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Coutant F, Touret F, Pin JJ, Alonzo M, Baronti C, Munier S, Attia M, de Lamballerie X, Ferry T, Miossec P. Neutralizing and enhancing monoclonal antibodies in SARS-CoV-2 convalescent patients: lessons from early variant infection and impact on shaping emerging variants. Emerg Microbes Infect 2024; 13:2307510. [PMID: 38240255 PMCID: PMC10829827 DOI: 10.1080/22221751.2024.2307510] [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: 10/03/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Serological studies of COVID-19 convalescent patients have identified polyclonal lineage-specific and cross-reactive antibodies (Abs), with varying effector functions against virus variants. Individual specificities of anti-SARS-CoV-2 Abs and their impact on infectivity by other variants have been little investigated to date. Here, we dissected at a monoclonal level neutralizing and enhancing Abs elicited by early variants and how they affect infectivity of emerging variants. B cells from 13 convalescent patients originally infected by D614G or Alpha variants were immortalized to isolate 445 naturally-produced anti-SARS-CoV-2 Abs. Monoclonal antibodies (mAbs) were tested for their abilities to impact the cytopathic effect of D614G, Delta, and Omicron (BA.1) variants. Ninety-eight exhibited robust neutralization against at least one of the three variant types, while 309 showed minimal or no impact on infectivity. Thirty-eight mAbs enhanced infectivity of SARS-CoV-2. Infection with D614G/Alpha variants generated variant-specific (65 neutralizing Abs, 35 enhancing Abs) and cross-reactive (18 neutralizing Abs, 3 enhancing Abs) mAbs. Interestingly, among the neutralizing mAbs with cross-reactivity restricted to two of the three variants tested, none demonstrated specific neutralization of the Delta and Omicron variants. In contrast, cross-reactive mAbs enhancing infectivity (n = 3) were found exclusively specific to Delta and Omicron variants. Notably, two mAbs that amplified in vitro the cytopathic effect of the Delta variant also exhibited neutralization against Omicron. These findings shed light on functional diversity of cross-reactive Abs generated during SARS-CoV-2 infection and illustrate how the balance between neutralizing and enhancing Abs facilitate variant emergence.
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Affiliation(s)
- Frédéric Coutant
- Immunogenomics and Inflammation Research Team, University of Lyon, Edouard Herriot Hospital, Lyon, France
- Immunology Department, Lyon-Sud Hospital, Hospices Civils of Lyon, Pierre-Bénite, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Jean-Jacques Pin
- Eurobio Scientific/Dendritics – Edouard Herriot Hospital, Lyon, France
| | - Marina Alonzo
- Immunogenomics and Inflammation Research Team, University of Lyon, Edouard Herriot Hospital, Lyon, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Sandie Munier
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses Unit, Paris, France
| | - Mikaël Attia
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses Unit, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Tristan Ferry
- Department of Infectious and Tropical Diseases, Hospices Civils of Lyon - Croix-Rousse Hospital, Lyon, France
- CIRI, Inserm U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon I, Lyon, France
| | - Pierre Miossec
- Immunogenomics and Inflammation Research Team, University of Lyon, Edouard Herriot Hospital, Lyon, France
- Department of Immunology and Rheumatology, Edouard Herriot Hospital, Lyon, France
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Martins DOS, Ruiz UEA, Santos IA, Oliveira IS, Guevara-Vega M, de Paiva REF, Abbehausen C, Sabino-Silva R, Corbi PP, Jardim ACG. Exploring the antiviral activities of the FDA-approved drug sulfadoxine and its derivatives against Chikungunya virus. Pharmacol Rep 2024; 76:1147-1159. [PMID: 39150661 DOI: 10.1007/s43440-024-00635-z] [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: 02/16/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND Currently, there is no antiviral licensed to treat chikungunya fever, a disease caused by the infection with Alphavirus chikungunya (CHIKV). Treatment is based on analgesic and anti-inflammatory drugs to relieve symptoms. Our study aimed to evaluate the antiviral activity of sulfadoxine (SFX), an FDA-approved drug, and its derivatives complexed with silver(I) (AgSFX), salicylaldehyde Schiff base (SFX-SL), and with both Ag and SL (AgSFX-SL) against CHIKV. METHODS The anti-CHIKV activity of SFX and its derivatives was investigated using BHK-21 cells infected with CHIKV-nanoluc, a marker virus-carrying nanoluciferase reporter. Dose-response and time of drug-addition assays were performed in order to assess the antiviral effects of the compounds, as well as in silico data and ATR-FTIR analysis for insights on their mechanisms of action. RESULTS The SFX inhibited 34% of CHIKV replication, while AgSFX, SFX-SL, and AgSFX-SL enhanced anti-CHIKV activity to 84%, 89%, and 95%, respectively. AgSFX, SFX-SL, and AgSFX-SL significantly decreased viral entry and post-entry to host cells, and the latter also protected cells against infection. Additionally, molecular docking calculations and ATR-FTIR analysis demonstrated interactions of SFX-SL, AgSFX, and AgSFX-SL with CHIKV. CONCLUSIONS Collectively, our findings suggest that the addition of metal ions and/or Schiff base to SFX improved its antiviral activity against CHIKV.
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Affiliation(s)
- Daniel Oliveira Silva Martins
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
- Institute of Bioscience, Language and Exact Sciences - IBILCE, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Uriel Enrique Aquino Ruiz
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | - Igor Andrade Santos
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | | | - Marco Guevara-Vega
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | | | - Camilla Abbehausen
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Robinson Sabino-Silva
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | - Pedro Paulo Corbi
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil.
- Institute of Bioscience, Language and Exact Sciences - IBILCE, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil.
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Ghorbanalipoor S, Matsumoto K, Gross N, Heimberg L, Krause M, Veldkamp W, Magens M, Zanken J, Neuschutz KJ, De Luca DA, Kridin K, Vidarsson G, Chakievska L, Visser R, Kunzel S, Recke A, Gupta Y, Boch K, Vorobyev A, Kalies K, Manz RA, Bieber K, Ludwig RJ. High throughput screening identifies repurposable drugs for modulation of innate and acquired immune responses. J Autoimmun 2024; 148:103302. [PMID: 39163739 DOI: 10.1016/j.jaut.2024.103302] [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: 12/06/2023] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 08/22/2024]
Abstract
A balanced immune system is essential to maintain adequate host defense and effective self-tolerance. While an immune system that fails to generate appropriate response will permit infections to develop, uncontrolled activation may lead to autoinflammatory or autoimmune diseases. To identify drug candidates capable of modulating immune cell functions, we screened 1200 small molecules from the Prestwick Chemical Library for their property to inhibit innate or adaptive immune responses. Our studies focused specifically on drug interactions with T cells, B cells, and polymorphonuclear leukocytes (PMNs). Candidate drugs that were validated in vitro were examined in preclinical models to determine their immunomodulatory impact in chronic inflammatory diseases, here investigated in chronic inflammatory skin diseases. Using this approach, we identified several candidate drugs that were highly effective in preclinical models of chronic inflammatory disease. For example, we found that administration of pyrvinium pamoate, an FDA-approved over-the-counter anthelmintic drug, suppressed B cell activation in vitro and halted the progression of B cell-dependent experimental pemphigoid by reducing numbers of autoantigen-specific B cell responses. In addition, in studies performed in gene-deleted mouse strains provided additional insight into the mechanisms underlying these effects, for example, the receptor-dependent actions of tamoxifen that inhibit immune-complex-mediated activation of PMNs. Collectively, our methods and findings provide a vast resource that can be used to identify drugs that may be repurposed and used to promote or inhibit cellular immune responses.
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Affiliation(s)
| | - Kazuko Matsumoto
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Natalie Gross
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Linda Heimberg
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Malin Krause
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Wendelien Veldkamp
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Moritz Magens
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Johannes Zanken
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Kerstin J Neuschutz
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - David A De Luca
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Khalaf Kridin
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Gestur Vidarsson
- Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Lenche Chakievska
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Remco Visser
- Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Sven Kunzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andreas Recke
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Yask Gupta
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Katharina Boch
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Artem Vorobyev
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Rudolf A Manz
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
| | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Department of Dermatology, University of Lübeck, Lübeck, Germany
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Driouich JS, Cochin M, Lingas G, Luciani L, Baronti C, Bernadin O, Gilles M, Villarroel PMS, Moureau G, Petit PR, Dupont A, Izopet J, Kamar N, Autran B, Paintaud G, Caillard S, le Bourgeois A, Richez C, Couzi L, Xhaard A, Marjanovic Z, Avouac J, Jacquet C, Anglicheau D, Cheminant M, Nguyen S, Terrier B, Gottenberg JE, Besson C, Letrou S, Tine J, Basilua JM, Angoulvant D, Tardivon C, Blancho G, Martin-Blondel G, Yazdanpanah Y, Mentré F, Lévy V, Touret F, Guedj J, de Lamballerie X, Nougairède A. Preclinical in vivo assessment of the activity of AZD7442 anti-SARS-CoV-2 monoclonal antibodies against Omicron sublineages. Biomed Pharmacother 2024; 177:116988. [PMID: 38897157 DOI: 10.1016/j.biopha.2024.116988] [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: 12/05/2023] [Revised: 06/11/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024] Open
Abstract
Therapeutic monoclonal antibodies have been successful in protecting vulnerable populations against SARS-CoV-2. However, their effectiveness has been hampered by the emergence of new variants. To adapt the therapeutic landscape, health authorities have based their recommendations mostly on in vitro neutralization tests. However, these do not provide a reliable understanding of the changes in the dose-effect relationship and how they may translate into clinical efficacy. Taking the example of EvusheldTM (AZD7442), we aimed to investigate how in vivo data can provide critical quantitative results and project clinical effectiveness. We used the Golden Syrian hamster model to estimate 90 % effective concentrations (EC90) of AZD7442 in vivo against SARS-CoV-2 Omicron BA.1, BA.2 and BA.5 variants. While our in vivo results confirmed the partial loss of AZD7442 activity for BA.1 and BA.2, they showed a much greater loss of efficacy against BA.5 than that obtained in vitro. We analyzed in vivo EC90s in perspective with antibody levels measured in a cohort of immunocompromised patients who received 300 mg of AZD7442. We found that a substantial proportion of patients had serum levels of anti-SARS-CoV-2 spike protein IgG above the estimated in vivo EC90 for BA.1 and BA.2 (21 % and 92 % after 1 month, respectively), but not for BA.5. These findings suggest that AZD7442 is likely to retain clinical efficacy against BA.2 and BA.1, but not against BA.5. Overall, the present study illustrates the importance of complementing in vitro investigations by preclinical studies in animal models to help predict the efficacy of monoclonal antibodies in humans.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- SARS-CoV-2/drug effects
- Mesocricetus
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/immunology
- COVID-19/immunology
- COVID-19/virology
- Humans
- Cricetinae
- COVID-19 Drug Treatment
- Female
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Male
- Disease Models, Animal
- Betacoronavirus/immunology
- Betacoronavirus/drug effects
- Drug Evaluation, Preclinical/methods
- Antiviral Agents/pharmacology
- Antiviral Agents/therapeutic use
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Affiliation(s)
- Jean-Sélim Driouich
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France.
| | - Maxime Cochin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | | | - Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Ornéllie Bernadin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Magali Gilles
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | | | - Grégory Moureau
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Paul-Rémi Petit
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Axelle Dupont
- Université de Paris Cité, IAME, INSERM, Paris F-75018, France; AP-HP, Hôpital Bichat, Département d'Épidémiologie, Biostatistique et Recherche Clinique, Paris F-75018, France
| | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, National Reference Center for Hepatitis E, Toulouse 31300, France; Inserm UMR 1291, CNRS UMR5051, Université Toulouse III, Toulouse 31000, France
| | - Nassim Kamar
- Département de Néphrologie et Transplantation d'Organes, CHU Rangueil, Toulouse 31059, France
| | - Brigitte Autran
- Sorbonne-Université, Cimi-Paris, Inserm U1135, CNRS ERL8255, UPMC CR7, Team "NK and T Cell Immunity, Infections and Cancer", Paris, France
| | - Gilles Paintaud
- Université de Tours, EA4245 Transplantation, Immunology and Inflammation, Tours, France
| | - Sophie Caillard
- Department of Nephrology and Transplantation, Strasbourg University Hospital, Strasbourg 67000, France; Inserm UMR S1109 Labex Transplantex, Fédération de Médecine Translationnelle, Strasbourg University, Strasbourg, France
| | - Amandine le Bourgeois
- Service d'hématologie clinique, CHU Nantes, 1 place Alexis Ricordeau, Nantes 44000, France
| | - Christophe Richez
- Hôpital Pellegrin, CHU de Bordeaux, Service de Rhumatologie, Centre de référence des maladies autoimmunes systémiques rares (RESO), UMR-CNRS 5164, Université de Bordeaux, Bordeaux, France
| | - Lionel Couzi
- Nephrologie-Transplantation-Dialyse, CHU Bordeaux, Bordeaux, France; CNRS-UMR 5164 Immuno ConcEpT, Université de Bordeaux, Bordeaux, France
| | - Aliénor Xhaard
- Service d'hématologie greffe Hôpital Saint-Louis, APHP, Université de Paris Cité, Paris, France
| | - Zora Marjanovic
- Sorbonne University, Paris, France; Service d'Hématologie Clinique et Thérapie Cellulaire, Hôpital Saint-Antoine, AP-HP, Paris, France; INSERM, UMRs 938, Paris, France
| | - Jerome Avouac
- Université de Paris Service de Rhumatologie, Hôpital Cochin, AP-HP, CUP, 27 rue du Faubourg Saint-Jacques, Paris 75014, France
| | - Caroline Jacquet
- Service d'Hématologie, CHRU Nancy, Hôpitaux Brabois, Vandoeuvre les Nancy, France
| | - Dany Anglicheau
- Department of Nephrology and kidney transplantation, Necker Hospital, APHP and Université de Paris Cité, Paris, France
| | - Morgane Cheminant
- Clinical Hematology, Necker-Enfants Malades University Hospital, AP-HP, F-75015, Université de Paris Cité, Paris, France
| | - Stéphanie Nguyen
- Sorbonne université, Groupe Hospitalier Pitié-Salpêtrière APHP, Service d'Hématologie clinique, Pavillon Georges Heuyer, 47-83 boulevard de l'Hôpital, Paris Cedex 13 75651, France; Sorbonne Université, Inserm CNRS 1135 "NK and T Cell Immunity, Virus and Cancer", Centre d'Immunologie et des Pathologies Infectieuses (CIMI), UPMC UMRS CR7-Inserm U1135-CNRS ERL 8255, faculté de Médecine Sorbonne Université, Site Pitié-Salpêtrière, 91 boulevard de l'Hôpital, Paris 75013, France
| | - Benjamin Terrier
- Assistance Publique-Hôpitaux de Paris, Département de Médecine Interne, Centre de Référence National pour les maladies auto-immunes systémiques rares, Hôpital Cochin Paris, Université Paris, France
| | - Jacques Eric Gottenberg
- Service de Rhumatologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; CNR RESO, Hôpitaux Universitaires de Strasbourg, Strasbourg 67000, France; Laboratoire d'Immunopathologie et de Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR3572, Strasbourg, France
| | - Caroline Besson
- Université Paris-Saclay, UVSQ, CESP-INSERM1018, CH de Versailles, Le Chesnay 78150, France
| | - Sophie Letrou
- AP-HP, Hôpital Bichat, Département d'Épidémiologie, Biostatistique et Recherche Clinique, Paris F-75018, France
| | - Josephine Tine
- ANRS|Emerging Infectious Diseases, Department of Clinical Research, Paris, France
| | | | - Denis Angoulvant
- Service de Cardiologie, CHRU de Tours & UMR Inserm 1327 ISCHEMIA "Membrane Signaling and Inflammation in Reperfusion Injuries", Université de Tours, Tours F37000, France
| | - Coralie Tardivon
- AP-HP, Hôpital Bichat, Département d'Épidémiologie, Biostatistique et Recherche Clinique, Paris F-75018, France
| | - Gilles Blancho
- CHU Nantes, Nantes Université, Service de Néphrologie - Immunologie Clinique, ITUN, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes F-44000, France
| | - Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, CHU de Toulouse & Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, France
| | | | - France Mentré
- Université de Paris Cité, IAME, INSERM, Paris F-75018, France; AP-HP, Hôpital Bichat, Département d'Épidémiologie, Biostatistique et Recherche Clinique, Paris F-75018, France
| | - Vincent Lévy
- Département de Recherche Clinique, Hôpital Avicenne, APHP, Université Sorbonne Paris Nord and CRESS INSERM U1153, ECSTRRA Team, Paris, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Jérémie Guedj
- Université de Paris Cité, IAME, INSERM, Paris F-75018, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), France.
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Franco LS, de Jesus BDSM, Pinheiro PDSM, Fraga CAM. Remapping the Chemical Space and the Pharmacological Space of Drugs: What Can We Expect from the Road Ahead? Pharmaceuticals (Basel) 2024; 17:742. [PMID: 38931408 PMCID: PMC11207054 DOI: 10.3390/ph17060742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/26/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
This work examines the current landscape of drug discovery and development, with a particular focus on the chemical and pharmacological spaces. It emphasizes the importance of understanding these spaces to anticipate future trends in drug discovery. The use of cheminformatics and data analysis enabled in silico exploration of these spaces, allowing a perspective of drugs, approved drugs after 2020, and clinical candidates, which were extracted from the newly released ChEMBL34 (March 2024). This perspective on chemical and pharmacological spaces enables the identification of trends and areas to be occupied, thereby creating opportunities for more effective and targeted drug discovery and development strategies in the future.
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Affiliation(s)
- Lucas Silva Franco
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
- Instituto Nacional de Ciência e Tecnologia de Fármacos e Medicamentos (INCT-INOFAR), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal (PPGFQM), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Bárbara da Silva Mascarenhas de Jesus
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
- Programa de Pós-Graduação em Farmacologia e Química Medicinal (PPGFQM), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil; (L.S.F.); (B.d.S.M.d.J.)
- Instituto Nacional de Ciência e Tecnologia de Fármacos e Medicamentos (INCT-INOFAR), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal (PPGFQM), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
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Zhang Y, Chen S, Tian Y, Fu X. Host factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects. Front Cell Infect Microbiol 2024; 14:1407261. [PMID: 38846354 PMCID: PMC11155306 DOI: 10.3389/fcimb.2024.1407261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
SARS-CoV-2 is the causative virus of the devastating COVID-19 pandemic that results in an unparalleled global health and economic crisis. Despite unprecedented scientific efforts and therapeutic interventions, the fight against COVID-19 continues as the rapid emergence of different SARS-CoV-2 variants of concern and the increasing challenge of long COVID-19, raising a vast demand to understand the pathomechanisms of COVID-19 and its long-term sequelae and develop therapeutic strategies beyond the virus per se. Notably, in addition to the virus itself, the replication cycle of SARS-CoV-2 and clinical severity of COVID-19 is also governed by host factors. In this review, we therefore comprehensively overview the replication cycle and pathogenesis of SARS-CoV-2 from the perspective of host factors and host-virus interactions. We sequentially outline the pathological implications of molecular interactions between host factors and SARS-CoV-2 in multi-organ and multi-system long COVID-19, and summarize current therapeutic strategies and agents targeting host factors for treating these diseases. This knowledge would be key for the identification of new pathophysiological aspects and mechanisms, and the development of actionable therapeutic targets and strategies for tackling COVID-19 and its sequelae.
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Affiliation(s)
| | | | - Yan Tian
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
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7
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Abolhasani FS, Moein M, Rezaie N, Sheikhimehrabadi P, Shafiei M, Afkhami H, Modaresi M. Occurrence of COVID-19 in cystic fibrosis patients: a review. Front Microbiol 2024; 15:1356926. [PMID: 38694803 PMCID: PMC11061495 DOI: 10.3389/fmicb.2024.1356926] [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: 12/16/2023] [Accepted: 03/11/2024] [Indexed: 05/04/2024] Open
Abstract
Cystic fibrosis (CF) is a genetic ailment caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This autosomal recessive disorder is characterized by diverse pathobiological abnormalities, such as the disorder of CFTR channels in mucosal surfaces, caused by inadequate clearance of mucus and sputum, in addition to the malfunctioning of mucous organs. However, the primary motive of mortality in CF patients is pulmonary failure, which is attributed to the colonization of opportunistic microorganisms, formation of resistant biofilms, and a subsequent decline in lung characteristics. In December 2019, the World Health Organization (WHO) declared the outbreak of the radical coronavirus disease 2019 (COVID-19) as a worldwide public health crisis, which unexpectedly spread not only within China but also globally. Given that the respiration system is the primary target of the COVID-19 virus, it is crucial to investigate the impact of COVID-19 on the pathogenesis and mortality of CF patients, mainly in the context of acute respiratory distress syndrome (ARDS). Therefore, the goal of this review is to comprehensively review the present literature on the relationship between cystic fibrosis, COVID-19 contamination, and development of ARDS. Several investigations performed during the early stages of the virus outbreak have discovered unexpected findings regarding the occurrence and effectiveness of COVID-19 in individuals with CF. Contrary to initial expectancies, the rate of infection and the effectiveness of the virus in CF patients are lower than those in the overall population. This finding may be attributed to different factors, including the presence of thick mucus, social avoidance, using remedies that include azithromycin, the fairly younger age of CF patients, decreased presence of ACE-2 receptors, and the effect of CFTR channel disorder on the replication cycle and infectivity of the virus. However, it is important to notice that certain situations, which include undergoing a transplant, can also doubtlessly boost the susceptibility of CF patients to COVID-19. Furthermore, with an increase in age in CF patients, it is vital to take into account the prevalence of the SARS-CoV-2 virus in this population. Therefore, ordinary surveillance of CF patients is vital to evaluate and save the population from the capability of transmission of the virus given the various factors that contribute to the spread of the SARS-CoV-2 outbreak in this precise organization.
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Affiliation(s)
- Fatemeh Sadat Abolhasani
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masood Moein
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Rezaie
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Department of Medical Microbiology, School of Medicine, Shahed University, Tehran, Iran
| | - Mohammadreza Modaresi
- Pediatric Pulmonary Disease and Sleep Medicine Research Center, Pediatric Center of Excellence, Children's Medical Center, Tehran, Iran
- Cystic Fibrosis Research Center, Iran CF Foundation (ICFF), Tehran, Iran
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8
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Jung SB, Choi G, Kim HJ, Moon KS, Lee G, Na KH, Kwon YM, Moon J, Shin MY, Yu JY, Baek YB, Park JG, Park SI. A Noble Extract of Pseudomonas sp. M20A4R8 Efficiently Controlling the Influenza Virus-Induced Cell Death. Microorganisms 2024; 12:677. [PMID: 38674621 PMCID: PMC11051866 DOI: 10.3390/microorganisms12040677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Epidemic diseases that arise from infectious RNA viruses, particularly influenza viruses, pose a constant threat to the global economy and public health. Viral evolution has undermined the efficacy of acquired immunity from vaccines and the antiviral effects of FDA-approved drugs. As such, there is an urgent need to develop new antiviral lead agents. Natural compounds, owing to their historical validation of application and safety, have become a promising solution. In this light, a novel marine bacterium, Pseudomonas sp. M20A4R8, has been found to exhibit significant antiviral activity [half maximal inhibitory concentration (IC50) = 1.3 µg/mL, selectivity index (SI) = 919.4] against influenza virus A/Puerto Rico/8/34, surpassing the activity of chloroquine. The antiviral response via M20A4R8 extract was induced during post-entry stages of the influenza virus, indicating suitability for post-application after the establishment of viral infection. Furthermore, post-treatment with M20A4R8 extract protected the host from virus-induced apoptosis, suggesting its potential use in acute respiratory disease complexes resulting from immune effectors' overstimulation and autophagy-mediated self-apoptosis. The extract demonstrated an outstanding therapeutic index against influenza virus A/Wisconsin/15/2009 (IC50 = 8.1 µg/mL, SI = 146.2) and B/Florida/78/2015 Victoria lineage (IC50 = 3.5 µg/mL, SI = 343.8), indicating a broad anti-influenza virus activity with guaranteed safety and effectiveness. This study provides a new perspective on mechanisms for preventing a broad spectrum of viral infections through antiviral agents from novel and natural origins. Future studies on a single or combined compound from the extract hold promise, encouraging its use in preclinical challenge tests with various influenza virus strains.
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Affiliation(s)
- Su-Bin Jung
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Grace Choi
- Department of Biological Application and Technology, National Marine Biodiversity Institute of Korea, Seocheon 33662, Republic of Korea; (G.C.); (Y.M.K.)
| | - Hyo-Jin Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; (H.-J.K.); (Y.-B.B.)
| | - Kyeong-Seo Moon
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Gun Lee
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Kyeong-Hak Na
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
| | - Yong Min Kwon
- Department of Biological Application and Technology, National Marine Biodiversity Institute of Korea, Seocheon 33662, Republic of Korea; (G.C.); (Y.M.K.)
| | - Jimin Moon
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Mi Yeong Shin
- Department of Health Research, Jeollanam-do Institute of Health and Environment, Muan 58568, Republic of Korea; (M.Y.S.); (J.-Y.Y.)
| | - Jae-Yeong Yu
- Department of Health Research, Jeollanam-do Institute of Health and Environment, Muan 58568, Republic of Korea; (M.Y.S.); (J.-Y.Y.)
| | - Yeong-Bin Baek
- Department of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea; (H.-J.K.); (Y.-B.B.)
| | - Jun-Gyu Park
- Department of Veterinary Zoonotic Diseases, College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang-Ik Park
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (S.-B.J.); (K.-S.M.); (G.L.); (K.-H.N.)
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9
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Fernández DI, Troitiño S, Sobota V, Tullemans BME, Zou J, van den Hurk H, García Á, Honarnejad S, Kuijpers MJE, Heemskerk JWM. Ultra-high throughput-based screening for the discovery of antiplatelet drugs affecting receptor dependent calcium signaling dynamics. Sci Rep 2024; 14:6229. [PMID: 38486006 PMCID: PMC10940705 DOI: 10.1038/s41598-024-56799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Distinct platelet activation patterns are elicited by the tyrosine kinase-linked collagen receptor glycoprotein VI (GPVI) and the G-protein coupled protease-activated receptors (PAR1/4) for thrombin. This is reflected in the different platelet Ca2+ responses induced by the GPVI agonist collagen-related peptide (CRP) and the PAR1/4 agonist thrombin. Using a 96 well-plate assay with human Calcium-6-loaded platelets and a panel of 22 pharmacological inhibitors, we assessed the cytosolic Ca2+ signaling domains of these receptors and developed an automated Ca2+ curve algorithm. The algorithm was used to evaluate an ultra-high throughput (UHT) based screening of 16,635 chemically diverse small molecules with orally active physicochemical properties for effects on platelets stimulated with CRP or thrombin. Stringent agonist-specific selection criteria resulted in the identification of 151 drug-like molecules, of which three hit compounds were further characterized. The dibenzyl formamide derivative ANO61 selectively modulated thrombin-induced Ca2+ responses, whereas the aromatic sulfonyl imidazole AF299 and the phenothiazine ethopropazine affected CRP-induced responses. Platelet functional assays confirmed selectivity of these hits. Ethopropazine retained its inhibitory potential in the presence of plasma, and suppressed collagen-dependent thrombus buildup at arterial shear rate. In conclusion, targeting of platelet Ca2+ signaling dynamics in a screening campaign has the potential of identifying novel platelet-inhibiting molecules.
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Affiliation(s)
- Delia I Fernández
- The Department of Biochemistry, CARIM, Maastricht University, 6229 ER, Maastricht, The Netherlands
- Platelet Proteomics Group, CiMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Sara Troitiño
- Platelet Proteomics Group, CiMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Vladimír Sobota
- IHU-LIRYC, Electrophysiology and Heart Modeling Institute, Fondation Bordeaux Université, 33604, Bordeaux, France
- Institut de Mathématiques de Bordeaux, UMR5251, University of Bordeaux, 33 405, Talence, France
| | - Bibian M E Tullemans
- The Department of Biochemistry, CARIM, Maastricht University, 6229 ER, Maastricht, The Netherlands
- Synapse Research Institute, Kon. Emmaplein 7, 6217 KD, Maastricht, The Netherlands
| | - Jinmi Zou
- The Department of Biochemistry, CARIM, Maastricht University, 6229 ER, Maastricht, The Netherlands
- Synapse Research Institute, Kon. Emmaplein 7, 6217 KD, Maastricht, The Netherlands
| | | | - Ángel García
- Platelet Proteomics Group, CiMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | | | - Marijke J E Kuijpers
- The Department of Biochemistry, CARIM, Maastricht University, 6229 ER, Maastricht, The Netherlands.
- Thrombosis Expertise Centre, Heart and Vascular Centre, Maastricht University Medical Centre+, 6229 HX, Maastricht, The Netherlands.
| | - Johan W M Heemskerk
- The Department of Biochemistry, CARIM, Maastricht University, 6229 ER, Maastricht, The Netherlands.
- Synapse Research Institute, Kon. Emmaplein 7, 6217 KD, Maastricht, The Netherlands.
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10
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Kim HJ, Park JG, Moon KS, Jung SB, Kwon YM, Kang NS, Kim JH, Nam SJ, Choi G, Baek YB, Park SI. Identification and characterization of a marine bacterium extract from Mameliella sp. M20D2D8 with antiviral effects against influenza A and B viruses. Arch Virol 2024; 169:41. [PMID: 38326489 PMCID: PMC10850258 DOI: 10.1007/s00705-024-05979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/24/2023] [Indexed: 02/09/2024]
Abstract
Despite significant improvements in vaccines and chemotherapeutic drugs, pathogenic RNA viruses continue to have a profound impact on the global economy and pose a serious threat to animal and human health through emerging and re-emerging outbreaks of diseases. To overcome the challenge of viral adaptation and evolution, increased vigilance is required. Particularly, antiviral drugs derived from new, natural sources provide an attractive strategy for controlling problematic viral diseases. In this antiviral study, we discovered a previously unknown bacterium, Mameliella sp. M20D2D8, by conducting an antiviral screening of marine microorganisms. An extract from M20D2D8 exhibited antiviral activity with low cytotoxicity and was found to be effective in vitro against multiple influenza virus strains: A/PR8 (IC50 = 2.93 µg/mL, SI = 294.85), A/Phil82 (IC50 = 1.42 µg/mL, SI = 608.38), and B/Yamagata (IC50 = 1.59 µg/mL, SI = 543.33). The antiviral action was found to occur in the post-entry stages of viral replication and to suppress viral replication by inducing apoptosis in infected cells. Moreover, it efficiently suppressed viral genome replication, protein synthesis, and infectivity in MDCK and A549 cells. Our findings highlight the antiviral capabilities of a novel marine bacterium, which could potentially be useful in the development of drugs for controlling viral diseases.
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Affiliation(s)
- Hyo-Jin Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jun-Gyu Park
- Laboratory of Veterinary Zoonotic Diseases, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kyeong-Seo Moon
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Bin Jung
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, South Korea
| | - Yong Min Kwon
- Department of Microbial Resources, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Nam Seon Kang
- Department of Microbial Resources, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea
| | - Jeong-Hyeon Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Grace Choi
- Department of Microbial Resources, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101beon-gil, Seocheon-gun, Chungcheongnam-do, 33662, Republic of Korea.
| | - Yeong-Bin Baek
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Sang-Ik Park
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea.
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, 61186, South Korea.
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11
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Alkafaas SS, Abdallah AM, Hassan MH, Hussien AM, Elkafas SS, Loutfy SA, Mikhail A, Murad OG, Elsalahaty MI, Hessien M, Elshazli RM, Alsaeed FA, Ahmed AE, Kamal HK, Hafez W, El-Saadony MT, El-Tarabily KA, Ghosh S. Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS- CoV-2 infectivity. BMC Public Health 2024; 24:395. [PMID: 38321448 PMCID: PMC10848368 DOI: 10.1186/s12889-024-17747-z] [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: 10/24/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Recently, COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, caused > 6 million deaths. Symptoms included respiratory strain and complications, leading to severe pneumonia. SARS-CoV-2 attaches to the ACE-2 receptor of the host cell membrane to enter. Targeting the SARS-CoV-2 entry may effectively inhibit infection. Acid sphingomyelinase (ASMase) is a lysosomal protein that catalyzes the conversion of sphingolipid (sphingomyelin) to ceramide. Ceramide molecules aggregate/assemble on the plasma membrane to form "platforms" that facilitate the viral intake into the cell. Impairing the ASMase activity will eventually disrupt viral entry into the cell. In this review, we identified the metabolism of sphingolipids, sphingolipids' role in cell signal transduction cascades, and viral infection mechanisms. Also, we outlined ASMase structure and underlying mechanisms inhibiting viral entry 40 with the aid of inhibitors of acid sphingomyelinase (FIASMAs). In silico molecular docking analyses of FIASMAs with inhibitors revealed that dilazep (S = - 12.58 kcal/mol), emetine (S = - 11.65 kcal/mol), pimozide (S = - 11.29 kcal/mol), carvedilol (S = - 11.28 kcal/mol), mebeverine (S = - 11.14 kcal/mol), cepharanthine (S = - 11.06 kcal/mol), hydroxyzin (S = - 10.96 kcal/mol), astemizole (S = - 10.81 kcal/mol), sertindole (S = - 10.55 kcal/mol), and bepridil (S = - 10.47 kcal/mol) have higher inhibition activity than the candidate drug amiodarone (S = - 10.43 kcal/mol), making them better options for inhibition.
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Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Abanoub Mosaad Abdallah
- Narcotic Research Department, National Center for Social and Criminological Research (NCSCR), Giza, 11561, Egypt
| | - Mai H Hassan
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Aya Misbah Hussien
- Biotechnology department at Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design Department, Faculty of Engineering, Menofia University, Menofia, Egypt
- Faculty of Control System and Robotics, ITMO University, Saint-Petersburg, 197101, Russia
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center, British University, Cairo, Egypt
| | - Abanoub Mikhail
- Department of Physics, Faculty of Science, Minia University, Minia, Egypt
- Faculty of Physics, ITMO University, Saint Petersburg, Russia
| | - Omnia G Murad
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed I Elsalahaty
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed Hessien
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, 34517, Egypt
| | - Fatimah A Alsaeed
- Department of Biology, College of Science, King Khalid University, Muhayl, Saudi Arabia
| | - Ahmed Ezzat Ahmed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Hani K Kamal
- Anatomy and Histology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Wael Hafez
- NMC Royal Hospital, 16Th Street, 35233, Khalifa City, Abu Dhabi, United Arab Emirates
- Medical Research Division, Department of Internal Medicine, The National Research Centre, 12622, 33 El Buhouth St, Ad Doqi, Dokki, Cairo Governorate, Egypt
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
- Natural & Medical Science Research Center, University of Nizwa, Nizwa, Oman
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12
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Shida H, Komamine M, Kajiyama K, Waki T, Maruyama H, Uyama Y. Real-world prescription of anti-COVID-19 drugs in hospitalized patients with COVID-19 in Japan. PLoS One 2024; 19:e0297679. [PMID: 38277429 PMCID: PMC10817178 DOI: 10.1371/journal.pone.0297679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
OBJECTIVE Prescription trends and patterns of anti-COVID-19 drugs in hospitalized patients were examined based on real world data to understand the use of anti-COVID-19 drugs in clinical practice in Japan. DESIGN The longitudinal and cross-sectional study was conducted utilizing data from January 1, 2019 to December 31, 2021 of the MID-NET® medical information database, which stored the electronic medical records, administrative claim data, and diagnosis procedure combination data of patients in Japan. PARTICIPANTS Hospitalized patients with a COVID-19-related diagnosis who received at least one anti-COVID-19 drug between April 1, 2020 and December 31, 2021. EXPOSURES The following 14 drugs were included in this study: remdesivir, baricitinib, combination product of casirivimab and imdevimab, favipiravir, dexamethasone, ivermectin, azithromycin, nafamostat mesylate, camostat mesylate, ciclesonide, tocilizumab, sarilumab, combination product of lopinavir and ritonavir, and hydroxychloroquine. RESULTS We identified 5,717 patients hospitalized with COVID-19 and prescribed at least one anti-COVID-19 drug. The entire cohort generally included patients over 41-50 years and more males. The most common prescription pattern was dexamethasone monotherapy (22.9%), followed by the concomitant use of remdesivir and dexamethasone (15.0%), azithromycin monotherapy (15.0%), remdesivir monotherapy (10.2%), and nafamostat mesylate monotherapy (8.5%). However, an often prescribed anti-COVID-19 drug differed depending on the period. CONCLUSIONS AND RELEVANCE This study revealed the real-world situation of anti-COVID-19 drug prescriptions in hospitalized COVID-19 patients in Japan. A prescribed drug would depend on the latest scientific evidence, such as efficacy, safety, and approval status, at the time of prescription. Understanding the prescription of anti-COVID-19 drugs will be important for providing the most up-to-date treatments to patients and evaluating the benefit and/or risk of anti-COVID-19 drugs based on the utilization of an electronic medical record database.
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Affiliation(s)
- Haruka Shida
- Office of Medical Informatics and Epidemiology, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
| | - Maki Komamine
- Office of Medical Informatics and Epidemiology, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
| | - Kazuhiro Kajiyama
- Office of Medical Informatics and Epidemiology, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
| | - Takashi Waki
- Office of Medical Informatics and Epidemiology, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
| | - Hotaka Maruyama
- Office of Medical Informatics and Epidemiology, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
| | - Yoshiaki Uyama
- Office of Medical Informatics and Epidemiology, Pharmaceuticals and Medical Devices Agency, Tokyo, Japan
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13
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Khalifa HO, Al Ramahi YM. After the Hurricane: Anti-COVID-19 Drugs Development, Molecular Mechanisms of Action and Future Perspectives. Int J Mol Sci 2024; 25:739. [PMID: 38255813 PMCID: PMC10815681 DOI: 10.3390/ijms25020739] [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: 12/03/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a new coronavirus in the Coronaviridae family. The COVID-19 pandemic, caused by SARS-CoV-2, has undoubtedly been the largest crisis of the twenty-first century, resulting in over 6.8 million deaths and 686 million confirmed cases, creating a global public health issue. Hundreds of notable articles have been published since the onset of this pandemic to justify the cause of viral spread, viable preventive measures, and future therapeutic approaches. As a result, this review was developed to provide a summary of the current anti-COVID-19 drugs, as well as their timeline, molecular mode of action, and efficacy. It also sheds light on potential future treatment options. Several medications, notably hydroxychloroquine and lopinavir/ritonavir, were initially claimed to be effective in the treatment of SARS-CoV-2 but eventually demonstrated inadequate activity, and the Food and Drug Administration (FDA) withdrew hydroxychloroquine. Clinical trials and investigations, on the other hand, have demonstrated the efficacy of remdesivir, convalescent plasma, and monoclonal antibodies, 6-Thioguanine, hepatitis C protease inhibitors, and molnupiravir. Other therapeutics, including inhaled medicines, flavonoids, and aptamers, could pave the way for the creation of novel anti-COVID-19 therapies. As future pandemics are unavoidable, this article urges immediate action and extensive research efforts to develop potent specialized anti-COVID-19 medications.
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Affiliation(s)
- Hazim O. Khalifa
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates;
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Yousef M. Al Ramahi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates;
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Pham TX, Huynh TTX, Choi J, Lee JB, Park SC, Kim B, Lim YS, Hwang SB. SARS-CoV-2 exploits cellular RAD51 to promote viral propagation: implication of RAD51 inhibitor as a potential drug candidate against COVID-19. J Virol 2023; 97:e0173723. [PMID: 38051260 PMCID: PMC10734463 DOI: 10.1128/jvi.01737-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Viruses are constantly evolving to promote propagation in the host. Here, we show that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes host RAD51 for replication. Silencing of RAD51 impaired SARS-CoV-2 propagation. Viral RNA colocalized with RAD51 in the cytoplasm of SARS-CoV-2-infected cells, suggesting that both viral RNA and RAD51 may form a replication complex. We, therefore, evaluated RAD51 inhibitors as possible therapeutic agents against SARS-CoV-2. Indeed, RAD51 inhibitors exerted antiviral activities against not only Wuhan but also variants of SARS-CoV-2. Molecular docking model shows that RAD51 inhibitors impede SARS-CoV-2 propagation by interfering with dimerization of RAD51. These data suggest that RAD51 may represent a novel host-based drug target for coronavirus disease 2019 treatment.
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Affiliation(s)
- Thuy X. Pham
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
| | - Trang T. X. Huynh
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
| | - Jiwon Choi
- College of Pharmacy, Dongduk Women’s University, Seoul, South Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
| | - Seok-Chan Park
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan, South Korea
| | - Bumseok Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan, South Korea
| | - Yun-Sook Lim
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
| | - Soon B. Hwang
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Ilsong Institute of Life Science, Hallym University, Seoul, South Korea
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15
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Li Y, Touret F, de Lamballerie X, Nguyen M, Laurent M, Benoit-Vical F, Robert A, Liu Y, Meunier B. Hybrid molecules based on an emodin scaffold. Synthesis and activity against SARS-CoV-2 and Plasmodium. Org Biomol Chem 2023; 21:7382-7394. [PMID: 37655748 DOI: 10.1039/d3ob01122d] [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: 09/02/2023]
Abstract
Since the Covid-19 epidemic, it has been clear that the availability of small and affordable drugs that are able to efficiently control viral infections in humans is still a challenge in medicinal chemistry. The synthesis and biological activities of a series of hybrid molecules that combine an emodin moiety and other structural moieties expected to act as possible synergistic pharmacophores in a single molecule were studied. Emodin has been reported to block the entry of the SARS-CoV-2 virus into human cells and might also inhibit cytokine production, resulting in the reduction of pulmonary injury induced by SARS-CoV-2. The pharmacophore associated with emodin was either a polyamine residue (emodin-PA series), a choice driven by the fact that a natural alkyl PA like spermine and spermidine play regulatory roles in immune cell functions, or a diphenylmethylpiperazine derivative of the norchlorcyclizine series (emoxyzine series). In fact, diphenylmethylpiperazine antagonists of the H1 histamine receptor display activity against several viruses by multiple interrelated mechanisms. In the emoxyzine series, the most potent drug against SARS-CoV-2 was (R)-emoxyzine-2, with an EC50 value = 1.9 μM, which is in the same range as that of the reference drug remdesivir. However, the selectivity index was rather low, indicating that the dissociation of antiviral potency and cytotoxicity remains a challenge. In addition, since emodin was also reported to be a relatively high-affinity inhibitor of the virulence regulator FIKK kinase from the malaria parasite Plasmodium vivax, the antimalarial activity of the synthesized hybrid compounds has been evaluated. However, these molecules cannot efficiently compete with the currently used antimalarial drugs.
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Affiliation(s)
- Youzhi Li
- Education Mega Center, Guangdong University of Technology, School of Chemical Engineering and Light Industry, No. 100 Waihuan Xi Road, Guangzhou, P. R. China.
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Franck Touret
- Unité des Virus Émergents (UVE), Aix Marseille Univ, IRD 190, Inserm 1207, 27 Boulevard Jean Moulin, 13005 Marseille Cedex 05, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE), Aix Marseille Univ, IRD 190, Inserm 1207, 27 Boulevard Jean Moulin, 13005 Marseille Cedex 05, France
| | - Michel Nguyen
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Marion Laurent
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Françoise Benoit-Vical
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Anne Robert
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Yan Liu
- Education Mega Center, Guangdong University of Technology, School of Chemical Engineering and Light Industry, No. 100 Waihuan Xi Road, Guangzhou, P. R. China.
| | - Bernard Meunier
- Education Mega Center, Guangdong University of Technology, School of Chemical Engineering and Light Industry, No. 100 Waihuan Xi Road, Guangzhou, P. R. China.
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
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16
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Huang Y, Huang HY, Chen Y, Lin YCD, Yao L, Lin T, Leng J, Chang Y, Zhang Y, Zhu Z, Ma K, Cheng YN, Lee TY, Huang HD. A Robust Drug-Target Interaction Prediction Framework with Capsule Network and Transfer Learning. Int J Mol Sci 2023; 24:14061. [PMID: 37762364 PMCID: PMC10531393 DOI: 10.3390/ijms241814061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Drug-target interactions (DTIs) are considered a crucial component of drug design and drug discovery. To date, many computational methods were developed for drug-target interactions, but they are insufficiently informative for accurately predicting DTIs due to the lack of experimentally verified negative datasets, inaccurate molecular feature representation, and ineffective DTI classifiers. Therefore, we address the limitations of randomly selecting negative DTI data from unknown drug-target pairs by establishing two experimentally validated datasets and propose a capsule network-based framework called CapBM-DTI to capture hierarchical relationships of drugs and targets, which adopts pre-trained bidirectional encoder representations from transformers (BERT) for contextual sequence feature extraction from target proteins through transfer learning and the message-passing neural network (MPNN) for the 2-D graph feature extraction of compounds to accurately and robustly identify drug-target interactions. We compared the performance of CapBM-DTI with state-of-the-art methods using four experimentally validated DTI datasets of different sizes, including human (Homo sapiens) and worm (Caenorhabditis elegans) species datasets, as well as three subsets (new compounds, new proteins, and new pairs). Our results demonstrate that the proposed model achieved robust performance and powerful generalization ability in all experiments. The case study on treating COVID-19 demonstrates the applicability of the model in virtual screening.
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Affiliation(s)
- Yixian Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Yigang Chen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Lantian Yao
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Tianxiu Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Junlin Leng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Yuan Chang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Yuntian Zhang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Zihao Zhu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Kun Ma
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
| | - Yeong-Nan Cheng
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (Y.-N.C.)
| | - Tzong-Yi Lee
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (Y.-N.C.)
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (Y.H.); (Y.C.); (J.L.)
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen 518172, China; (L.Y.); (Y.C.)
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17
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Sharma A, Kaur M, Yadav P, Singh G, Barnwal RP. Expediting the drug discovery for ideal leads against SARS-CoV-2 via molecular docking of repurposed drugs. J Biomol Struct Dyn 2023; 41:7949-7965. [PMID: 36165445 DOI: 10.1080/07391102.2022.2127903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
SARS-CoV-2, the novel coronavirus spreading worldwide urges the need to repurpose drugs that can quickly enter clinical trials to combat the on-going global pandemic. A cluster of proteins are encoded for by the viral genome, each assuming a critical role in pathogen endurance inside the host. To handle the adverse circumstances, robust virtual strategies such as repurposing are coming to the fore due to being economical, efficient and rapid. Five FDA approved repurposed drugs proposed to act as inhibitors by targeting SARS-CoV-2 were used for initial evaluation via molecular docking. Moreover, a comparative analysis of the selected SARS-CoV-2 proteins against five ligands (Clemizole hydrochloride, Exemestane, Nafamostat, Pregnenolone and Umifenovir) was designed. In this regard, non-structural proteins (nsp3, nsp5, nsp10, nsp12 and nsp15), structural proteins (Spike, Nucleocapsid protein) and accessory proteins (ORF 3a, ORF 7a and ORF 9 b) were selected. Here, we aim to expedite the search for a potential drug from the five FDA approved repurposing drugs already in use for treatment of multiple diseases. Based on docking analysis, Umifenovir and Pregnenolone are suggested to show potential inhibitory effects against most of the SARS-CoV-2 proteins. These drugs are noteworthy since they exhibit high binding towards target proteins and should be used as lead compounds towards in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Priya Yadav
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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18
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Yoon SH, Lee HL, Jeong DU, Lim KM, Park SJ, Kim KS. Assessment of the proarrhythmic effects of repurposed antimalarials for COVID-19 treatment using a comprehensive in vitro proarrhythmia assay (CiPA). Front Pharmacol 2023; 14:1220796. [PMID: 37649890 PMCID: PMC10464612 DOI: 10.3389/fphar.2023.1220796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023] Open
Abstract
Due to the outbreak of the SARS-CoV-2 virus, drug repurposing and Emergency Use Authorization have been proposed to treat the coronavirus disease 2019 (COVID-19) during the pandemic. While the efficiency of the drugs has been discussed, it was identified that certain compounds, such as chloroquine and hydroxychloroquine, cause QT interval prolongation and potential cardiotoxic effects. Drug-induced cardiotoxicity and QT prolongation may lead to life-threatening arrhythmias such as torsades de pointes (TdP), a potentially fatal arrhythmic symptom. Here, we evaluated the risk of repurposed pyronaridine or artesunate-mediated cardiac arrhythmias alone and in combination for COVID-19 treatment through in vitro and in silico investigations using the Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative. The potential effects of each drug or in combinations on cardiac action potential (AP) and ion channels were explored using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and Chinese hamster ovary (CHO) cells transiently expressing cardiac ion channels (Nav1.5, Cav1.2, and hERG). We also performed in silico computer simulation using the optimized O'Hara-Rudy human ventricular myocyte model (ORd model) to classify TdP risk. Artesunate and dihydroartemisinin (DHA), the active metabolite of artesunate, are classified as a low risk of inducing TdP based on the torsade metric score (TMS). Moreover, artesunate does not significantly affect the cardiac APs of hiPSC-CMs even at concentrations up to 100 times the maximum serum concentration (Cmax). DHA modestly prolonged at APD90 (10.16%) at 100 times the Cmax. When considering Cmax, pyronaridine, and the combination of both drugs (pyronaridine and artesunate) are classified as having an intermediate risk of inducing TdP. However, when considering the unbound concentration (the free fraction not bound to carrier proteins or other tissues inducing pharmacological activity), both drugs are classified as having a low risk of inducing TdP. In summary, pyronaridine, artesunate, and a combination of both drugs have been confirmed to pose a low proarrhythmogenic risk at therapeutic and supratherapeutic (up to 4 times) free Cmax. Additionally, the CiPA initiative may be suitable for regulatory use and provide novel insights for evaluating drug-induced cardiotoxicity.
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Affiliation(s)
- Seung-Hyun Yoon
- R&D Center for Advanced Pharmaceuticals and Evaluation, Korea Institute of Toxicology, Daejeon, Republic of Korea
- College of Veterinary Medicine, Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hyun-Lee Lee
- R&D Center for Advanced Pharmaceuticals and Evaluation, Korea Institute of Toxicology, Daejeon, Republic of Korea
| | - Da Un Jeong
- Intelligent Human Twin Research Center, Electronics and Telecommunications Research Institute, Daejeon, Republic of Korea
| | - Ki Moo Lim
- Department of IT Convergence Engineering, Kumoh National Institute of Technology, Gumi, Republic of Korea
| | - Seong-Jun Park
- College of Veterinary Medicine, Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Ki-Suk Kim
- R&D Center for Advanced Pharmaceuticals and Evaluation, Korea Institute of Toxicology, Daejeon, Republic of Korea
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Solanky D, McGovern OL, Edwards JR, Mahon G, Patel TS, Lessa FC, Hicks LA, Patel PK. Prescribing of Outpatient Antibiotics Commonly Used for Respiratory Infections Among Adults Before and During the Coronavirus Disease 2019 Pandemic in Brazil. Clin Infect Dis 2023; 77:S12-S19. [PMID: 37406052 DOI: 10.1093/cid/ciad183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic may have impacted outpatient antibiotic prescribing in low- and middle-income countries such as Brazil. However, outpatient antibiotic prescribing in Brazil, particularly at the prescription level, is not well-described. METHODS We used the IQVIA MIDAS database to characterize changes in prescribing rates of antibiotics commonly prescribed for respiratory infections (azithromycin, amoxicillin-clavulanate, levofloxacin/moxifloxacin, cephalexin, and ceftriaxone) among adults in Brazil overall and stratified by age and sex, comparing prepandemic (January 2019-March 2020) and pandemic periods (April 2020-December 2021) using uni- and multivariate Poisson regression models. The most common prescribing provider specialties for these antibiotics were also identified. RESULTS In the pandemic period compared to the prepandemic period, outpatient azithromycin prescribing rates increased across all age-sex groups (incidence rate ratio [IRR] range, 1.474-3.619), with the greatest increase observed in males aged 65-74 years; meanwhile, prescribing rates for amoxicillin-clavulanate and respiratory fluoroquinolones mostly decreased, and changes in cephalosporin prescribing rates varied across age-sex groups (IRR range, 0.134-1.910). For all antibiotics, the interaction of age and sex with the pandemic in multivariable models was an independent predictor of prescribing changes comparing the pandemic versus prepandemic periods. General practitioners and gynecologists accounted for the majority of increases in azithromycin and ceftriaxone prescribing during the pandemic period. CONCLUSIONS Substantial increases in outpatient prescribing rates for azithromycin and ceftriaxone were observed in Brazil during the pandemic with prescribing rates being disproportionally different by age and sex. General practitioners and gynecologists were the most common prescribers of azithromycin and ceftriaxone during the pandemic, identifying them as potential specialties for antimicrobial stewardship interventions.
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Affiliation(s)
- Dipesh Solanky
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Olivia L McGovern
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonathan R Edwards
- Surveillance Branch, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Garrett Mahon
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- CACI International Inc., Reston, Virginia, USA
| | - Twisha S Patel
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Chenega Enterprise Systems and Solutions, Chesapeake, Virginia, USA
| | - Fernanda C Lessa
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauri A Hicks
- Prevention and Response Branch, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Payal K Patel
- International Infection Control Program, Division of Healthcare Quality Promotion, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Clinical Epidemiology and Infectious Diseases, Intermountain Healthcare, Salt Lake City, Utah, USA
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Tomezsko PJ, Phillipson CW, Walsh ME. Lessons Learned From Limited Overlap of 15 In Vitro COVID-19 Drug Repurposing Screens. Health Secur 2023; 21:249-257. [PMID: 37196212 PMCID: PMC10357111 DOI: 10.1089/hs.2022.0132] [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: 10/03/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/19/2023] Open
Abstract
Drug repurposing can quickly and cost-effectively identify medical countermeasures against pathogens with pandemic potential and could be used as a down-selection method for selecting US Food and Drug Administration-approved drugs to test in clinical trials. We compared results from 15 high-throughput in vitro screening efforts that tested approved and clinically evaluated drugs for activity against SARS-CoV-2 replication. From the 15 studies, 304 drugs were identified as displaying the highest level of confidence from the individual screens. Of those 304 drugs, 30 were identified in 2 or more screens, while only 3 drugs (apilimod, tetrandrine, and salinomycin) were identified in 4 screens. The lack of concordance in high-confidence hits and variations in protocols makes it challenging to use the collective data as down-selection criteria for identifying repurposing candidates to move into a clinical trial.
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Affiliation(s)
- Phillip J. Tomezsko
- Phillip J. Tomezsko, PhD, is Technical Staff, Counter WMD Systems Group, MIT Lincoln Laboratory, Lexington, MA
| | | | - Matthew E. Walsh
- Matthew E. Walsh was Associate Technical Staff, Biological and Chemical Technologies Group, MIT Lincoln Laboratory, Lexington, MA
- Matthew E. Walsh is currently a PhD Student, Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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21
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Vaz ES, Vassiliades SV, Giarolla J, Polli MC, Parise-Filho R. Drug repositioning in the COVID-19 pandemic: fundamentals, synthetic routes, and overview of clinical studies. Eur J Clin Pharmacol 2023; 79:723-751. [PMID: 37081137 PMCID: PMC10118228 DOI: 10.1007/s00228-023-03486-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023]
Abstract
INTRODUCTION Drug repositioning is a strategy to identify a new therapeutic indication for molecules that have been approved for other conditions, aiming to speed up the traditional drug development process and reduce its costs. The high prevalence and incidence of coronavirus disease 2019 (COVID-19) underline the importance of searching for a safe and effective treatment for the disease, and drug repositioning is the most rational strategy to achieve this goal in a short period of time. Another advantage of repositioning is the fact that these compounds already have established synthetic routes, which facilitates their production at the industrial level. However, the hope for treatment cannot allow the indiscriminate use of medicines without a scientific basis. RESULTS The main small molecules in clinical trials being studied to be potentially repositioned to treat COVID-19 are chloroquine, hydroxychloroquine, ivermectin, favipiravir, colchicine, remdesivir, dexamethasone, nitazoxanide, azithromycin, camostat, methylprednisolone, and baricitinib. In the context of clinical tests, in general, they were carried out under the supervision of large consortiums with a methodology based on and recognized in the scientific community, factors that ensure the reliability of the data collected. From the synthetic perspective, compounds with less structural complexity have more simplified synthetic routes. Stereochemical complexity still represents the major challenge in the preparation of dexamethasone, ivermectin, and azithromycin, for instance. CONCLUSION Remdesivir and baricitinib were approved for the treatment of hospitalized patients with severe COVID-19. Dexamethasone and methylprednisolone should be used with caution. Hydroxychloroquine, chloroquine, ivermectin, and azithromycin are ineffective for the treatment of the disease, and the other compounds presented uncertain results. Preclinical and clinical studies should not be analyzed alone, and their methodology's accuracy should also be considered. Regulatory agencies are responsible for analyzing the efficacy and safety of a treatment and must be respected as the competent authorities for this decision, avoiding the indiscriminate use of medicines.
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Affiliation(s)
- Elisa Souza Vaz
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil
| | - Sandra Valeria Vassiliades
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil
| | - Michelle Carneiro Polli
- Pharmacy Course, São Francisco University (USF), Waldemar César da Silveira St, 105, SP, Campinas, Brazil
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil.
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22
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Hausdorff M, Delpal A, Barelier S, Nicollet L, Canard B, Touret F, Colmant A, Coutard B, Vasseur JJ, Decroly E, Debart F. Structure-guided optimization of adenosine mimetics as selective and potent inhibitors of coronavirus nsp14 N7-methyltransferases. Eur J Med Chem 2023; 256:115474. [PMID: 37192550 DOI: 10.1016/j.ejmech.2023.115474] [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: 02/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic reveals the urgent need to develop new therapeutics targeting the SARS-CoV-2 replication machinery. The first antiviral drugs were nucleoside analogues targeting RdRp and protease inhibitors active on nsp5 Mpro. In addition to these common antiviral targets, SARS-CoV-2 codes for the highly conserved protein nsp14 harbouring N7-methyltransferase (MTase) activity. Nsp14 is involved in cap N7-methylation of viral RNA and its inhibition impairs viral RNA translation and immune evasion, making it an attractive new antiviral target. In this work, we followed a structure-guided drug design approach to design bisubstrates mimicking the S-adenosylmethionine methyl donor and RNA cap. We developed adenosine mimetics with an N-arylsulfonamide moiety in the 5'-position, recently described as a guanine mimicking the cap structure in a potent adenosine-derived nsp14 inhibitor. Here, the adenine moiety was replaced by hypoxanthine, N6-methyladenine, or C7-substituted 7-deaza-adenine. 26 novel adenosine mimetics were synthesized, one of which selectively inhibits nsp14 N7-MTase activity with a subnanomolar IC50 (and seven with a single-digit nanomolar IC50). In the most potent inhibitors, adenine was replaced by two different 7-deaza-adenines bearing either a phenyl or a 3-quinoline group at the C7-position via an ethynyl linker. These more complex compounds are barely active on the cognate human N7-MTase and docking experiments reveal that their selectivity of inhibition might result from the positioning of their C7 substitution in a SAM entry tunnel present in the nsp14 structure and absent in the hN7-MTase. These compounds show moderate antiviral activity against SARS-CoV-2 replication in cell culture, suggesting delivery or stability issue.
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Affiliation(s)
- Marcel Hausdorff
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Adrien Delpal
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Sarah Barelier
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Laura Nicollet
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Franck Touret
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | - Agathe Colmant
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | - Bruno Coutard
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | | | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France.
| | - Françoise Debart
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France.
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23
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Morán Blanco JI, Alvarenga Bonilla JA, Fremont-Smith P, Villar Gómez de Las Heras K. Antihistamines as an early treatment for Covid-19. Heliyon 2023; 9:e15772. [PMID: 37128299 PMCID: PMC10129342 DOI: 10.1016/j.heliyon.2023.e15772] [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: 08/09/2022] [Revised: 03/31/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023] Open
Abstract
Infection with SARs-COV-2 results in COVID-19 disease. Between March 2020 and August 2021, 468 COVID-19 patients confirmed by PCR or antigen test, in Yepes, Spain, received early treatment with antihistamines, adding azithromycin in selected cases. The primary endpoint is the hospitalization rate of COVID-19 patients, and the secondary endpoints are ICU admission and mortality rates. All endpoints are compared with the official Spanish rates during the time period of the study. There were 20 hospital admissions (hospitalization rate 4,3%), 5 ICU admissions (ICU admission rate 1,1%) and 3 deaths (fatality rate of 0,6%). No patients in the study required follow up treatment, which suggest they did not develop long COVID. Results from this retrospective trail indicate that early treatment of SARS-COV-2 positive patients with antihistamines may reduce the odds of hospitalization (OR: 0.490, CI: 0.313-0.767, p-value: 0.001). Randomized controlled clinical trials are needed to further evaluate the effects of early antihistamine treatment of SARS-CoV-2 patients to prevent hospitalization, ICU admission, mortality and long-covid.
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Affiliation(s)
- Juan Ignacio Morán Blanco
- Servicio de Salud de Castilla-La Mancha (SESCAM), Toledo, Spain
- Centro de Salud de Yepes, Toledo, Spain
| | | | | | - Karina Villar Gómez de Las Heras
- Servicio de Salud de Castilla-La Mancha (SESCAM), Toledo, Spain
- Gerencia de Urgencias, Emergencias y Transporte Sanitario, Toledo, Spain
- Universidad de Alcalá de Henares, Facultad de Medicina y Ciencias de la Salud, Alcalá de Henares, Madrid, Spain
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24
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Lim SYM, Al Bishtawi B, Lim W. Role of Cytochrome P450 2C9 in COVID-19 Treatment: Current Status and Future Directions. Eur J Drug Metab Pharmacokinet 2023; 48:221-240. [PMID: 37093458 PMCID: PMC10123480 DOI: 10.1007/s13318-023-00826-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 04/25/2023]
Abstract
The major human liver drug metabolising cytochrome P450 (CYP) enzymes are downregulated during inflammation and infectious disease state, especially during coronavirus disease 2019 (COVID-19) infection. The influx of proinflammatory cytokines, known as a 'cytokine storm', during severe COVID-19 leads to the downregulation of CYPs and triggers new cytokine release, which further dampens CYP expression. Impaired drug metabolism, along with the inevitable co-administration of drugs or 'combination therapy' in patients with COVID-19 with various comorbidities, could cause drug-drug interactions, thus worsening the disease condition. Genetic variability or polymorphism in CYP2C9 across different ethnicities could contribute to COVID-19 susceptibility. A number of drugs used in patients with COVID-19 are inducers or inhibitors of, or are metabolised by, CYP2C9, and co-administration might cause pharmacokinetic and pharmacodynamic interactions. It is also worth mentioning that some of the COVID-19 drug interactions are due to altered activity of other CYPs including CYP3A4. Isoniazid/rifampin for COVID-19 and tuberculosis co-infection; lopinavir/ritonavir and cobicistat/remdesivir combination therapy; or multi-drug therapy including ivermectin, azithromycin, montelukast and acetylsalicylic acid, known as TNR4 therapy, all improved recovery in patients with COVID-19. However, a combination of CYP2C9 inducers, inhibitors or both, and plausibly different CYP isoforms could lead to treatment failure, hepatotoxicity or serious side effects including thromboembolism or bleeding, as observed in the combined use of azithromycin/warfarin. Further, herbs that are CYP2C9 inducers and inhibitors, showed anti-COVID-19 properties, and in silico predictions postulated that phytochemical compounds could inhibit SARS-CoV-2 virus particles. COVID-19 vaccines elicit immune responses that activate cytokine release, which in turn suppresses CYP expression that could be the source of compromised CYP2C9 drug metabolism and the subsequent drug-drug interaction. Future studies are recommended to determine CYP regulation in COVID-19, while recognising the involvement of CYP2C9 and possibly utilising CYP2C9 as a target gene to tackle the ever-mutating SARS-CoV-2.
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Affiliation(s)
- Sharoen Yu Ming Lim
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500, Semenyih, Malaysia.
| | - Basel Al Bishtawi
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500, Semenyih, Malaysia
| | - Willone Lim
- Faculty of Engineering, Computing and Science, Swinburne University of Technology, 93350, Kuching, Malaysia
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25
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Touret F, Giraud E, Bourret J, Donati F, Tran-Rajau J, Chiaravalli J, Lemoine F, Agou F, Simon-Lorière E, van der Werf S, de Lamballerie X. Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages. iScience 2023; 26:106413. [PMID: 36968074 PMCID: PMC10015083 DOI: 10.1016/j.isci.2023.106413] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple subvariants originating from BA.2, BA.4, and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1, and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1, and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1, and XBB variants.
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Affiliation(s)
- Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Emilie Giraud
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Jérôme Bourret
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France
| | - Jaouen Tran-Rajau
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Jeanne Chiaravalli
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Fabrice Agou
- Institut Pasteur, Université Paris Cité, CNRS UMR 3523, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses, National Reference Center for Respiratory Viruses, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
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26
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Ortiz-Miravalles L, Sánchez-Angulo M, Sanz JM, Maestro B. Drug Repositioning as a Therapeutic Strategy against Streptococcus pneumoniae: Cell Membrane as Potential Target. Int J Mol Sci 2023; 24:ijms24065831. [PMID: 36982905 PMCID: PMC10058218 DOI: 10.3390/ijms24065831] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
A collection of repurposing drugs (Prestwick Chemical Library) containing 1200 compounds was screened to investigate the drugs' antimicrobial effects against planktonic cultures of the respiratory pathogen Streptococcus pneumoniae. After four discrimination rounds, a set of seven compounds was finally selected, namely (i) clofilium tosylate; (ii) vanoxerine; (iii) mitoxantrone dihydrochloride; (iv) amiodarone hydrochloride; (v) tamoxifen citrate; (vi) terfenadine; and (vii) clomiphene citrate (Z, E). These molecules arrested pneumococcal growth in a liquid medium and induced a decrease in bacterial viability between 90.0% and 99.9% at 25 µM concentration, with minimal inhibitory concentrations (MICs) also in the micromolar range. Moreover, all compounds but mitoxantrone caused a remarkable increase in the permeability of the bacterial membrane and share a common, minimal chemical structure consisting of an aliphatic amine linked to a phenyl moiety via a short carbon/oxygen linker. These results open new possibilities to tackle pneumococcal disease through drug repositioning and provide clues for the design of novel membrane-targeted antimicrobials with a related chemical structure.
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Affiliation(s)
- Laura Ortiz-Miravalles
- Protein Engineering against Antimicrobial Resistance Group, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Manuel Sánchez-Angulo
- Department of Vegetal Production and Microbiology, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Jesús M Sanz
- Protein Engineering against Antimicrobial Resistance Group, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Beatriz Maestro
- Protein Engineering against Antimicrobial Resistance Group, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain
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27
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Shukla AK, Seth T, Muhuri PK. Artificial intelligence centric scientific research on COVID-19: an analysis based on scientometrics data. MULTIMEDIA TOOLS AND APPLICATIONS 2023; 82:1-33. [PMID: 37362722 PMCID: PMC9978294 DOI: 10.1007/s11042-023-14642-4] [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: 02/07/2022] [Revised: 07/01/2022] [Accepted: 02/03/2023] [Indexed: 06/28/2023]
Abstract
With the spread of the deadly coronavirus disease throughout the geographies of the globe, expertise from every field has been sought to fight the impact of the virus. The use of Artificial Intelligence (AI), especially, has been the center of attention due to its capability to produce trustworthy results in a reasonable time. As a result, AI centric based research on coronavirus (or COVID-19) has been receiving growing attention from different domains ranging from medicine, virology, and psychiatry etc. We present this comprehensive study that closely monitors the impact of the pandemic on global research activities related exclusively to AI. In this article, we produce highly informative insights pertaining to publications, such as the best articles, research areas, most productive and influential journals, authors, and institutions. Studies are made on top 50 most cited articles to identify the most influential AI subcategories. We also study the outcome of research from different geographic areas while identifying the research collaborations that have had an impact. This study also compares the outcome of research from the different countries around the globe and produces insights on the same.
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Affiliation(s)
- Amit K. Shukla
- Faculty of Information Technology, University of Jyväskylä, Box 35 (Agora), Jyväskylä, 40014 Finland
| | - Taniya Seth
- Department of Computer Science, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi 110021 India
| | - Pranab K. Muhuri
- Department of Computer Science, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi 110021 India
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28
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Maria NI, Rapicavoli RV, Alaimo S, Bischof E, Stasuzzo A, Broek JA, Pulvirenti A, Mishra B, Duits AJ, Ferro A. Application of the PHENotype SIMulator for rapid identification of potential candidates in effective COVID-19 drug repurposing. Heliyon 2023; 9:e14115. [PMID: 36911878 PMCID: PMC9986505 DOI: 10.1016/j.heliyon.2023.e14115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
The current, rapidly diversifying pandemic has accelerated the need for efficient and effective identification of potential drug candidates for COVID-19. Knowledge on host-immune response to SARS-CoV-2 infection, however, remains limited with few drugs approved to date. Viable strategies and tools are rapidly arising to address this, especially with repurposing of existing drugs offering significant promise. Here we introduce a systems biology tool, the PHENotype SIMulator, which -by leveraging available transcriptomic and proteomic databases-allows modeling of SARS-CoV-2 infection in host cells in silico to i) determine with high sensitivity and specificity (both>96%) the viral effects on cellular host-immune response, resulting in specific cellular SARS-CoV-2 signatures and ii) utilize these cell-specific signatures to identify promising repurposable therapeutics. Powered by this tool, coupled with domain expertise, we identify several potential COVID-19 drugs including methylprednisolone and metformin, and further discern key cellular SARS-CoV-2-affected pathways as potential druggable targets in COVID-19 pathogenesis.
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Key Words
- 2DG, 2-Deoxy-Glucose
- ACE2, Angiotensin-converting enzyme 2
- COVID-19
- COVID-19, Coronavirus disease 2019
- Caco-2, Human colon epithelial carcinoma cell line
- Calu-3, Epithelial cell line
- Cellular SARS-CoV-2 signatures
- Cellular host-immune response
- Cellular simulation models
- DEGs, Differentially Expressed Genes
- DEPs, Differentially expressed proteins
- Drug repurposing
- HCQ-CQ, (Hydroxy)chloroquine
- IFN, Interferon
- ISGs, IFN-stimulated genes
- MITHrIL, Mirna enrIched paTHway Impact anaLysis
- MOI, Multiplicity of infection
- MP, Methylprednisolone
- NHBE, Normal human bronchial epithelial cells
- PHENSIM, PHENotype SIMulator
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- Systems biology
- TLR, Toll-like Receptor
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Affiliation(s)
- Naomi I. Maria
- Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra, Northwell Health, Manhasset, NY, USA
- Red Cross Blood Bank Foundation Curaçao, Willemstad, Curaçao
- Department of Medical Microbiology and Immunology, St. Antonius Ziekenhuis, Niewegein, the Netherlands
- Corresponding author. Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA.
| | - Rosaria Valentina Rapicavoli
- Department of Physics and Astronomy, University of Catania, Italy
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Salvatore Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Evelyne Bischof
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Via Pansini, Naples, Italy
- School of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Pudong, Shanghai, China
- Insilico Medicine, Hong Kong Special Administrative Region, China
| | | | - Jantine A.C. Broek
- Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA
| | - Alfredo Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Bud Mishra
- Department of Computer Science, Mathematics, Engineering and Cell Biology, Courant Institute, Tandon and School of Medicine, New York University, New York, USA
- Simon Center for Quantitative Biology, Cold Spring Harbor Lab, Long Island, USA
- Corresponding author. Courant Institute of Mathematical Sciences, Room 405, 251 Mercer Street, NY, USA.
| | - Ashley J. Duits
- Red Cross Blood Bank Foundation Curaçao, Willemstad, Curaçao
- Curaçao Biomedical Health Research Institute, Willemstad, Curaçao
- Institute for Medical Education, University Medical Center Groningen, Groningen, the Netherlands
| | - Alfredo Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Italy
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29
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Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform. iScience 2023; 26:105944. [PMID: 36644320 PMCID: PMC9822553 DOI: 10.1016/j.isci.2023.105944] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/07/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a readout for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in numerous cell culture models, independently of cytopathogenic effect formation. Compared to other models, the Caco-2 subline Caco-2-F03 displayed superior performance. It possesses a stable SARS-CoV-2 susceptibility phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (HK2) inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2-F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false-positive hits.
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30
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Plant Extracts and SARS-CoV-2: Research and Applications. Life (Basel) 2023; 13:life13020386. [PMID: 36836744 PMCID: PMC9965937 DOI: 10.3390/life13020386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/28/2023] [Indexed: 02/01/2023] Open
Abstract
The recent pandemic of COVID-19 caused by the SARS-CoV-2 virus has brought upon the world an unprecedented challenge. During its acute dissemination, a rush for vaccines started, making the scientific community come together and contribute to the development of efficient therapeutic agents and vaccines. Natural products have been used as sources of individual molecules and extracts capable of inhibiting/neutralizing several microorganisms, including viruses. Natural extracts have shown effective results against the coronavirus family, when first tested in the outbreak of SARS-CoV-1, back in 2002. In this review, the relationship between natural extracts and SARS-CoV is discussed, while also providing insight into misinformation regarding the use of plants as possible therapeutic agents. Studies with plant extracts on coronaviruses are presented, as well as the main inhibition assays and trends for the future regarding the yet unknown long-lasting effects post-infection with SARS-CoV-2.
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31
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The Trimeric Artesunate Analog TF27, a Broadly Acting Anti-Infective Model Drug, Exerts Pronounced Anti-SARS-CoV-2 Activity Spanning Variants and Host Cell Types. Pharmaceutics 2022; 15:pharmaceutics15010115. [PMID: 36678744 PMCID: PMC9866877 DOI: 10.3390/pharmaceutics15010115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Starting in 2019, the spread of respiratory syndrome coronavirus 2 (SARS-CoV-2) and the associated pandemic of the corona virus disease (COVID-19) has led to enormous efforts in the development of medical countermeasures. Although innovative vaccines have scaled back the number of severe COVID cases, the emergence of the omicron variant (B.1.1.529) illustrates how vaccine development struggles to keep pace with viral evolution. On the other hand, while the recently approved antiviral drugs remdesivir, molnupiravir, and Paxlovid are considered as broadly acting anti-coronavirus therapeutics, only molnupiravir and Paxlovid are orally available and none of these drugs are recommended for prophylactic use. Thus, so far unexploited small molecules, targeting strategies, and antiviral mechanisms are urgently needed to address issues in the current pandemic and in putative future outbreaks of newly emerging variants of concern. Recently, we and others have described the anti-infective potential and particularly the pronounced antiviral activity of artesunate and related compounds of the trioxane/sesquiterpene class. In particular, the trimeric derivative TF27 demonstrated strong anti-cytomegalovirus activity at nanomolar concentrations in vitro as well as in vivo efficacy after oral administration in therapeutic and even prophylactic treatment settings. Here, we extended this analysis by evaluating TF27 for its anti-SARS-CoV-2 potential. Our main findings are as follows: (i) compound TF27 exerted strong anti-SARS-CoV-2 activity in vitro (EC50 = 0.46 ± 0.20 µM), (ii) antiviral activity was clearly distinct from the induction of cytotoxicity, (iii) pretreatment with TF27 prevented virus replication in cultured cells, (iv) antiviral activity has likewise been demonstrated in Calu-3 human lung and Caco-2 human colon cells infected with wild-type, delta, or omicron SARS-CoV-2, respectively, and (v) analysis of TF27 combination treatments has revealed synergistic interaction with GC376, but antagonistic interaction with EIDD-1931. Combined, the data demonstrated the pronounced anti-SARS-CoV-2 activity of TF27 and thus highlight the potential of trioxane compounds for further pharmacologic development towards improved options for COVID-specific medication.
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32
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Sharma G, Song LF, Merz KM. Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. J Chem Inf Model 2022; 62:6574-6585. [PMID: 35118864 PMCID: PMC8848506 DOI: 10.1021/acs.jcim.1c01283] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Indexed: 01/07/2023]
Abstract
The recent outbreak of COVID-19 infection started in Wuhan, China, and spread across China and beyond. Since the WHO declared COVID-19 a pandemic (March 11, 2020), three vaccines and only one antiviral drug (remdesivir) have been approved (Oct 22, 2020) by the FDA. The coronavirus enters human epithelial cells by the binding of the densely glycosylated fusion spike protein (S protein) to a receptor (angiotensin-converting enzyme 2, ACE2) on the host cell surface. Therefore, inhibiting the viral entry is a promising treatment pathway for preventing or ameliorating the effects of COVID-19 infection. In the current work, we have used all-atom molecular dynamics (MD) simulations to investigate the influence of the MLN-4760 inhibitor on the conformational properties of ACE2 and its interaction with the receptor-binding domain (RBD) of SARS-CoV-2. We have found that the presence of an inhibitor tends to completely/partially open the ACE2 receptor where the two subdomains (I and II) move away from each other, while the absence results in partial or complete closure. The current study increases our understanding of ACE inhibition by MLN-4760 and how it modulates the conformational properties of ACE2.
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Affiliation(s)
- Gaurav Sharma
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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33
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Bram Y, Duan X, Nilsson-Payant BE, Chandar V, Wu H, Shore D, Fajardo A, Sinha S, Hassan N, Weinstein H, TenOever BR, Chen S, Schwartz RE. Dual-Reporter System for Real-Time Monitoring of SARS-CoV-2 Main Protease Activity in Live Cells Enables Identification of an Allosteric Inhibition Path. ACS BIO & MED CHEM AU 2022; 2:627-641. [PMID: 36570071 PMCID: PMC9603010 DOI: 10.1021/acsbiomedchemau.2c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
The SARS-CoV-2 pandemic is an ongoing threat to global health, and the continuing emergence of contagious variants highlights the urgent need for additional antiviral therapy to attenuate COVID-19 disease. The SARS-CoV-2 main protease (3CLpro) presents an attractive target for such therapy due to its high sequence conservation and key role in the viral life cycle. In this study, we designed a fluorescent-luminescent cell-based reporter for the detection and quantification of 3CLpro intracellular activity. Employing this platform, we examined the efficiency of known protease inhibitors against 3CLpro and further identified potent inhibitors through high-throughput chemical screening. Computational analysis confirmed a direct interaction of the lead compounds with the protease catalytic site and identified a prototype for efficient allosteric inhibition. These developments address a pressing need for a convenient sensor and specific targets for both virus detection and rapid discovery of potential inhibitors.
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Affiliation(s)
- Yaron Bram
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Xiaohua Duan
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Benjamin E. Nilsson-Payant
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States
| | - Vasuretha Chandar
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Hao Wu
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Derek Shore
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Alvaro Fajardo
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Saloni Sinha
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Nora Hassan
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Harel Weinstein
- Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Benjamin R. TenOever
- Department
of Microbiology, Icahn School of Medicine
at Mount Sinai, One Gustav L Levy Place, New York, New York 10029, United
States,
| | - Shuibing Chen
- Department
of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,
| | - Robert E. Schwartz
- Division
of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States,Department
of Physiology, Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10065, United States,
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Hu F, Wang D, Huang H, Hu Y, Yin P. Bridging the Gap between Target-Based and Cell-Based Drug Discovery with a Graph Generative Multitask Model. J Chem Inf Model 2022; 62:6046-6056. [PMID: 36401569 DOI: 10.1021/acs.jcim.2c01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of new drugs is crucial for protecting humans from disease. In the past several decades, target-based screening has been one of the most popular methods for developing new drugs. This method efficiently screens potential inhibitors of a target protein in vitro, but it frequently fails in vivo due to insufficient activity of the selected drugs. There is a need for accurate computational methods to bridge this gap. Here, we present a novel graph multi-task deep learning model to identify compounds with both target inhibitory and cell active (MATIC) properties. On a carefully curated SARS-CoV-2 data set, the proposed MATIC model shows advantages compared with the traditional method in screening effective compounds in vivo. Following this, we investigated the interpretability of the model and discovered that the learned features for target inhibition (in vitro) or cell active (in vivo) tasks are different with molecular property correlations and atom functional attention. Based on these findings, we utilized a Monte Carlo-based reinforcement learning generative model to generate novel multiproperty compounds with both in vitro and in vivo efficacy, thus bridging the gap between target-based and cell-based drug discovery. The tool is freely accessible at https://github.com/SIAT-code/MATIC.
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Affiliation(s)
- Fan Hu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Dongqi Wang
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Huazhen Huang
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Yishen Hu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Peng Yin
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
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Torres Neto L, Monteiro MLG, Fernández-Romero J, Teleshova N, Sailer J, Conte Junior CA. Essential oils block cellular entry of SARS-CoV-2 delta variant. Sci Rep 2022; 12:20639. [PMID: 36450916 PMCID: PMC9709744 DOI: 10.1038/s41598-022-25342-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Aiming to fill a gap in the literature, we aimed to identify the most promising EOs blocking in vitro cellular entry of SARS-CoV-2 delta variant without conferring human cytotoxicity and provide insights into the influence of their composition on these activities. Twelve EOs were characterized by gas chromatography coupled to mass spectrometry. The antiviral and cytotoxicity activities were determined using the cell-based pseudoviral entry with SARS-CoV-2 delta pseudovirus and the XTT assay in HeLa cells expressing human angiotensin-converting enzyme 2 (HeLa ACE-2), respectively. Syzygium aromaticum, Cymbopogon citratus, Citrus limon, Pelargonium graveolens, Origanum vulgare, "Illicium verum", and Matricaria recutita showed EC50 lowered or close to 1 µg/mL but also the lowest CC50 (0.20-1.70 µg/mL), except "I. verum" (30.00 µg/mL). Among these, "I. verum", C. limon, P. graveolens and S. aromaticum proved to be promising alternatives for SARS-CoV-2 delta variant inhibition (therapeutic index above 4), which possibly was related to the compounds (E)-anetole, limonene and beta-pinene, citronellol, and eugenol, respectively.
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Affiliation(s)
- Luiz Torres Neto
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil.
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil.
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Avenida Athos da Silveira Ramos, N. 149, Bloco A, 5° Andar, Rio de Janeiro, RJ, 21941-909, Brazil.
| | - Maria Lúcia Guerra Monteiro
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil.
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil.
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Avenida Athos da Silveira Ramos, N. 149, Bloco A, 5° Andar, Rio de Janeiro, RJ, 21941-909, Brazil.
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, 24220-000, Brazil.
| | - José Fernández-Romero
- Science Department, Borough of Manhattan Community College, The City University of New York, 199 Chambers Street, Science Department Room N699, New York, NY, 10007, USA
- Center for Biomedical Research, Population Council, 1230 York Avenue, New York, NY, 10065, USA
| | - Natalia Teleshova
- Center for Biomedical Research, Population Council, 1230 York Avenue, New York, NY, 10065, USA
| | - James Sailer
- Center for Biomedical Research, Population Council, 1230 York Avenue, New York, NY, 10065, USA
| | - Carlos Adam Conte Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Avenida Athos da Silveira Ramos, N. 149, Bloco A, 5° Andar, Rio de Janeiro, RJ, 21941-909, Brazil
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, 24220-000, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
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Alrashedi MG, Ali AS, Ahmed OA, Ibrahim IM. Local Delivery of Azithromycin Nanoformulation Attenuated Acute Lung Injury in Mice. Molecules 2022; 27:8293. [PMID: 36500388 PMCID: PMC9739299 DOI: 10.3390/molecules27238293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Humanity has suffered from the coronavirus disease 2019 (COVID-19) pandemic over the past two years, which has left behind millions of deaths. Azithromycin (AZ), an antibiotic used for the treatment of several bacterial infections, has shown antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as against the dengue, Zika, Ebola, and influenza viruses. Additionally, AZ has shown beneficial effects in non-infective diseases such as cystic fibrosis and bronchiectasis. However, the systemic use of AZ in several diseases showed low efficacy and potential cardiac toxicity. The application of nanotechnology to formulate a lung delivery system of AZ could prove to be one of the solutions to overcome these drawbacks. Therefore, we aimed to evaluate the attenuation of acute lung injury in mice via the local delivery of an AZ nanoformulation. The hot emulsification-ultrasonication method was used to prepare nanostructured lipid carrier of AZ (AZ-NLC) pulmonary delivery systems. The developed formulation was evaluated and characterized in vitro and in vivo. The efficacy of the prepared formulation was tested in the bleomycin (BLM) -mice model for acute lung injury. AZ-NLC was given by the intratracheal (IT) route for 6 days at a dose of about one-eighth oral dose of AZ suspension. Samples of lung tissues were taken at the end of the experiment for immunological and histological assessments. AZ-NLC showed an average particle size of 453 nm, polydispersity index of 0.228 ± 0.07, zeta potential of -30 ± 0.21 mV, and a sustained release pattern after the initial 50% drug release within the first 2 h. BLM successfully induced a marked increase in pro-inflammatory markers and also induced histological changes in pulmonary tissues. All these alterations were significantly reversed by the concomitant administration of AZ-NLC (IT). Pulmonary delivery of AZ-NLC offered delivery of the drug locally to lung tissues. Its attenuation of lung tissue inflammation and histological injury induced by bleomycin was likely through the downregulation of the p53 gene and the modulation of Bcl-2 expression. This novel strategy could eventually improve the effectiveness and diminish the adverse drug reactions of AZ. Lung delivery could be a promising treatment for acute lung injury regardless of its cause. However, further work is needed to explore the stability of the formulation, its pharmacokinetics, and its safety.
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Affiliation(s)
- Mohsen G. Alrashedi
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Ministry of Health, Riyadh 12628, Saudi Arabia
| | - Ahmed Shaker Ali
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Osama Abdelhakim Ahmed
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ibrahim M. Ibrahim
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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37
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Koçak ÇC, Aslışen B, Karabiberoğlu Ş, Özdokur KV, Aslan A, Koçak S. Electrochemical Determination of Levofloxacin Using Poly(Pyrogallol Red) Modified Glassy Carbon Electrode. ChemistrySelect 2022. [DOI: 10.1002/slct.202201864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Burak Aslışen
- Applied Science Research Center Manisa Celal Bayar University 45040 Manisa Turkey
| | - Şükriye Karabiberoğlu
- Department of Chemistry Ege University Faculty of Science 35100 Bornova İzmir Turkey
| | - Kemal Volkan Özdokur
- Department of Chemistry Erzincan Binali Yıldırım University Science Faculty 24100 Erzincan Turkey
| | - Avni Aslan
- Department of Chemistry Manisa Celal Bayar University Science and Art Faculty 45040 Manisa Turkey
| | - Süleyman Koçak
- Department of Chemistry Manisa Celal Bayar University Science and Art Faculty 45040 Manisa Turkey
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38
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Nguyenla X, Wehri E, Van Dis E, Biering SB, Yamashiro LH, Zhu C, Stroumza J, Dugast-Darzacq C, Graham TGW, Wang X, Jockusch S, Tao C, Chien M, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Russo JJ, Ju J, Näär AM, Stanley S, Schaletzky J. Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells. Sci Rep 2022; 12:18506. [PMID: 36323770 PMCID: PMC9628577 DOI: 10.1038/s41598-022-21034-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/21/2022] [Indexed: 11/07/2022] Open
Abstract
SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy is only moderate, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. This identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir's apparent potency > 25-fold. We report that HCV NS5A inhibitors act on the SARS-CoV-2 exonuclease proofreader, providing a possible explanation for the synergy observed with nucleoside analog remdesivir. FDA-approved Hepatitis C therapeutics Epclusa® (velpatasvir/sofosbuvir) and Zepatier® (elbasvir/grazoprevir) could be further optimized to achieve potency and pharmacokinetic properties that support clinical evaluation in combination with remdesivir.
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Affiliation(s)
- Xammy Nguyenla
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Livia H Yamashiro
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Chi Zhu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Julien Stroumza
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA, 94720, USA
| | - Thomas G W Graham
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA, 94720, USA
| | - Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA
| | - Anders M Näär
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Sarah Stanley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA.
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA.
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39
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Use of Human Lung Tissue Models for Screening of Drugs against SARS-CoV-2 Infection. Viruses 2022; 14:v14112417. [PMID: 36366514 PMCID: PMC9693925 DOI: 10.3390/v14112417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
The repurposing of licenced drugs for use against COVID-19 is one of the most rapid ways to develop new and alternative therapeutic options to manage the ongoing pandemic. Given circa 7817 licenced compounds available from Compounds Australia that can be screened, this paper demonstrates the utility of commercially available ex vivo/3D airway and alveolar tissue models. These models are a closer representation of in vivo studies than in vitro models, but retain the benefits of rapid in vitro screening for drug efficacy. We demonstrate that several existing drugs appear to show anti-SARS-CoV-2 activity against both SARS-CoV-2 Delta and Omicron Variants of Concern in the airway model. In particular, fluvoxamine, as well as aprepitant, everolimus, and sirolimus, has virus reduction efficacy comparable to the current standard of care (remdesivir, molnupiravir, nirmatrelvir). Whilst these results are encouraging, further testing and efficacy studies are required before clinical use can be considered.
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40
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Baek YB, Kwon HJ, Sharif M, Lim J, Lee IC, Ryu YB, Lee JI, Kim JS, Lee YS, Kim DH, Park SI, Kim DK, Kim JS, Choy HE, Lee S, Choi HS, Osborne TF, Jeon TI, Cho KO. Therapeutic strategy targeting host lipolysis limits infection by SARS-CoV-2 and influenza A virus. Signal Transduct Target Ther 2022; 7:367. [PMID: 36253361 PMCID: PMC9575645 DOI: 10.1038/s41392-022-01223-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/21/2022] [Accepted: 10/09/2022] [Indexed: 11/08/2022] Open
Abstract
The biosynthesis of host lipids and/or lipid droplets (LDs) has been studied extensively as a putative therapeutic target in diverse viral infections. However, directly targeting the LD lipolytic catabolism in virus-infected cells has not been widely investigated. Here, we show the linkage of the LD-associated lipase activation to the breakdown of LDs for the generation of free fatty acids (FFAs) at the late stage of diverse RNA viral infections, which represents a broad-spectrum antiviral target. Dysfunction of membrane transporter systems due to virus-induced cell injury results in intracellular malnutrition at the late stage of infection, thereby making the virus more dependent on the FFAs generated from LD storage for viral morphogenesis and as a source of energy. The replication of SARS-CoV-2 and influenza A virus (IAV), which is suppressed by the treatment with LD-associated lipases inhibitors, is rescued by supplementation with FFAs. The administration of lipase inhibitors, either individually or in a combination with virus-targeting drugs, protects mice from lethal IAV infection and mitigates severe lung lesions in SARS-CoV-2-infected hamsters. Moreover, the lipase inhibitors significantly reduce proinflammatory cytokine levels in the lungs of SARS-CoV-2- and IAV-challenged animals, a cause of a cytokine storm important for the critical infection or mortality of COVID-19 and IAV patients. In conclusion, the results reveal that lipase-mediated intracellular LD lipolysis is commonly exploited to facilitate RNA virus replication and furthermore suggest that pharmacological inhibitors of LD-associated lipases could be used to curb current COVID-19- and future pandemic outbreaks of potentially troublesome RNA virus infection in humans.
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Affiliation(s)
- Yeong-Bin Baek
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience & Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Muhammad Sharif
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeongah Lim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - In-Chul Lee
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience & Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Young Bae Ryu
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience & Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Jae-In Lee
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience & Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience & Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Young-Seung Lee
- Department of Animal Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Dong-Hoon Kim
- Department of Pharmacology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Sang-Ik Park
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Don-Kyu Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61486, Republic of Korea
| | - Sunwoo Lee
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hueng-Sik Choi
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Timothy F Osborne
- Institute for Fundamental Biomedical Research, Department of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA
| | - Tae-Il Jeon
- Department of Animal Science, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Kyoung-Oh Cho
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Ratnapriya S, Braun AR, Cervera H, Carlson D, Ding S, Paulson C, Mishra N, Sachs JN, Aldrich C, Finzi A, Herschhorn A. Broad Tricyclic Ring Inhibitors Block SARS-CoV-2 Spike Function Required for Viral Entry. ACS Infect Dis 2022; 8:2045-2058. [PMID: 36153947 PMCID: PMC9528568 DOI: 10.1021/acsinfecdis.1c00658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 01/29/2023]
Abstract
The entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells requires binding of the viral spike glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor, which triggers subsequent conformational changes to facilitate viral and cellular fusion at the plasma membrane or following endocytosis. Here, we experimentally identified selective and broad inhibitors of SARS-CoV-2 entry that share a tricyclic ring (or similar) structure. The inhibitory effect was restricted to early steps during infection and the entry inhibitors interacted with the receptor binding domain of the SARS-CoV-2 spike but did not significantly interfere with receptor (ACE2) binding. Instead, some of these compounds induced conformational changes or affected spike assembly and blocked SARS-CoV-2 spike cell-cell fusion activity. The broad inhibitors define a highly conserved binding pocket that is present on the spikes of SARS-CoV-1, SARS-CoV-2, and all circulating SARS-CoV-2 variants tested and block SARS-CoV spike activity required for mediating viral entry. These compounds provide new insights into the SARS-CoV-2 spike topography, as well as into critical steps on the entry pathway, and can serve as lead candidates for the development of broad-range entry inhibitors against SARS-CoVs.
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Affiliation(s)
- Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Anthony R. Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Héctor Cervera
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Danielle Carlson
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Carolyn Paulson
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Jonathan N. Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Courtney Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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MacRaild CA, Mohammed MUR, Faheem, Murugesan S, Styles IK, Peterson AL, Kirkpatrick CMJ, Cooper MA, Palombo EA, Simpson MM, Jain HA, Agarwal V, McAuley AJ, Kumar A, Creek DJ, Trevaskis NL, Vasan SS. Systematic Down-Selection of Repurposed Drug Candidates for COVID-19. Int J Mol Sci 2022; 23:11851. [PMID: 36233149 PMCID: PMC9569752 DOI: 10.3390/ijms231911851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 01/09/2023] Open
Abstract
SARS-CoV-2 is the cause of the COVID-19 pandemic which has claimed more than 6.5 million lives worldwide, devastating the economy and overwhelming healthcare systems globally. The development of new drug molecules and vaccines has played a critical role in managing the pandemic; however, new variants of concern still pose a significant threat as the current vaccines cannot prevent all infections. This situation calls for the collaboration of biomedical scientists and healthcare workers across the world. Repurposing approved drugs is an effective way of fast-tracking new treatments for recently emerged diseases. To this end, we have assembled and curated a database consisting of 7817 compounds from the Compounds Australia Open Drug collection. We developed a set of eight filters based on indicators of efficacy and safety that were applied sequentially to down-select drugs that showed promise for drug repurposing efforts against SARS-CoV-2. Considerable effort was made to evaluate approximately 14,000 assay data points for SARS-CoV-2 FDA/TGA-approved drugs and provide an average activity score for 3539 compounds. The filtering process identified 12 FDA-approved molecules with established safety profiles that have plausible mechanisms for treating COVID-19 disease. The methodology developed in our study provides a template for prioritising drug candidates that can be repurposed for the safe, efficacious, and cost-effective treatment of COVID-19, long COVID, or any other future disease. We present our database in an easy-to-use interactive interface (CoviRx that was also developed to enable the scientific community to access to the data of over 7000 potential drugs and to implement alternative prioritisation and down-selection strategies.
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Affiliation(s)
- Christopher A. MacRaild
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
| | - Muzaffar-Ur-Rehman Mohammed
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Pilani 333031, Rajasthan, India
| | - Faheem
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Pilani 333031, Rajasthan, India
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Sankaranarayanan Murugesan
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Pilani 333031, Rajasthan, India
| | - Ian K. Styles
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
| | - Amanda L. Peterson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Carl M. J. Kirkpatrick
- Centre for Medicine Use and Safety, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Moana M. Simpson
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Hardik A. Jain
- Department of Electrical and Electronics Engineering, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Vinti Agarwal
- Department of Computer Science and Information Systems, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Alexander J. McAuley
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Portarlington Road, Geelong, VIC 3220, Australia
| | - Anupama Kumar
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Campus, SA 5064, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
| | - Natalie L. Trevaskis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3800, Australia
| | - Seshadri S. Vasan
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Portarlington Road, Geelong, VIC 3220, Australia
- Department of Health, 189 Royal Street, East Perth, WA 6004, Australia
- Department of Health Sciences, University of York, York YO10 5DD, UK
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Aljarba NH, Hasnain MS, Bin-Meferij MM, Alkahtani S. An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:102214. [PMID: 35811756 PMCID: PMC9250415 DOI: 10.1016/j.jksus.2022.102214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/28/2022] [Indexed: 05/04/2023]
Abstract
The deadliest recent pandemic outbreak of COVID-19 disease has severely damaged the socio-economic health of the people globally. Due to unavailability of any effective vaccine or treatment the human beings are still struggling to overcome the pandemic condition. In an attempt to discover anti-COVID molecule, we used in-silico approach and reported 160 natural polyphenols to identify the most promising druggable HITs that can further used for drug discovery process. The co-crystallized structure COVID protease enzyme (PDB id 6LU7) was used. HTVS, MD simulation, binding energy calculations and in-silico ADME calculation were done and analyzed. Depending upon the scores three compounds galangin, nalsudaldain and rhamnezine were identified and the docking score were found to be -7.704, -6.51, -4.212 respectively. These docked complexes were further subjected to MD simulation runs over a 100 ns time and the RMSD and RMSF values were determined. The RMSD values of three compounds were found to be 2.9 Å, 7.6 Å & 9.5 Å respectively and the lowest RMSF values suggested the steady stability of ligand-protein complexes. The binding free energies (ΔG) of compounds with protein were found to be -49.8, -56.45, -62.87 kJ/mole. Moreover, in-silico ADME calculations indicated the drug likeliness properties of these molecules. By considering all these in-silico results the identified HITs would be the most probable anti-COVID drug molecules that can be further taken in wet lab and can act as lead for development of newer inhibitor of COVID-19 main protease enzyme.
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Affiliation(s)
- Nada H Aljarba
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Md Saquib Hasnain
- Department of Pharmacy, Palamau Institute of Pharmacy, Chianki, Daltonganj 822102, Jharkhand, India
| | | | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
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Proposal to Consider Chemical/Physical Microenvironment as a New Therapeutic Off-Target Approach. Pharmaceutics 2022; 14:pharmaceutics14102084. [PMID: 36297518 PMCID: PMC9611316 DOI: 10.3390/pharmaceutics14102084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022] Open
Abstract
The molecular revolution could lead drug discovery from chance observation to the rational design of new classes of drugs that could simultaneously be more effective and less toxic. Unfortunately, we are witnessing some failure in this sense, and the causes of the crisis involve a wide range of epistemological and scientific aspects. In pharmacology, one key point is the crisis of the paradigm the “magic bullet”, which is to design therapies based on specific molecular targets. Drug repurposing is one of the proposed ways out of the crisis and is based on the off-target effects of known drugs. Here, we propose the microenvironment as the ideal place to direct the off-targeting of known drugs. While it has been extensively investigated in tumors, the generation of a harsh microenvironment is also a phenotype of the vast majority of chronic diseases. The hostile microenvironment, on the one hand, reduces the efficacy of both chemical and biological drugs; on the other hand, it dictates a sort of “Darwinian” selection of those cells armed to survive in such hostile conditions. This opens the way to the consideration of the microenvironment as a convenient target for pharmacological action, with a clear example in proton pump inhibitors.
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Mousavi S, Zare S, Mirzaei M, Feizi A. Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Affiliation(s)
- Sarah Mousavi
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Zare
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahmoud Mirzaei
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
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Nepali K, Sharma R, Sharma S, Thakur A, Liou JP. Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal. J Biomed Sci 2022; 29:65. [PMID: 36064696 PMCID: PMC9444709 DOI: 10.1186/s12929-022-00847-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/16/2022] [Indexed: 02/08/2023] Open
Abstract
Unprecedented efforts of the researchers have been witnessed in the recent past towards the development of vaccine platforms for the control of the COVID-19 pandemic. Albeit, vaccination stands as a practical strategy to prevent SARS-CoV-2 infection, supplementing the anti-COVID19 arsenal with therapeutic options such as small molecules/peptides and antibodies is being conceived as a prudent strategy to tackle the emerging SARS-CoV-2 variants. Noteworthy to mention that collective efforts from numerous teams have led to the generation of a voluminous library composed of chemically and mechanistically diverse small molecules as anti-COVID19 scaffolds. This review article presents an overview of medicinal chemistry campaigns and drug repurposing programs that culminated in the identification of a plethora of small molecule-based anti-COVID19 drugs mediating their antiviral effects through inhibition of proteases, S protein, RdRp, ACE2, TMPRSS2, cathepsin and other targets. In light of the evidence ascertaining the potential of small molecule drugs to approach conserved proteins required for the viral replication of all coronaviruses, accelerated FDA approvals are anticipated for small molecules for the treatment of COVID19 shortly. Though the recent attempts invested in this direction in pursuit of enrichment of the anti-COVID-19 armoury (chemical tools) are praiseworthy, some strategies need to be implemented to extract conclusive benefits of the recently reported small molecule viz. (i) detailed preclinical investigation of the generated anti-COVID19 scaffolds (ii) in-vitro profiling of the inhibitors against the emerging SARS-CoV-2 variants (iii) development of assays enabling rapid screening of the libraries of anti-COVID19 scaffold (iv) leveraging the applications of machine learning based predictive models to expedite the anti-COVID19 drug discovery campaign (v) design of antibody-drug conjugates.
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Affiliation(s)
- Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan.
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan.
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Plebani R, Bai H, Si L, Li J, Zhang C, Romano M. 3D Lung Tissue Models for Studies on SARS-CoV-2 Pathophysiology and Therapeutics. Int J Mol Sci 2022; 23:ijms231710071. [PMID: 36077471 PMCID: PMC9456220 DOI: 10.3390/ijms231710071] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19), has provoked more than six million deaths worldwide and continues to pose a major threat to global health. Enormous efforts have been made by researchers around the world to elucidate COVID-19 pathophysiology, design efficacious therapy and develop new vaccines to control the pandemic. To this end, experimental models are essential. While animal models and conventional cell cultures have been widely utilized during these research endeavors, they often do not adequately reflect the human responses to SARS-CoV-2 infection. Therefore, models that emulate with high fidelity the SARS-CoV-2 infection in human organs are needed for discovering new antiviral drugs and vaccines against COVID-19. Three-dimensional (3D) cell cultures, such as lung organoids and bioengineered organs-on-chips, are emerging as crucial tools for research on respiratory diseases. The lung airway, small airway and alveolus organ chips have been successfully used for studies on lung response to infection by various pathogens, including corona and influenza A viruses. In this review, we provide an overview of these new tools and their use in studies on COVID-19 pathogenesis and drug testing. We also discuss the limitations of the existing models and indicate some improvements for their use in research against COVID-19 as well as future emerging epidemics.
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Affiliation(s)
- Roberto Plebani
- Center on Advanced Studies and Technology (CAST), Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
- Correspondence:
| | - Haiqing Bai
- Xellar Biosystems Inc., Cambridge, MA 02138, USA
| | - Longlong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chunhe Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mario Romano
- Center on Advanced Studies and Technology (CAST), Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
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Thébault S, Lejal N, Dogliani A, Donchet A, Urvoas A, Valerio-Lepiniec M, Lavie M, Baronti C, Touret F, Da Costa B, Bourgon C, Fraysse A, Saint-Albin-Deliot A, Morel J, Klonjkowski B, de Lamballerie X, Dubuisson J, Roussel A, Minard P, Le Poder S, Meunier N, Delmas B. Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals. PLoS Pathog 2022; 18:e1010799. [PMID: 36067253 PMCID: PMC9481167 DOI: 10.1371/journal.ppat.1010799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/16/2022] [Accepted: 08/06/2022] [Indexed: 12/04/2022] Open
Abstract
The binding of the SARS-CoV-2 spike to angiotensin-converting enzyme 2 (ACE2) promotes virus entry into the cell. Targeting this interaction represents a promising strategy to generate antivirals. By screening a phage-display library of biosynthetic protein sequences build on a rigid alpha-helicoidal HEAT-like scaffold (named αReps), we selected candidates recognizing the spike receptor binding domain (RBD). Two of them (F9 and C2) bind the RBD with affinities in the nM range, displaying neutralisation activity in vitro and recognizing distinct sites, F9 overlapping the ACE2 binding motif. The F9-C2 fusion protein and a trivalent αRep form (C2-foldon) display 0.1 nM affinities and EC50 of 8-18 nM for neutralization of SARS-CoV-2. In hamsters, F9-C2 instillation in the nasal cavity before or during infections effectively reduced the replication of a SARS-CoV-2 strain harbouring the D614G mutation in the nasal epithelium. Furthermore, F9-C2 and/or C2-foldon effectively neutralized SARS-CoV-2 variants (including delta and omicron variants) with EC50 values ranging from 13 to 32 nM. With their high stability and their high potency against SARS-CoV-2 variants, αReps provide a promising tool for SARS-CoV-2 therapeutics to target the nasal cavity and mitigate virus dissemination in the proximal environment.
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Affiliation(s)
- Stéphanie Thébault
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nathalie Lejal
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alexis Dogliani
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, UMR, Marseille, France
| | - Amélie Donchet
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Agathe Urvoas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette cedex, France
| | - Marie Valerio-Lepiniec
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette cedex, France
| | - Muriel Lavie
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Bruno Da Costa
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Bourgon
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Audrey Fraysse
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Audrey Saint-Albin-Deliot
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jessica Morel
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernard Klonjkowski
- UMR Virologie, INRAE-ENVA-ANSES, École Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, Marseille, France
| | - Jean Dubuisson
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Alain Roussel
- Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, UMR, Marseille, France
| | - Philippe Minard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette cedex, France
| | - Sophie Le Poder
- UMR Virologie, INRAE-ENVA-ANSES, École Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, Paris, France
| | - Nicolas Meunier
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Bernard Delmas
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
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Na-Bangchang K, Porasuphatana S, Karbwang J. Perspective: repurposed drugs for COVID-19. Arch Med Sci 2022; 18:1378-1391. [PMID: 36160358 PMCID: PMC9479713 DOI: 10.5114/aoms/152467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction The article aims to emphasize the necessity of proper research design, both scientifically and ethically, in order to provide good evidence for physicians to base their decisions on when prescribing drug treatment. Methods Research articles and guidelines related to therapy of COVID-19 were searched from the PubMed database. Results Only remdesivir and tocilizumab are medicines that have been approved by the US FDA's decision to approve their clinical use in moderate and severe COVID-19. Conclusions Favipiravir, ivermectin and andrographolide need further well-conducted research to confirm the efficacy and safety against COVID-19 at different stages.
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Affiliation(s)
- Kesara Na-Bangchang
- Drug Discovery and Development Center, Office of Advanced Science and Technology, Thammasat University, Pathumthani, Thailand
| | - Supatra Porasuphatana
- Department of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Juntra Karbwang
- Drug Discovery and Development Center, Office of Advanced Science and Technology, Thammasat University, Pathumthani, Thailand
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Wotring JW, McCarty SM, Shafiq K, Zhang CJ, Nguyen T, Meyer SR, Fursmidt R, Mirabelli C, Clasby MC, Wobus CE, O’Meara MJ, Sexton JZ. In Vitro Evaluation and Mitigation of Niclosamide's Liabilities as a COVID-19 Treatment. Vaccines (Basel) 2022; 10:1284. [PMID: 36016172 PMCID: PMC9412300 DOI: 10.3390/vaccines10081284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Niclosamide, an FDA-approved oral anthelmintic drug, has broad biological activity including anticancer, antibacterial, and antiviral properties. Niclosamide has also been identified as a potent inhibitor of SARS-CoV-2 infection in vitro, generating interest in its use for the treatment or prevention of COVID-19. Unfortunately, there are several potential issues with using niclosamide for COVID-19, including low bioavailability, significant polypharmacology, high cellular toxicity, and unknown efficacy against emerging SARS-CoV-2 variants of concern. In this study, we used high-content imaging-based immunofluorescence assays in two different cell models to assess these limitations and evaluate the potential for using niclosamide as a COVID-19 antiviral. We show that despite promising preliminary reports, the antiviral efficacy of niclosamide overlaps with its cytotoxicity giving it a poor in vitro selectivity index for anti-SARS-CoV-2 inhibition. We also show that niclosamide has significantly variable potency against the different SARS-CoV-2 variants of concern and is most potent against variants with enhanced cell-to-cell spread including the B.1.1.7 (alpha) variant. Finally, we report the activity of 33 niclosamide analogs, several of which have reduced cytotoxicity and increased potency relative to niclosamide. A preliminary structure-activity relationship analysis reveals dependence on a protonophore for antiviral efficacy, which implicates nonspecific endolysosomal neutralization as a dominant mechanism of action. Further single-cell morphological profiling suggests niclosamide also inhibits viral entry and cell-to-cell spread by syncytia. Altogether, our results suggest that niclosamide is not an ideal candidate for the treatment of COVID-19, but that there is potential for developing improved analogs with higher clinical translational potential in the future.
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Affiliation(s)
- Jesse W. Wotring
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sean M. McCarty
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khadija Shafiq
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles J. Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Theophilus Nguyen
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | - Sophia R. Meyer
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Reid Fursmidt
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martin C. Clasby
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan Z. Sexton
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
- U-M Center for Drug Repurposing, University of Michigan, Ann Arbor, MI 48109, USA
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