1
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W. An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. Int J Biol Macromol 2024; 265:130644. [PMID: 38462102 DOI: 10.1016/j.ijbiomac.2024.130644] [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: 10/26/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
The main proteinase (Mpro) of SARS-CoV-2 plays a critical role in cleaving viral polyproteins into functional proteins required for viral replication and assembly, making it a prime drug target for COVID-19. It is well known that noncompetitive inhibition offers potential therapeutic options for treating COVID-19, which can effectively reduce the likelihood of cross-reactivity with other proteins and increase the selectivity of the drug. Therefore, the discovery of allosteric sites of Mpro has both scientific and practical significance. In this study, we explored the binding characteristics and inhibiting process of Mpro activity by two recently reported allosteric inhibitors, pelitinib and AT7519 which were obtained by the X-ray screening experiments, to probe the allosteric mechanism via molecular dynamic (MD) simulations. We found that pelitinib and AT7519 can stably bind to Mpro far from the active site. The binding affinity is estimated to be -24.37 ± 4.14 and - 26.96 ± 4.05 kcal/mol for pelitinib and AT7519, respectively, which is considerably stable compared with orthosteric drugs. Furthermore, the strong binding caused clear changes in the catalytic site of Mpro, thus decreasing the substrate accessibility. The community network analysis also validated that pelitinib and AT7519 strengthened intra- and inter-domain communication of Mpro dimer, resulting in a rigid Mpro, which could negatively impact substrate binding. In summary, our findings provide the detailed working mechanism for the two experimentally observed allosteric sites of Mpro. These allosteric sites greatly enhance the 'druggability' of Mpro and represent attractive targets for the development of new Mpro inhibitors.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Yang Liu
- School of Physics, Shandong University, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, China
| | | | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, China.
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2
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Halip L, Avram S, Curpan R, Borota A, Bora A, Bologa C, Oprea TI. Exploring DrugCentral: from molecular structures to clinical effects. J Comput Aided Mol Des 2023; 37:681-694. [PMID: 37707619 PMCID: PMC10692006 DOI: 10.1007/s10822-023-00529-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
DrugCentral, accessible at https://drugcentral.org , is an open-access online drug information repository. It covers over 4950 drugs, incorporating structural, physicochemical, and pharmacological details to support drug discovery, development, and repositioning. With around 20,000 bioactivity data points, manual curation enhances information from several major digital sources. Approximately 724 mechanism-of-action (MoA) targets offer updated drug target insights. The platform captures clinical data: over 14,300 on- and off-label uses, 27,000 contraindications, and around 340,000 adverse drug events from pharmacovigilance reports. DrugCentral encompasses information from molecular structures to marketed formulations, providing a comprehensive pharmaceutical reference. Users can easily navigate basic drug information and key features, making DrugCentral a versatile, unique resource. Furthermore, we present a use-case example where we utilize experimentally determined data from DrugCentral to support drug repurposing. A minimum activity threshold t should be considered against novel targets to repurpose a drug. Analyzing 1156 bioactivities for human MoA targets suggests a general threshold of 1 µM: t = 6 when expressed as - log[Activity(M)]). This applies to 87% of the drugs. Moreover, t can be refined empirically based on water solubility (S): t = 3 - logS, for logS < - 3. Alongside the drug repurposing classification scheme, which considers intellectual property rights, market exclusivity protections, and market accessibility, DrugCentral provides valuable data to prioritize candidates for drug repurposing programs efficiently.
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Affiliation(s)
- Liliana Halip
- Department of Computational Chemistry, "Coriolan Dragulescu" Institute of Chemistry, Timisoara, Romania
| | - Sorin Avram
- Department of Computational Chemistry, "Coriolan Dragulescu" Institute of Chemistry, Timisoara, Romania
| | - Ramona Curpan
- Department of Computational Chemistry, "Coriolan Dragulescu" Institute of Chemistry, Timisoara, Romania
| | - Ana Borota
- Department of Computational Chemistry, "Coriolan Dragulescu" Institute of Chemistry, Timisoara, Romania
| | - Alina Bora
- Department of Computational Chemistry, "Coriolan Dragulescu" Institute of Chemistry, Timisoara, Romania
| | - Cristian Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA.
- Expert Systems Inc, San Diego, CA, USA.
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3
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Zhai C, Wang M, Jin Y, Chung HJ, Kim S, Kim HJ, Hong ST. Oral delivery of a host-directed antiviral, niclosamide, as a cholate-coated nanoformulation. Int J Antimicrob Agents 2023; 62:106973. [PMID: 37741586 DOI: 10.1016/j.ijantimicag.2023.106973] [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: 01/19/2023] [Revised: 07/21/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023]
Abstract
Potentially significant drug candidates often face elimination from consideration due to the lack of an effective method for systemic delivery. The poor solubility of these candidates has posed a major obstacle for their development as oral pills or injectables. Niclosamide, a host-directed antiviral, is a good example. In this study, a nanoformulation technology that allows for the non-covalent formulation of niclosamide with cholic acids was developed. This formulation enables efficient systemic delivery through endocytosis and enterohepatic circulation of bile-acid-coated nanoparticles. The oral bioavailability of niclosamide-delivery nanoparticles (NDNs) was significantly enhanced to 38.3%, representing an eight-fold increase compared with pure niclosamide. Consequently, the plasma concentration of niclosamide for the NDN formulation reached 1179.6 ng/mL, which is 11 times higher than the therapeutic plasma level. This substantial increase in plasma level contributed to the complete resolution of clinical symptoms in animals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This nanoformulation not only provides an orally deliverable antiviral drug for SARS-CoV-2 with improved pharmaceutical bioavailability, but also offers a solution to the systemic delivery challenges faced by potentially significant drug candidates.
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Affiliation(s)
- Chongkai Zhai
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk, South Korea; Animal Diseases and Public Health Engineering Research Centre of Henan Province, Luoyang Polytechnic, Luoyang, China
| | - Mingda Wang
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk, South Korea
| | - Yanyan Jin
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Hea-Jong Chung
- Gwangju Centre, Korea Basic Science Institute, Gwangju, South Korea
| | - Sura Kim
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk, South Korea
| | - Hyeon-Jin Kim
- SNJ Pharma Inc., BioLabs-LA at the Lundquist Institute for BioMedical Innovation at Harbor UCLA, Torrance, CA, USA.
| | - Seong-Tshool Hong
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk, South Korea.
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4
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Sasaki M, Tabata K, Kishimoto M, Itakura Y, Kobayashi H, Ariizumi T, Uemura K, Toba S, Kusakabe S, Maruyama Y, Iida S, Nakajima N, Suzuki T, Yoshida S, Nobori H, Sanaki T, Kato T, Shishido T, Hall WW, Orba Y, Sato A, Sawa H. S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and ameliorates COVID-19 severity in hamsters. Sci Transl Med 2023; 15:eabq4064. [PMID: 36327352 PMCID: PMC9765455 DOI: 10.1126/scitranslmed.abq4064] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622 (ensitrelvir), an inhibitor of SARS-CoV-2 main protease (Mpro; also known as 3C-like protease), decreases viral load and ameliorates disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to submicromolar concentrations in cells. Oral administration of S-217622 demonstrated favorable pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern, including the highly pathogenic Delta variant and the recently emerged Omicron BA.5 and BA.2.75 variants. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase 3 clinical trial (clinical trial registration no. jRCT2031210350), has remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Corresponding author. (M.S.); (H.S.)
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Hiroko Kobayashi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Takuma Ariizumi
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shinsuke Toba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shinji Kusakabe
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Yuki Maruyama
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | | | | | | | | | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,National Virus Reference Laboratory, School of Medicine, University College of Dublin, 4, Ireland.,Global Virus Network, Baltimore, MD, 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Akihiko Sato
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,Shionogi & Co., Ltd., Osaka 561-0825, Japan.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-220, Japan.,International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.,Global Virus Network, Baltimore, MD, 21201, USA.,Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, 001-0021, Japan.,One Health Research Center, Hokkaido University, Sapporo, 001-0020, Japan.,Corresponding author. (M.S.); (H.S.)
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5
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Ma C, Zhou Z, Liu H, Koslicki D. KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description. Gigascience 2022; 12:giad057. [PMID: 37602759 PMCID: PMC10441000 DOI: 10.1093/gigascience/giad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/05/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Computational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan diseases due to its cheaper investment and shorter research cycle compared with traditional wet-lab drug discovery approaches. However, the underlying mechanisms of action (MOAs) between repurposed drugs and their target diseases remain largely unknown, which is still a main obstacle for computational drug repurposing methods to be widely adopted in clinical settings. RESULTS In this work, we propose KGML-xDTD: a Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases. It is a 2-module framework that not only predicts the treatment probabilities between drugs/compounds and diseases but also biologically explains them via knowledge graph (KG) path-based, testable MOAs. We leverage knowledge-and-publication-based information to extract biologically meaningful "demonstration paths" as the intermediate guidance in the Graph-based Reinforcement Learning (GRL) path-finding process. Comprehensive experiments and case study analyses show that the proposed framework can achieve state-of-the-art performance in both predictions of drug repurposing and recapitulation of human-curated drug MOA paths. CONCLUSIONS KGML-xDTD is the first model framework that can offer KG path explanations for drug repurposing predictions by leveraging the combination of prediction outcomes and existing biological knowledge and publications. We believe it can effectively reduce "black-box" concerns and increase prediction confidence for drug repurposing based on predicted path-based explanations and further accelerate the process of drug discovery for emerging diseases.
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Affiliation(s)
- Chunyu Ma
- Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Zhihan Zhou
- Department of Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - Han Liu
- Department of Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - David Koslicki
- Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
- Department of Computer Science and Engineering, Pennsylvania State University, State College, PA 16801, USA
- Department of Biology, Pennsylvania State University, State College, PA 16801, USA
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6
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Bhullar KS, Nael MA, Elokely KM, Drews SJ, Wu J. Structurally Modified Bioactive Peptide Inhibits SARS-CoV-2 Lentiviral Particles Expression. Pharmaceutics 2022; 14:pharmaceutics14102045. [PMID: 36297481 PMCID: PMC9607082 DOI: 10.3390/pharmaceutics14102045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), the current global pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various pharmaceuticals are being developed to counter the spread of the virus. The strategy of repurposing known drugs and bioactive molecules is a rational approach. A previously described molecule, Ile-Arg-Trp (IRW), is a bioactive tripeptide that exhibits an ability to boost angiotensin converting enzyme-2 (ACE2) expression in animals and cells. Given the importance of SARS-CoV-2 S receptor binding domain (RBD)-ACE2 interaction in SARS-CoV-2 pathophysiology, we synthesized various IRW analogs intending to mitigate the RBD-ACE-2 interaction. Herein, we describe two analogs of IRW, A9 (Acetyl-Ile-Arg-Trp-Amide) and A14 (Formyl-Ile-Arg-Trp-Amide) which lowered the SARS-CoV-2 S RBD-ACE2 (at 50 µM) in vitro. The free energy of binding suggested that A9 and A14 interacted with the SARS-CoV-2 S RBD more favorably than ACE2. The calculated MMGBSA ΔG of spike binding for A9 was −57.22 kcal/mol, while that of A14 was −52.44 kcal/mol. A14 also inhibited furin enzymatic activity at various tested concentrations (25, 50, and 100 µM). We confirmed the effect of the two potent analogs using SARS-CoV-2 spike protein overexpressing cells. Both peptides lowered the protein expression of SARS-CoV-2 spike protein at the tested concentration (50 µM). Similarly, both peptides, A9 and A14 (50 µM), also inhibited pseudotyped lentiviral particles with SARS-CoV-2 Spike in ACE2 overexpressing cells. Further, the molecular dynamics (MD) calculations showed the interaction of A9 and A14 with multiple residues in spike S1 RBD. In conclusion, novel peptide analogs of ACE2 boosting IRW were prepared and confirmed through in vitro, cellular, and computational evaluations to be potential seed candidates for SARS-CoV-2 host cell binding inhibition.
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Affiliation(s)
- Khushwant S. Bhullar
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Manal A. Nael
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta 31527, Egypt
| | - Khaled M. Elokely
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Steven J. Drews
- Canadian Blood Services, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Jianping Wu
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 2R7, Canada
- Correspondence:
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7
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Lieber CM, Plemper RK. 4'-Fluorouridine Is a Broad-Spectrum Orally Available First-Line Antiviral That May Improve Pandemic Preparedness. DNA Cell Biol 2022; 41:699-704. [PMID: 35788144 PMCID: PMC9416544 DOI: 10.1089/dna.2022.0312] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The COVID-19 pandemic has highlighted the urgent need for the development of broad-spectrum antivirals to enhance preparedness against future spillover of zoonotic viruses with pandemic potential into the human population. Currently, the direct-acting orally available SARS-CoV-2 inhibitors molnupiravir and paxlovid are approved for human use under emergency use authorization. A promising next-generation therapeutic candidate is the orally available ribonucleoside analog 4'-fluorouridine (4'-FlU) that had potent antiviral efficacy against different viral targets, including SARS-CoV-2 in human organoids and animal models. Although a nucleoside analog inhibitor such as molnupiravir that targets the viral RNA-dependent RNA polymerase (RdRP) complex, 4'-FlU showed a distinct mechanism of activity, delayed chain termination, compared with molnupiravir's induction of viral error catastrophe. This review will focus on some currently approved and emerging medicines developed against SARS-CoV-2, examining their potential to form a pharmacological first-line defense against zoonotic viruses with pandemic potential.
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Affiliation(s)
- Carolin M Lieber
- Center for Translational Antiviral Research, Georgia State University, Atlanta, Georgia, USA
| | - Richard K Plemper
- Center for Translational Antiviral Research, Georgia State University, Atlanta, Georgia, USA
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8
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Chiu W, Verschueren L, Van den Eynde C, Buyck C, De Meyer S, Jochmans D, Bojkova D, Ciesek S, Cinatl J, De Jonghe S, Leyssen P, Neyts J, Van Loock M, Van Damme E. Development and optimization of a high-throughput screening assay for in vitro anti-SARS-CoV-2 activity: Evaluation of 5676 Phase 1 Passed Structures. J Med Virol 2022; 94:3101-3111. [PMID: 35229317 PMCID: PMC9088669 DOI: 10.1002/jmv.27683] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 01/09/2023]
Abstract
Although vaccines are currently used to control the coronavirus disease 2019 (COVID-19) pandemic, treatment options are urgently needed for those who cannot be vaccinated and for future outbreaks involving new severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) strains or coronaviruses not covered by current vaccines. Thus far, few existing antivirals are known to be effective against SARS-CoV-2 and clinically successful against COVID-19. As part of an immediate response to the COVID-19 pandemic, a high-throughput, high content imaging-based SARS-CoV-2 infection assay was developed in VeroE6 African green monkey kidney epithelial cells expressing a stable enhanced green fluorescent protein (VeroE6-eGFP cells) and was used to screen a library of 5676 compounds that passed Phase 1 clinical trials. Eight drugs (nelfinavir, RG-12915, itraconazole, chloroquine, hydroxychloroquine, sematilide, remdesivir, and doxorubicin) were identified as inhibitors of in vitro anti-SARS-CoV-2 activity in VeroE6-eGFP and/or Caco-2 cell lines. However, apart from remdesivir, toxicity and pharmacokinetic data did not support further clinical development of these compounds for COVID-19 treatment.
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Affiliation(s)
- Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | | | | | | | | | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | - Denisa Bojkova
- Institute of Medical VirologyUniversity Hospital Frankfurt, Goethe UniversityFrankfurt am MainGermany
| | - Sandra Ciesek
- Institute of Medical VirologyUniversity Hospital Frankfurt, Goethe UniversityFrankfurt am MainGermany
| | - Jindrich Cinatl
- Institute of Medical VirologyUniversity Hospital Frankfurt, Goethe UniversityFrankfurt am MainGermany
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and TransplantationRega Institute, Laboratory of Virology and ChemotherapyLeuvenBelgium
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9
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Hussein RK, Khouqeer G, Alkaoud AM, El-Khayatt AM. Probing the Action of Screened Anticancer Triazole–Tetrazole Derivatives Against COVID-19 Using Molecular Docking and DFT Investigations. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221093915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Drugs are continuously being evaluated for novel therapeutic uses. The purpose of this work was to screen anticancer triazole/tetrazole derivatives for effectiveness against the SARS-CoV-2 main protease (Mpro). First, the chemical structures’ activity was derived from conceptual quantum chemical calculations. According to molecular docking analysis, the compounds scored good interactions against SAR-COV-2's Mpro, with binding energies extending from −8.21 to −8.97 kcal/mol. The docked complexes included various bindings with His41 and Cys145, both catalytic residues responsible for cleavage of the SARS-CoV-2 Mpro. Among the 4 studied compounds, TD3 exhibited the highest affinity by achieving the most stable binding energy and lowest value for the inhibition constant. Most striking was that TD3 not only formed strong bonds with the catalytic residues His41 and Cys145, but also captured the residues of the catalytic loop (Cys44 to Pro52), which flank the catalytic dyads in Mpro's active site. As a result, the studied triazole/tetrazole derivatives, notably TD3, must be reviewed as potent drugs that could be repurposed for SARS-CoV-2 treatment.
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Affiliation(s)
- Rageh K. Hussein
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ghada Khouqeer
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ahmed M. Alkaoud
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ahmed M. El-Khayatt
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
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10
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Hou B, Zhang YM, Liao HY, Fu LF, Li DD, Zhao X, Qi JX, Yang W, Xiao GF, Yang L, Zuo ZY, Wang L, Zhang XL, Bai F, Yang L, Gao GF, Song H, Hu JM, Shang WJ, Zhou J. Target-Based Virtual Screening and LC/MS-Guided Isolation Procedure for Identifying Phloroglucinol-Terpenoid Inhibitors of SARS-CoV-2. JOURNAL OF NATURAL PRODUCTS 2022; 85:327-336. [PMID: 35084181 PMCID: PMC8806002 DOI: 10.1021/acs.jnatprod.1c00805] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 05/09/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to more than 5 million deaths worldwide to date. Due to the limited therapeutic options so far available, target-based virtual screening with LC/MS support was applied to identify the novel and high-content compounds 1-4 with inhibitory effects on SARS-CoV-2 in Vero E6 cells from the plant Dryopteris wallichiana. These compounds were also evaluated against SARS-CoV-2 in Calu-3 cells and showed unambiguous inhibitory activity. The inhibition assay of targets showed that compounds 3 and 4 mainly inhibited SARS-CoV-2 3CLpro, with effective Kd values. Through docking and molecular dynamics modeling, the binding site is described, providing a comprehensive understanding of 3CLpro and interactions for 3, including hydrogen bonds, hydrophobic bonds, and the spatial occupation of the B ring. Compounds 3 and 4 represent new, potential lead compounds for the development of anti-SARS-CoV-2 drugs. This study has led to the development of a target-based virtual screening method for exploring the potency of natural products and for identifying natural bioactive compounds for possible COVID-19 treatment.
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Affiliation(s)
- Bo Hou
- State Key Laboratory of Phytochemistry and Plant
Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry,
Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, People’s Republic of China
| | - Yu-Min Zhang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan 430071, People’s Republic of
China
| | - Han-Yi Liao
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Li-Feng Fu
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - De-Dong Li
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Xin Zhao
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Jian-Xun Qi
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Wei Yang
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Geng-Fu Xiao
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan 430071, People’s Republic of
China
| | - Lian Yang
- State Key Laboratory of Phytochemistry and Plant
Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry,
Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, People’s Republic of China
| | - Zheng-Yu Zuo
- State Key Laboratory of Phytochemistry and Plant
Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry,
Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, People’s Republic of China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies
and School of Life Science and Technology, Shanghai Tech
University, Shanghai 201210, People’s Republic of
China
| | - Xiang-Lei Zhang
- Shanghai Institute for Advanced Immunochemical Studies
and School of Life Science and Technology, Shanghai Tech
University, Shanghai 201210, People’s Republic of
China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies
and School of Life Science and Technology, Shanghai Tech
University, Shanghai 201210, People’s Republic of
China
| | - Liu Yang
- State Key Laboratory of Phytochemistry and Plant
Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry,
Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, People’s Republic of China
| | - George F. Gao
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Hao Song
- CAS Key Laboratory of Pathogenic Microbiology and
Immunology, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
- Research Network of Immunity and Health (RNIH),
Beijing Institutes of Life Science, Chinese Academy of
Sciences, Beijing 100101, People’s Republic of
China
| | - Jiang-Miao Hu
- State Key Laboratory of Phytochemistry and Plant
Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry,
Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, People’s Republic of China
| | - Wei-Juan Shang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan 430071, People’s Republic of
China
| | - Jun Zhou
- State Key Laboratory of Phytochemistry and Plant
Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry,
Kunming Institute of Botany, Chinese Academy of Sciences,
Kunming 650201, People’s Republic of China
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11
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Schultz É, Atlani-Duault L, Peretti-Watel P, Ward JK. Does the public know when a scientific controversy is over? Public perceptions of hydroxychloroquine in France between April 2020 and June 2021. Therapie 2022; 77:591-602. [PMID: 35101281 PMCID: PMC8801974 DOI: 10.1016/j.therap.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022]
Abstract
Objectives In the early stages of the coronavirus disease 2019 (COVID-19) pandemic, chloroquine and its derivatives such as hydroxychloroquine (HCQ) were widely commented upon both within the scientific community and in the media. This paper explores the different factors that influenced public perceptions in France of the efficacy of HCQ as well as their evolution between April 2020 and June 2021. Methods This article draws on 5 surveys conducted among representative samples of the French population (projects COCONEL and TRACTRUST; quota method, n = 1006; 1004; 2006; 1014 and 1005). We asked questions on the effectiveness of chloroquine against COVID-19. We also collected sociodemographic variables and attitudes toward politics and science. Results Between April and June 2021, the proportion of respondents who believed in the efficacy of HCQ decreased rapidly from 35% to 14%. The proportion of respondents who believed that HCQ is ineffective rose gradually from 6% to 21%. After adjusting for the temporal effect, the logistic regression showed a very strong association between political orientation and the belief in the efficacy of HCQ. Respondents who felt closest to the more radical parties (far-right and far-left) were more likely to believe in the efficacy of HCQ than those who felt closest to the political center (O.R. 2.48 [1.95–3.15] and 1.87 [1.44–2.43]). The role of trust in the government and in science and of the degree of political engagement were investigated in the two waves conducted after the scientific consensus was established during the summer of 2020. High levels of trust in the government and in science and of politicization are associated with belief of HCQ proven inefficacy. Across the whole period, a majority of respondents were uncertain. Even in 2021, 41.5% stated that the data were insufficient to decide whether or not HCQ is effective and 25.2% stating that they did not know. Conclusion Because media coverage of scientific controversies is higher in times of uncertainty than after these controversies have died down, the publicization of therapeutic promises can have lasting consequences on attitudes towards science and medicine.
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Affiliation(s)
- Émilien Schultz
- Université de Paris, IRD, Inserm, CEPED (UMR 196), 75006 Paris, France; Aix Marseille Univ, INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, ISSPAM, Equipe CANBIOS Labellisée Ligue Contre le Cancer, 13005 Marseille, France.
| | - Laëtitia Atlani-Duault
- Université de Paris, IRD, Inserm, CEPED (UMR 196), 75006 Paris, France; Institut COVID-19 Add Memoriam, université de Paris, 75006 Paris, France; WHO Collaborative Center for Research on Health and Humanitarian Policies and Practices, IRD, université de Paris, 75006 Paris, France; Columbia University, Mailman School of Public Health, New York, NY, USA
| | - Patrick Peretti-Watel
- VITROME, Aix-Marseille université, IRD, AP-HM, SSA, 13005 Marseille, France; Observatoire régional de la santé PACA (ORS Paca), Aix-Marseille université, 13385 Marseille, France
| | - Jeremy K Ward
- VITROME, Aix-Marseille université, IRD, AP-HM, SSA, 13005 Marseille, France; CERMES3, Inserm, CNRS, EHESS, université de Paris, 94801 Villejuif, France
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12
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Schultz É, Mignot L, Ward JK, Boaventura Bomfim D, Chabannon C, Mancini J. Public perceptions of the association between drug effectiveness and drug novelty in France during the COVID-19 pandemic. Therapie 2022; 77:693-701. [PMID: 35599194 PMCID: PMC9077798 DOI: 10.1016/j.therap.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/11/2022] [Accepted: 05/02/2022] [Indexed: 12/16/2022]
Abstract
OBJECTIVES During the coronavirus disease 2019 (COVID-19) pandemic, public debates overtly addressed the promises of new innovative drugs. Many of these debates pitted those who advocated for the development of new drugs by pharmaceutical companies against those who favored the repositioning of existing drugs. Our study explored perceptions of the association between drug novelty and effectiveness as well as perceptions of the role of the pharmaceutical industry in drug development. METHODS Data were collected in January 2021 from a quota sample of the French population aged 18-75years (n=1,000) during the second round of the "Health Literacy Survey 2019" (HLS19). RESULTS We tested the hypothesis that individuals with a high level of familiarity with the health care system and those with a high level of trust in institutions are more likely to agree that new drugs are more effective than old ones and that drug development should be driven by the pharmaceutical industry. A quarter (25%) of respondents agreed that new drugs are always more effective than old ones. Agreement with this statement was stronger among respondents with a high level of familiarity with the health care system (as measured by the navigational health literacy score, OR 3.34 [2.13-5.24]). Respondents with a low level of trust in pharmaceutical companies or politicians were two times less likely to agree that new drugs are always more effective than old ones (OR 0.63 [0.42-0.95] and OR 0.68 [0.49-0.94], respectively). A high level of trust in pharmaceutical companies was reported by 42% of respondents, and 43% agreed that drug development should be driven by the pharmaceutical industry. CONCLUSION Our study shows that the perceived effectiveness of innovative drugs is associated with familiarity with the health care system and trust in institutions.
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Affiliation(s)
- Émilien Schultz
- Université Paris Cité, IRD, Ceped, 75006 Paris, France,SESSTIM, Sciences Économiques & Sociales de la Santé & Traitement de l’Information Médicale, CANBIOS team (équipe labellisée LIGUE 2019), Aix-Marseille Université, Inserm, IRD, 13009 Marseille, France,Corresponding. CEPED, 45, rue des Saints-Pères, 75006 Paris, France
| | - Léo Mignot
- University of Bordeaux, CNRS, CED, UMR 5116, 33600 Pessac, France,Sciences Po Bordeaux, CNRS, CED, UMR 5116, 33600 Pessac, France
| | - Jeremy K. Ward
- CERMES3, Inserm, CNRS, EHESS, Université de Paris Cité, 94801 Villejuif, France,VITROME, Aix-Marseille University, IRD, AP-HM, SSA, 13005 Marseille, France
| | - Daniela Boaventura Bomfim
- University of Bordeaux, CNRS, CED, UMR 5116, 33600 Pessac, France,SIRIC BRIO, CHU de Bordeaux, Institut Bergonié, Université of Bordeaux, Inserm, CNRS, 33000 Bordeaux, France
| | - Christian Chabannon
- Module Biothérapies du Centre d’Investigations Cliniques en Biothérapies, Inserm CBT-1409, Aix-Marseille Université, Institut Paoli-Calmettes comprehensive cancer center, 13005 Marseille, France
| | - Julien Mancini
- SESSTIM, Sciences Économiques & Sociales de la Santé & Traitement de l’Information Médicale, CANBIOS team (équipe labellisée LIGUE 2019), Aix-Marseille Université, Inserm, IRD, 13009 Marseille, France,BioSTIC, AP–HM, Timone, 13005 Marseille, France
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13
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Jukič M, Kores K, Janežič D, Bren U. Repurposing of Drugs for SARS-CoV-2 Using Inverse Docking Fingerprints. Front Chem 2021; 9:757826. [PMID: 35028304 PMCID: PMC8748264 DOI: 10.3389/fchem.2021.757826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 is a virus that belongs to the Coronaviridae family. This group of viruses commonly causes colds but possesses a tremendous pathogenic potential. In humans, an outbreak of SARS caused by the SARS-CoV virus was first reported in 2003, followed by 2012 when the Middle East respiratory syndrome coronavirus (MERS-CoV) led to an outbreak of Middle East respiratory syndrome (MERS). Moreover, COVID-19 represents a serious socioeconomic and global health problem that has already claimed more than four million lives. To date, there are only a handful of therapeutic options to combat this disease, and only a single direct-acting antiviral, the conditionally approved remdesivir. Since there is an urgent need for active drugs against SARS-CoV-2, the strategy of drug repurposing represents one of the fastest ways to achieve this goal. An in silico drug repurposing study using two methods was conducted. A structure-based virtual screening of the FDA-approved drug database on SARS-CoV-2 main protease was performed, and the 11 highest-scoring compounds with known 3CLpro activity were identified while the methodology was used to report further 11 potential and completely novel 3CLpro inhibitors. Then, inverse molecular docking was performed on the entire viral protein database as well as on the Coronaviridae family protein subset to examine the hit compounds in detail. Instead of target fishing, inverse docking fingerprints were generated for each hit compound as well as for the five most frequently reported and direct-acting repurposed drugs that served as controls. In this way, the target-hitting space was examined and compared and we can support the further biological evaluation of all 11 newly reported hits on SARS-CoV-2 3CLpro as well as recommend further in-depth studies on antihelminthic class member compounds. The authors acknowledge the general usefulness of this approach for a full-fledged inverse docking fingerprint screening in the future.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
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14
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Cysteamine with In Vitro Antiviral Activity and Immunomodulatory Effects Has the Potential to Be a Repurposing Drug Candidate for COVID-19 Therapy. Cells 2021; 11:cells11010052. [PMID: 35011614 PMCID: PMC8750154 DOI: 10.3390/cells11010052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
The ongoing pandemic of coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), needs better treatment options both at antiviral and anti-inflammatory levels. It has been demonstrated that the aminothiol cysteamine, an already human applied drug, and its disulfide product of oxidation, cystamine, have anti-infective properties targeting viruses, bacteria, and parasites. To determine whether these compounds exert antiviral effects against SARS-CoV-2, we used different in vitro viral infected cell-based assays. Moreover, since cysteamine has also immune-modulatory activity, we investigated its ability to modulate SARS-CoV-2-specific immune response in vitro in blood samples from COVID-19 patients. We found that cysteamine and cystamine decreased SARS-CoV-2-induced cytopathic effects (CPE) in Vero E6 cells. Interestingly, the antiviral action was independent of the treatment time respect to SARS-CoV-2 infection. Moreover, cysteamine and cystamine significantly decreased viral production in Vero E6 and Calu-3 cells. Finally, cysteamine and cystamine have an anti-inflammatory effect, as they significantly decrease the SARS-CoV-2 specific IFN-γ production in vitro in blood samples from COVID-19 patients. Overall, our findings suggest that cysteamine and cystamine exert direct antiviral actions against SARS-CoV-2 and have in vitro immunomodulatory effects, thus providing a rational to test these compounds as a novel therapy for COVID-19.
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15
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White JM, Schiffer JT, Bender Ignacio RA, Xu S, Kainov D, Ianevski A, Aittokallio T, Frieman M, Olinger GG, Polyak SJ. Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses. mBio 2021; 12:e0334721. [PMID: 34933447 PMCID: PMC8689562 DOI: 10.1128/mbio.03347-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The world was unprepared for coronavirus disease 2019 (COVID-19) and remains ill-equipped for future pandemics. While unprecedented strides have been made developing vaccines and treatments for COVID-19, there remains a need for highly effective and widely available regimens for ambulatory use for novel coronaviruses and other viral pathogens. We posit that a priority is to develop pan-family drug cocktails to enhance potency, limit toxicity, and avoid drug resistance. We urge cocktail development for all viruses with pandemic potential both in the short term (<1 to 2 years) and longer term with pairs of drugs in advanced clinical testing or repurposed agents approved for other indications. While significant efforts were launched against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in vitro and in the clinic, many studies employed solo drugs and had disappointing results. Here, we review drug combination studies against SARS-CoV-2 and other viruses and introduce a model-driven approach to assess drug pairs with the highest likelihood of clinical efficacy. Where component agents lack sufficient potency, we advocate for synergistic combinations to achieve therapeutic levels. We also discuss issues that stymied therapeutic progress against COVID-19, including testing of agents with low likelihood of efficacy late in clinical disease and lack of focus on developing virologic surrogate endpoints. There is a need to expedite efficient clinical trials testing drug combinations that could be taken at home by recently infected individuals and exposed contacts as early as possible during the next pandemic, whether caused by a coronavirus or another viral pathogen. The approach herein represents a proactive plan for global viral pandemic preparedness.
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Affiliation(s)
- Judith M. White
- University of Virginia, Department of Cell Biology, Charlottesville, Virginia, USA
- University of Virginia, Department of Microbiology, Charlottesville, Virginia, USA
| | - Joshua T. Schiffer
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Rachel A. Bender Ignacio
- University of Washington, Division of Allergy and Infectious Diseases, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Shuang Xu
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Diseases Division, Seattle, Washington, USA
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Stephen J. Polyak
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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16
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Vasudevan S, Baraniuk JN. Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex. Pathogens 2021; 10:1634. [PMID: 34959589 PMCID: PMC8709492 DOI: 10.3390/pathogens10121634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Non-structural protein 1 (Nsp1) is a virulence factor found in all beta coronaviruses (b-CoVs). Recent studies have shown that Nsp1 of SARS-CoV-2 virus interacts with the nuclear export receptor complex, which includes nuclear RNA export factor 1 (NXF1) and nuclear transport factor 2-like export factor 1 (NXT1). The NXF1-NXT1 complex plays a crucial role in the transport of host messenger RNA (mRNA). Nsp1 interferes with the proper binding of NXF1 to mRNA export adaptors and its docking to the nuclear pore complex. We propose that drugs targeting the binding surface between Nsp1 and NXF1-NXT1 may be a useful strategy to restore host antiviral gene expression. Exploring this strategy forms the main goals of this paper. Crystal structures of Nsp1 and the heterodimer of NXF1-NXT1 have been determined. We modeled the docking of Nsp1 to the NXF1-NXT1 complex, and discovered repurposed drugs that may interfere with this binding. To our knowledge, this is the first attempt at drug-repurposing of this complex. We used structural analysis to screen 1993 FDA-approved drugs for docking to the NXF1-NXT1 complex. The top hit was ganirelix, with a docking score of -14.49. Ganirelix competitively antagonizes the gonadotropin releasing hormone receptor (GNRHR) on pituitary gonadotrophs, and induces rapid, reversible suppression of gonadotropin secretion. The conformations of Nsp1 and GNRHR make it unlikely that they interact with each other. Additional drug leads were inferred from the structural analysis of this complex, which are discussed in the paper. These drugs offer several options for therapeutically blocking Nsp1 binding to NFX1-NXT1, which may normalize nuclear export in COVID-19 infection.
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Affiliation(s)
- Sona Vasudevan
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, 3900 Reservoir Road NW, Washington, DC 20057, USA
| | - James N Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University Medical Center, 3900 Reservoir Road NW, Washington, DC 20007, USA
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17
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Terrier O, Si-Tahar M, Ducatez M, Chevalier C, Pizzorno A, Le Goffic R, Crépin T, Simon G, Naffakh N. Influenza viruses and coronaviruses: Knowns, unknowns, and common research challenges. PLoS Pathog 2021; 17:e1010106. [PMID: 34969061 PMCID: PMC8718010 DOI: 10.1371/journal.ppat.1010106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The development of safe and effective vaccines in a record time after the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a remarkable achievement, partly based on the experience gained from multiple viral outbreaks in the past decades. However, the Coronavirus Disease 2019 (COVID-19) crisis also revealed weaknesses in the global pandemic response and large gaps that remain in our knowledge of the biology of coronaviruses (CoVs) and influenza viruses, the 2 major respiratory viruses with pandemic potential. Here, we review current knowns and unknowns of influenza viruses and CoVs, and we highlight common research challenges they pose in 3 areas: the mechanisms of viral emergence and adaptation to humans, the physiological and molecular determinants of disease severity, and the development of control strategies. We outline multidisciplinary approaches and technological innovations that need to be harnessed in order to improve preparedeness to the next pandemic.
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Affiliation(s)
- Olivier Terrier
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Mustapha Si-Tahar
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Inserm U1100, Research Center for Respiratory Diseases (CEPR), Université de Tours, Tours, France
| | - Mariette Ducatez
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- IHAP, UMR1225, Université de Toulouse, ENVT, INRAE, Toulouse, France
| | - Christophe Chevalier
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Université Paris-Saclay, UVSQ, INRAE, VIM, Equipe Virus Influenza, Jouy-en-Josas, France
| | - Andrés Pizzorno
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Ronan Le Goffic
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Université Paris-Saclay, UVSQ, INRAE, VIM, Equipe Virus Influenza, Jouy-en-Josas, France
| | - Thibaut Crépin
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Gaëlle Simon
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Swine Virology Immunology Unit, Ploufragan-Plouzané-Niort Laboratory, ANSES, Ploufragan, France
| | - Nadia Naffakh
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
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18
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Plemper RK. Editorial overview: Special issue on antiviral strategies in Current Opinion in Virology. Curr Opin Virol 2021; 50:95-96. [PMID: 34419858 PMCID: PMC8376291 DOI: 10.1016/j.coviro.2021.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Richard K Plemper
- Center for Translational Antiviral Research, Georgia State University, Atlanta, GA, USA.
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