arnodo
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Paola Bucci
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Raoul Fioravanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Maedeh Kojouri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Matteo Bersani
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy
| | - Giulia D'Arrigo
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy
| | - Lydia Siragusa
- Molecular Discovery Ltd., Kinetic Business Centre, Elstree, Borehamwood, WD6 4PJ Hertfordshire, United Kingdom
- Molecular Horizon s.r.l., 06084 Bettona (PG), Italy
| | - Simone Ghinato
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, 28100 Novara, Italy
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Ivan Visentin
- Department of Agricultural, Forestry, and Food Sciences, University of Turin, 10095 Grugliasco, Turin, Italy
| | - Emilio D'Ugo
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Paolo Malune
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Cristina Prandi
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy
| | - Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
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21
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Anton DB, Galvez Bulhões Pedreira J, Zvirtes ML, Laufer SA, Ducati RG, Goettert M, Saraiva Macedo Timmers LF. Targeting SARS-CoV-2 Main Protease (MPro) with Kinase Inhibitors: A Promising Approach for Discovering Antiviral and Anti-inflammatory Molecules against SARS-CoV-2. J Chem Inf Model 2023. [PMID: 37329322 DOI: 10.1021/acs.jcim.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infected over 688 million people worldwide, causing public health concern and approximately 6.8 million deaths due to COVID-19. COVID-19, especially severe cases, is characterized by exacerbated lung inflammation with an increase of pro-inflammatory cytokines. In addition to antiviral drugs, there is a need for anti-inflammatory therapies to treat all phases of COVID-19. One of the most attractive drug targets for COVID-19 is the SARS-CoV-2 main protease (MPro), an enzyme responsible for cleaving polyproteins formed after the translation of viral RNA, which is essential for viral replication. MPro inhibitors, therefore, have the potential to stop viral replication and act as antiviral drugs. Considering that several kinase inhibitors are known for their action in inflammatory pathways, this could also be investigated toward a potential anti-inflammatory treatment for COVID-19. Therefore, the use of kinase inhibitors against SARS-CoV-2 MPro may be a promising strategy to find molecules with dual activity─antiviral and anti-inflammatory. Considering this, the potential of six kinase inhibitors against SARS-CoV-2 MPro were evaluated in silico and in vitro, including Baricitinib, Tofacitinib, Ruxolitinib, BIRB-796, Skepinone-L, and Sorafenib. To assess the inhibitory potential of the kinase inhibitors, a continuous fluorescent-based enzyme activity assay was optimized with SARS-CoV-2 MPro and MCA-AVLQSGFR-K(Dnp)-K-NH2 (substrate). BIRB-796 and Baricitinib were identified as inhibitors of SARS-CoV-2 MPro, presenting IC50 values of 7.99 and 25.31 μM, respectively. As they are also known for their anti-inflammatory action, both are prototype compounds with the potential to present antiviral and anti-inflammatory activity against SARS-CoV-2 infection.
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Affiliation(s)
- Débora Bublitz Anton
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Júlia Galvez Bulhões Pedreira
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Maria Luiza Zvirtes
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
| | - Rodrigo Gay Ducati
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Márcia Goettert
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
| | - Luis Fernando Saraiva Macedo Timmers
- Biotechnology Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Department of Medicine, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
- Medical Science Graduate Program, Universidade do Vale do Taquari (Univates), Lajeado CEP 95914-014, Brazil
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22
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Ambrosio FA, Costa G, Romeo I, Esposito F, Alkhatib M, Salpini R, Svicher V, Corona A, Malune P, Tramontano E, Ceccherini-Silberstein F, Alcaro S, Artese A. Targeting SARS-CoV-2 Main Protease: A Successful Story Guided by an In Silico Drug Repurposing Approach. J Chem Inf Model 2023; 63:3601-3613. [PMID: 37227780 DOI: 10.1021/acs.jcim.3c00282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is a crucial enzyme for viral replication and has been considered an attractive drug target for the treatment of COVID-19. In this study, virtual screening techniques and in vitro assays were combined to identify novel Mpro inhibitors starting from around 8000 FDA-approved drugs. The docking analysis highlighted 17 promising best hits, biologically characterized in terms of their Mpro inhibitory activity. Among them, 7 cephalosporins and the oral anticoagulant betrixaban were able to block the enzyme activity in the micromolar range with no cytotoxic effect at the highest concentration tested. After the evaluation of the degree of conservation of Mpro residues involved in the binding with the studied ligands, the ligands' activity on SARS-CoV-2 replication was assessed. The ability of betrixaban to affect SARS-CoV-2 replication associated to its antithrombotic effect could pave the way for its possible use in the treatment of hospitalized COVID-19 patients.
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Affiliation(s)
- Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Mohammad Alkhatib
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Via Montpellier, 1, 00133 Roma, Italy
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Via Montpellier, 1, 00133 Roma, Italy
| | - Valentina Svicher
- Dipartimento di Medicina Sperimentale, Università degli Studi di Roma "Tor Vergata", Via Montpellier, 1, 00133 Roma, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Paolo Malune
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | | | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
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23
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Fumagalli V, Di Lucia P, Ravà M, Marotta D, Bono E, Grassi S, Donnici L, Cannalire R, Stefanelli I, Ferraro A, Esposito F, Pariani E, Inverso D, Montesano C, Delbue S, Perlman S, Tramontano E, De Francesco R, Summa V, Guidotti LG, Iannacone M. Nirmatrelvir treatment of SARS-CoV-2-infected mice blunts antiviral adaptive immune responses. EMBO Mol Med 2023; 15:e17580. [PMID: 36946379 PMCID: PMC10165354 DOI: 10.15252/emmm.202317580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Alongside vaccines, antiviral drugs are becoming an integral part of our response to the SARS-CoV-2 pandemic. Nirmatrelvir-an orally available inhibitor of the 3-chymotrypsin-like cysteine protease-has been shown to reduce the risk of progression to severe COVID-19. However, the impact of nirmatrelvir treatment on the development of SARS-CoV-2-specific adaptive immune responses is unknown. Here, by using mouse models of SARS-CoV-2 infection, we show that nirmatrelvir administration blunts the development of SARS-CoV-2-specific antibody and T cell responses. Accordingly, upon secondary challenge, nirmatrelvir-treated mice recruited significantly fewer memory T and B cells to the infected lungs and mediastinal lymph nodes, respectively. Together, the data highlight a potential negative impact of nirmatrelvir treatment with important implications for clinical management and might help explain the virological and/or symptomatic relapse after treatment completion reported in some individuals.
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Affiliation(s)
- Valeria Fumagalli
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Pietro Di Lucia
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Micol Ravà
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Davide Marotta
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Elisa Bono
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Stefano Grassi
- Pathology UnitIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Lorena Donnici
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
| | - Rolando Cannalire
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Irina Stefanelli
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Anastasia Ferraro
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Elena Pariani
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | - Donato Inverso
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | | | - Serena Delbue
- Department of Biomedical, Surgical and Dental SciencesUniversity of MilanMilanItaly
| | - Stanley Perlman
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIAUSA
- Department of PediatricsUniversity of IowaIowa CityIAUSA
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Raffaele De Francesco
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
- Department of Pharmacological and Biomolecular SciencesUniversity of MilanMilanItaly
| | - Vincenzo Summa
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Luca G Guidotti
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Matteo Iannacone
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
- Experimental Imaging CenterIRCCS San Raffaele Scientific InstituteMilanItaly
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24
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Arafet K, Royo S, Schirmeister T, Barthels F, González FV, Moliner V. Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L. ACS Catal 2023; 13:6289-6300. [PMID: 37180968 PMCID: PMC10167892 DOI: 10.1021/acscatal.3c01035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/10/2023] [Indexed: 05/16/2023]
Abstract
Cysteine proteases (CPs) are an important class of enzymes, many of which are responsible for several human diseases. For instance, cruzain of protozoan parasite Trypanosoma cruzi is responsible for the Chagas disease, while the role of human cathepsin L is associated with some cancers or is a potential target for the treatment of COVID-19. However, despite paramount work carried out during the past years, the compounds that have been proposed so far show limited inhibitory action against these enzymes. We present a study of proposed covalent inhibitors of these two CPs, cruzain and cathepsin L, based on the design, synthesis, kinetic measurements, and QM/MM computational simulations on dipeptidyl nitroalkene compounds. The experimentally determined inhibition data, together with the analysis and the predicted inhibition constants derived from the free energy landscape of the full inhibition process, allowed describing the impact of the recognition part of these compounds and, in particular, the modifications on the P2 site. The designed compounds and, in particular, the one with a bulky group (Trp) at the P2 site show promising in vitro inhibition activities against cruzain and cathepsin L for use as a starting lead compound in the development of drugs with medical applications for the treatment of human diseases and future designs.
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Affiliation(s)
- Kemel Arafet
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, 43124 Parma, Italy
- BioComp
Group, Institute of Advanced Materials (INAM),
Universitat Jaume I, 12071 Castelló, Spain
| | - Santiago Royo
- Departament
de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Tanja Schirmeister
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Fabian Barthels
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Florenci V. González
- Departament
de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM),
Universitat Jaume I, 12071 Castelló, Spain
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25
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Ng R, Zhang G, Li JJ. An update on the discovery and development of reversible covalent inhibitors. Med Chem Res 2023; 32:1039-1062. [PMID: 37305209 PMCID: PMC10148018 DOI: 10.1007/s00044-023-03065-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/18/2023] [Indexed: 06/13/2023]
Abstract
Small molecule drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety. Graphical Abstract
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Affiliation(s)
- Raymond Ng
- Olema Oncology, 512 2nd St., 4th Floor, San Francisco, 94107 CA USA
| | - Guiping Zhang
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
| | - Jie Jack Li
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
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26
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Moghadasi SA, Heilmann E, Khalil AM, Nnabuife C, Kearns FL, Ye C, Moraes SN, Costacurta F, Esler MA, Aihara H, von Laer D, Martinez-Sobrido L, Palzkill T, Amaro RE, Harris RS. Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. SCIENCE ADVANCES 2023; 9:eade8778. [PMID: 36989354 PMCID: PMC10058310 DOI: 10.1126/sciadv.ade8778] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/28/2023] [Indexed: 05/05/2023]
Abstract
Vaccines and drugs have helped reduce disease severity and blunt the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ongoing virus transmission, continuous evolution, and increasing selective pressures have the potential to yield viral variants capable of resisting these interventions. Here, we investigate the susceptibility of natural variants of the main protease [Mpro; 3C-like protease (3CLpro)] of SARS-CoV-2 to protease inhibitors. Multiple single amino acid changes in Mpro confer resistance to nirmatrelvir (the active component of Paxlovid). An additional clinical-stage inhibitor, ensitrelvir (Xocova), shows a different resistance mutation profile. Importantly, phylogenetic analyses indicate that several of these resistant variants have pre-existed the introduction of these drugs into the human population and are capable of spreading. These results encourage the monitoring of resistance variants and the development of additional protease inhibitors and other antiviral drugs with different mechanisms of action and resistance profiles for combinatorial therapy.
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Affiliation(s)
- Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ahmed Magdy Khalil
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Christina Nnabuife
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | | | - Morgan A. Esler
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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27
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Stefanelli I, Corona A, Cerchia C, Cassese E, Improta S, Costanzi E, Pelliccia S, Morasso S, Esposito F, Paulis A, Scognamiglio S, Di Leva FS, Storici P, Brindisi M, Tramontano E, Cannalire R, Summa V. Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination. Eur J Med Chem 2023; 253:115311. [PMID: 37043904 PMCID: PMC10068823 DOI: 10.1016/j.ejmech.2023.115311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Despite the approval of vaccines, monoclonal antibodies and restrictions during the pandemic, the demand for new efficacious and safe antivirals is compelling to boost the therapeutic arsenal against the COVID-19. The viral 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for replication with high homology in the active site across CoVs and variants showing an almost unique specificity for Leu-Gln as P2-P1 residues, allowing the development of broad-spectrum inhibitors. The design, synthesis, biological activity, and cocrystal structural information of newly conceived peptidomimetic covalent reversible inhibitors are herein described. The inhibitors display an aldehyde warhead, a Gln mimetic at P1 and modified P2-P3 residues. Particularly, functionalized proline residues were inserted at P2 to stabilize the β-turn like bioactive conformation, modulating the affinity. The most potent compounds displayed low/sub-nM potency against the 3CLpro of SARS-CoV-2 and MERS-CoV and inhibited viral replication of three human CoVs, i.e. SARS-CoV-2, MERS-CoV, and HCoV 229 in different cell lines. Particularly, derivative 12 exhibited nM-low μM antiviral activity depending on the virus, and the highest selectivity index. Some compounds were co-crystallized with SARS-CoV-2 3CLpro validating our design. Altogether, these results foster future work toward broad-spectrum 3CLpro inhibitors to challenge CoVs related pandemics.
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28
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Shen JX, Du WW, Xia YL, Zhang ZB, Yu ZF, Fu YX, Liu SQ. Identification of and Mechanistic Insights into SARS-CoV-2 Main Protease Non-Covalent Inhibitors: An In-Silico Study. Int J Mol Sci 2023; 24:ijms24044237. [PMID: 36835648 PMCID: PMC9959744 DOI: 10.3390/ijms24044237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
The indispensable role of the SARS-CoV-2 main protease (Mpro) in the viral replication cycle and its dissimilarity to human proteases make Mpro a promising drug target. In order to identify the non-covalent Mpro inhibitors, we performed a comprehensive study using a combined computational strategy. We first screened the ZINC purchasable compound database using the pharmacophore model generated from the reference crystal structure of Mpro complexed with the inhibitor ML188. The hit compounds were then filtered by molecular docking and predicted parameters of drug-likeness and pharmacokinetics. The final molecular dynamics (MD) simulations identified three effective candidate inhibitors (ECIs) capable of maintaining binding within the substrate-binding cavity of Mpro. We further performed comparative analyses of the reference and effective complexes in terms of dynamics, thermodynamics, binding free energy (BFE), and interaction energies and modes. The results reveal that, when compared to the inter-molecular electrostatic forces/interactions, the inter-molecular van der Waals (vdW) forces/interactions are far more important in maintaining the association and determining the high affinity. Given the un-favorable effects of the inter-molecular electrostatic interactions-association destabilization by the competitive hydrogen bond (HB) interactions and the reduced binding affinity arising from the un-compensable increase in the electrostatic desolvation penalty-we suggest that enhancing the inter-molecular vdW interactions while avoiding introducing the deeply buried HBs may be a promising strategy in future inhibitor optimization.
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Affiliation(s)
- Jian-Xin Shen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Wen-Wen Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Bi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Ze-Fen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Human Genetics Center and Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
- Correspondence: (Y.-X.F.); (S.-Q.L.)
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
- Correspondence: (Y.-X.F.); (S.-Q.L.)
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29
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Structure-based lead optimization of peptide-based vinyl methyl ketones as SARS-CoV-2 main protease inhibitors. Eur J Med Chem 2023; 247:115021. [PMID: 36549112 PMCID: PMC9751013 DOI: 10.1016/j.ejmech.2022.115021] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Despite several major achievements in the development of vaccines and antivirals, the fight against SARS-CoV-2 and the health problems accompanying COVID-19 are still ongoing. SARS-CoV-2 main protease (Mpro), an essential viral cysteine protease, is a crucial target for the development of antiviral agents. A virtual screening analysis of in-house cysteine protease inhibitors against SARS-CoV-2 Mpro allowed us to identify two hits (i.e., 1 and 2) bearing a methyl vinyl ketone warhead. Starting from these compounds, we herein report the development of Michael acceptors targeting SARS-CoV-2 Mpro, which differ from each other for the warhead and for the amino acids at the P2 site. The most promising vinyl methyl ketone-containing analogs showed sub-micromolar activity against the viral protease. SPR38, SPR39, and SPR41 were fully characterized, and additional inhibitory properties towards hCatL, which plays a key role in the virus entry into host cells, were observed. SPR39 and SPR41 exhibited single-digit micromolar EC50 values in a SARS-CoV-2 infection model in cell culture.
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30
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Thabet RH, Massadeh NA, Badarna OB, Al-Momani OM. Highlights on molecular targets in the management of COVID-19: Possible role of pharmacogenomics. J Int Med Res 2023; 51:3000605231153764. [PMID: 36717541 PMCID: PMC9893104 DOI: 10.1177/03000605231153764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
By the end of 2022, there had been a reduction in new cases and deaths caused by coronavirus disease 2019 (COVID-19). At the same time, new variants of the severe acute respiratory syndrome coronavirus 2 virus were being discovered. Critically ill patients with COVID-19 have been found to have high serum levels of proinflammatory cytokines, especially interleukin (IL)-6. COVID-19-related mortality has been attributed in most cases to the cytokine storm caused by increased levels of inflammatory cytokines. Dexamethasone in low doses and immunomodulators such as IL-6 inhibitors are recommended to overcome the cytokine storm. This current narrative review highlights the place of other therapeutic choices such as proteasome inhibitors, protease inhibitors and nuclear factor kappa B inhibitors in the treatment of patients with COVID-19.
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Affiliation(s)
- Romany H. Thabet
- Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, Egypt,Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan,Romany H. Thabet, Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Shafiq Irshidat Street, Irbid 21163, Jordan.
| | - Noor A. Massadeh
- Internship, Princess Basma Hospital, Ministry of Health, Irbid, Jordan
| | - Omar B. Badarna
- Internship, Princess Basma Hospital, Ministry of Health, Irbid, Jordan
| | - Omar M. Al-Momani
- Internship, Princess Basma Hospital, Ministry of Health, Irbid, Jordan
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31
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Pelliccia S, Cerchia C, Esposito F, Cannalire R, Corona A, Costanzi E, Kuzikov M, Gribbon P, Zaliani A, Brindisi M, Storici P, Tramontano E, Summa V. Easy access to α-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route. Eur J Med Chem 2022; 244:114853. [PMID: 36332546 PMCID: PMC9575579 DOI: 10.1016/j.ejmech.2022.114853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 caused worldwide the current outbreak called COVID-19. Despite multiple countermeasures implemented, there is an urgent global need for new potent and efficient antiviral drugs against this pathogen. In this context, the main protease (Mpro) of SARS-CoV-2 is an essential viral enzyme and plays a pivotal role in viral replication and transcription. Its specific cleavage of polypeptides after a glutamine residue has been considered as a key element to design novel antiviral drugs. Herein, we reported the design, synthesis and structure-activity relationships of novel α-ketoamides as covalent reversible inhibitors of Mpro, exploiting the PADAM oxidation route. The reported compounds showed μM to nM activities in enzymatic and in the antiviral cell-based assays against SARS-CoV-2 Mpro. In order to assess inhibitors’ binding mode, two co-crystal structures of SARS-CoV-2 Mpro in complex with our inhibitors were solved, which confirmed the covalent binding of the keto amide moiety to the catalytic Cys145 residue of Mpro. Finally, in order to interrogate potential broad-spectrum properties, we assessed a selection of compounds against MERS Mpro where they showed nM inhibitory potency, thus highlighting their potential as broad-spectrum coronavirus inhibitors.
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Affiliation(s)
- Sveva Pelliccia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy,Corresponding author
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Angela Corona
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra - Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, Trieste, Basovizza, 34149, Italy
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759, Bremen, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Margherita Brindisi
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Paola Storici
- Protein Facility, Elettra - Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, Trieste, Basovizza, 34149, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy,Corresponding author
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32
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La Monica G, Bono A, Lauria A, Martorana A. Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives. J Med Chem 2022; 65:12500-12534. [PMID: 36169610 PMCID: PMC9528073 DOI: 10.1021/acs.jmedchem.2c01005] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Indexed: 02/07/2023]
Abstract
The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors.
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Affiliation(s)
| | | | - Antonino Lauria
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
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Hu Q, Xiong Y, Zhu GH, Zhang YN, Zhang YW, Huang P, Ge GB. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3‐chymotrypsin‐like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β‐coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus‐caused infectious diseases, including COVID‐19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS‐CoV‐2 3CLpro inhibitors. To better understand the characteristics of SARS‐CoV‐2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non‐peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti‐coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS‐CoV‐2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti‐coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China.,Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Guang-Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Ya-Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
| | - Yi-Wen Zhang
- Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Ping Huang
- Clinical Pharmacy Center Cancer Center Department of Pharmacy Zhejiang Provincial People's Hospital Affiliated People's Hospital Hangzhou Medical College, Hangzhou Zhejiang China
| | - Guang-Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology Institute of Interdisciplinary Integrative Medicine Research Shanghai University of Traditional Chinese Medicine Shanghai China
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Proteases and Their Potential Role as Biomarkers and Drug Targets in Dry Eye Disease and Ocular Surface Dysfunction. Int J Mol Sci 2022; 23:ijms23179795. [PMID: 36077189 PMCID: PMC9456293 DOI: 10.3390/ijms23179795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Dry eye disease (DED) is a multifactorial disorder that leads to ocular discomfort, visual disturbance, and tear film instability. DED is accompanied by an increase in tear osmolarity and ocular surface inflammation. The diagnosis and treatment of DED still present significant challenges. Therefore, novel biomarkers and treatments are of great interest. Proteases are present in different tissues on the ocular surface. In a healthy eye, proteases are highly regulated. However, dysregulation occurs in various pathologies, including DED. With this review, we provide an overview of the implications of different families of proteases in the development and severity of DED, along with studies involving protease inhibitors as potential therapeutic tools. Even though further research is needed, this review aims to give suggestions for identifying novel biomarkers and developing new protease inhibitors.
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Abstract
The main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here, we report quantitative reporters for Mpro function in living cells in which protease inhibition by genetic or chemical methods results in robust signal readouts by fluorescence (enhanced green fluorescent protein [eGFP]) or bioluminescence (firefly luciferase). These gain-of-signal systems are scalable to high-throughput platforms for quantitative discrimination between Mpro mutants and/or inhibitor potencies as evidenced by validation of several reported inhibitors. Additional utility is shown by single Mpro amino acid variants and structural information combining to demonstrate that both inhibitor conformational dynamics and amino acid differences are able to influence inhibitor potency. We further show that a recent variant of concern (Omicron) has an unchanged response to a clinically approved drug, nirmatrelvir, whereas proteases from divergent coronavirus species show differential susceptibility. Together, we demonstrate that these gain-of-signal systems serve as robust, facile, and scalable assays for live cell quantification of Mpro inhibition, which will help expedite the development of next-generation antivirals and enable the rapid testing of emerging variants. IMPORTANCE The main protease, Mpro, of SARS-CoV-2 is an essential viral protein required for the earliest steps of infection. It is therefore an attractive target for antiviral drug development. Here, we report the development and implementation of two complementary cell-based systems for quantification of Mpro inhibition by genetic or chemical approaches. The first is fluorescence based (eGFP), and the second is luminescence based (firefly luciferase). Importantly, both systems rely upon gain-of-signal readouts such that stronger inhibitors yield higher fluorescent or luminescent signal. The high versatility and utility of these systems are demonstrated by characterizing Mpro mutants and natural variants, including Omicron, as well as a panel of existing inhibitors. These systems rapidly, safely, and sensitively identify Mpro variants with altered susceptibilities to inhibition, triage-nonspecific, or off-target molecules and validate bona fide inhibitors, with the most potent thus far being the first-in-class drug nirmatrelvir.
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Hicks EG, Kandel SE, Lampe JN. Identification of Aloe-derived natural products as prospective lead scaffolds for SARS-CoV-2 main protease (M pro) inhibitors. Bioorg Med Chem Lett 2022; 66:128732. [PMID: 35427739 PMCID: PMC9004148 DOI: 10.1016/j.bmcl.2022.128732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
In the past two years, the COVID-19 pandemic has caused over 5 million deaths and 250 million infections worldwide. Despite successful vaccination efforts and emergency approval of small molecule therapies, a diverse range of antivirals is still needed to combat the inevitable resistance that will arise from new SARS-CoV-2 variants. The main protease of SARS-CoV-2 (Mpro) is an attractive drug target due to the clinical success of protease inhibitors against other viruses, such as HIV and HCV. However, in order to combat resistance, various chemical scaffolds need to be identified that have the potential to be developed into potent inhibitors. To this end, we screened a high-content protease inhibitor library against Mproin vitro, in order to identify structurally diverse compounds that could be further developed into antiviral leads. Our high-content screening efforts retrieved 27 hits each with > 50% inhibition in our Mpro FRET assay. Of these, four of the top inhibitor compounds were chosen for follow-up due to their potency and drugability (Lipinski's rules of five criteria): anacardic acid, aloesin, aloeresin D, and TCID. Further analysis via dose response curves revealed IC50 values of 6.8 μM, 38.9 μM, 125.3 μM, and 138.0 μM for each compound, respectively. Molecular docking studies demonstrated that the four inhibitors bound at the catalytic active site of Mpro with varying binding energies (-7.5 to -5.6 kcal/mol). Furthermore, Mpro FRET assay kinetic studies demonstrated that Mpro catalysis is better represented by a sigmoidal Hill model than the standard Michaelis-Menten hyperbola, indicating substantial cooperativity of the active enzyme dimer. This result suggests that the dimerization interface could be an attractive target for allosteric inhibitors. In conclusion, we identified two closely-related natural product compounds from the Aloe plant (aloesin and aloeresin D) that may serve as novel scaffolds for Mpro inhibitor design and additionally confirmed the strongly cooperative kinetics of Mpro proteolysis. These results further advance our knowledge of structure-function relationships in Mpro and offer new molecular scaffolds for inhibitor design.
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Affiliation(s)
- Emily G Hicks
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, CO 80045, United States
| | - Sylvie E Kandel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, CO 80045, United States
| | - Jed N Lampe
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy, University of Colorado, Aurora, CO 80045, United States.
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Potential Drug Discovery for COVID-19 Treatment Targeting Cathepsin L Using a Deep Learning-Based Strategy. Comput Struct Biotechnol J 2022; 20:2442-2454. [PMID: 35602976 PMCID: PMC9110316 DOI: 10.1016/j.csbj.2022.05.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 01/06/2023] Open
Abstract
Cathepsin L(CTSL) is a promising therapeutic target for COVID-19. A new deep learning model was used to predict CTSL inhibitor based on structure. 5 molecules for inhibiting CTSL and treating COVID-19 at nmol level were identified. Daptomycin can distinctly inhibit CTSL and has potential for COVID-19 treatment.
Cathepsin L (CTSL), a cysteine protease that can cleave and activate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, could be a promising therapeutic target for coronavirus disease 2019 (COVID-19). However, there is still no clinically available CTSL inhibitor that can be used. Here, we applied Chemprop, a newly trained directed-message passing deep neural network approach, to identify small molecules and FDA-approved drugs that can block CTSL activity to expand the discovery of CTSL inhibitors for drug development and repurposing for COVID-19. We found 5 molecules (Mg-132, Z-FA-FMK, leupeptin hemisulfate, Mg-101 and calpeptin) that were able to significantly inhibit the activity of CTSL in the nanomolar range and inhibit the infection of both pseudotype and live SARS-CoV-2. Notably, we discovered that daptomycin, an FDA-approved antibiotic, has a prominent CTSL inhibitory effect and can inhibit SARS-CoV-2 pseudovirus infection. Further, molecular docking calculation showed stable and robust binding of these compounds with CTSL. In conclusion, this study suggested for the first time that Chemprop is ideally suited to predict additional inhibitors of enzymes and revealed the noteworthy strategy for screening novel molecules and drugs for the treatment of COVID-19 and other diseases with unmet needs.
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Vázquez-Mendoza LH, Mendoza-Figueroa HL, García-Vázquez JB, Correa-Basurto J, García-Machorro J. In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking. Int J Mol Sci 2022; 23:ijms23073987. [PMID: 35409348 PMCID: PMC8999907 DOI: 10.3390/ijms23073987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The epidemic caused by the SARS-CoV-2 coronavirus, which has spread rapidly throughout the world, requires urgent and effective treatments considering that the appearance of viral variants limits the efficacy of vaccines. The main protease of SARS-CoV-2 (Mpro) is a highly conserved cysteine proteinase, fundamental for the replication of the coronavirus and with a specific cleavage mechanism that positions it as an attractive therapeutic target for the proposal of irreversible inhibitors. A structure-based strategy combining 3D pharmacophoric modeling, virtual screening, and covalent docking was employed to identify the interactions required for molecular recognition, as well as the spatial orientation of the electrophilic warhead, of various drugs, to achieve a covalent interaction with Cys145 of Mpro. The virtual screening on the structure-based pharmacophoric map of the SARS-CoV-2 Mpro in complex with an inhibitor N3 (reference compound) provided high efficiency by identifying 53 drugs (FDA and DrugBank databases) with probabilities of covalent binding, including N3 (Michael acceptor) and others with a variety of electrophilic warheads. Adding the energy contributions of affinity for non-covalent and covalent docking, 16 promising drugs were obtained. Our findings suggest that the FDA-approved drugs Vaborbactam, Cimetidine, Ixazomib, Scopolamine, and Bicalutamide, as well as the other investigational peptide-like drugs (DB04234, DB03456, DB07224, DB7252, and CMX-2043) are potential covalent inhibitors of SARS-CoV-2 Mpro.
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Affiliation(s)
- Luis Heriberto Vázquez-Mendoza
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Humberto L. Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
- Correspondence: (H.L.M.-F.); (J.B.G.-V.)
| | - Juan Benjamín García-Vázquez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
- Cátedras CONACyT-Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico
- Correspondence: (H.L.M.-F.); (J.B.G.-V.)
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Jazmín García-Machorro
- Laboratorio de Medicina de la Conservación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico;
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Narayanan A, Narwal M, Majowicz SA, Varricchio C, Toner SA, Ballatore C, Brancale A, Murakami KS, Jose J. Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay. Commun Biol 2022; 5:169. [PMID: 35217718 PMCID: PMC8881501 DOI: 10.1038/s42003-022-03090-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/01/2022] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 proteases Mpro and PLpro are promising targets for antiviral drug development. In this study, we present an antiviral screening strategy involving a novel in-cell protease assay, antiviral and biochemical activity assessments, as well as structural determinations for rapid identification of protease inhibitors with low cytotoxicity. We identified eight compounds with anti-SARS-CoV-2 activity from a library of 64 repurposed drugs and modeled at protease active sites by in silico docking. We demonstrate that Sitagliptin and Daclatasvir inhibit PLpro, and MG-101, Lycorine HCl, and Nelfinavir mesylate inhibit Mpro of SARS-CoV-2. The X-ray crystal structure of Mpro in complex with MG-101 shows a covalent bond formation between the inhibitor and the active site Cys145 residue indicating its mechanism of inhibition is by blocking the substrate binding at the active site. Thus, we provide methods for rapid and effective screening and development of inhibitors for blocking virus polyprotein processing as SARS-CoV-2 antivirals. Additionally, we show that the combined inhibition of Mpro and PLpro is more effective in inhibiting SARS-CoV-2 and the delta variant.
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Affiliation(s)
- Anoop Narayanan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Manju Narwal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sydney A Majowicz
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Carmine Varricchio
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - Shay A Toner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, CF10 3NB, Cardiff, UK
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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Saeed A, Ahmad B, Majaz S, Nouroz F, Ahmad A, Xie Y. Targeting Omicron and other reported SARS-CoV-2 lineages by Potent inhibitors of Main Protease 3CL Mpro: Molecular Simulation Analysis. J Infect 2022; 84:e133-e136. [PMID: 35183608 PMCID: PMC8851874 DOI: 10.1016/j.jinf.2022.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Aamir Saeed
- Department of Bioinformatics, Hazara University, Mansehra 21300, Pakistan
| | - Basharat Ahmad
- Department of Bioinformatics, Hazara University, Mansehra 21300, Pakistan
| | - Sidra Majaz
- Department of Bioinformatics, Hazara University, Mansehra 21300, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University, Mansehra 21300, Pakistan
| | - Ashfaq Ahmad
- Department of Bioinformatics, Hazara University, Mansehra 21300, Pakistan.
| | - Yingqiu Xie
- Biology Department, Nazarbayev University, Nur-Sultan 010000, Kazakhstan.
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