1
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Arduino I, Francese R, Civra A, Feyles E, Argenziano M, Volante M, Cavalli R, Mougharbel AM, Kortz U, Donalisio M, Lembo D. Polyoxometalate exerts broad-spectrum activity against human respiratory viruses hampering viral entry. Antiviral Res 2024; 226:105897. [PMID: 38685531 DOI: 10.1016/j.antiviral.2024.105897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Human respiratory viruses have an enormous impact on national health systems, societies, and economy due to the rapid airborne transmission and epidemic spread of such pathogens, while effective specific antiviral drugs to counteract infections are still lacking. Here, we identified two Keggin-type polyoxometalates (POMs), [TiW11CoO40]8- (TiW11Co) and [Ti2PW10O40]7- (Ti2PW10), endowed with broad-spectrum activity against enveloped and non-enveloped human respiratory viruses, i.e., coronavirus (HCoV-OC43), rhinovirus (HRV-A1), respiratory syncytial virus (RSV-A2), and adenovirus (AdV-5). Ti2PW10 showed highly favorable selectivity indexes against all tested viruses (SIs >700), and its antiviral potential was further investigated against human coronaviruses and rhinoviruses. This POM was found to inhibit replication of multiple HCoV and HRV strains, in different cell systems. Ti2PW10 did not affect virus binding or intracellular viral replication, but selectively inhibited the viral entry. Serial passaging of virus in presence of the POM revealed a high barrier to development of Ti2PW10-resistant variants of HRV-A1 or HCoV-OC43. Moreover, Ti2PW10 was able to inhibit HRV-A1 production in a 3D model of the human nasal epithelium and, importantly, the antiviral treatment did not determine cytotoxicity or tissue damage. A mucoadhesive thermosensitive in situ hydrogel formulation for nasal delivery was also developed for Ti2PW10. Overall, good biocompatibility on cell lines and human nasal epithelia, broad-spectrum activity, and absence of antiviral resistance development reveal the potential of Ti2PW10 as an antiviral candidate for the development of a treatment of acute respiratory viral diseases, warranting further studies to identify the specific target/s of the polyanion and assess its clinical potential.
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Affiliation(s)
- Irene Arduino
- Department of Clinical and Biological Sciences, Laboratory of Molecular Virology and Antiviral Research, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - Rachele Francese
- Department of Clinical and Biological Sciences, Laboratory of Molecular Virology and Antiviral Research, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - Andrea Civra
- Department of Clinical and Biological Sciences, Laboratory of Molecular Virology and Antiviral Research, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - Elisa Feyles
- Department of Clinical and Biological Sciences, Laboratory of Molecular Virology and Antiviral Research, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - Monica Argenziano
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10100, Torino, Italy.
| | - Marco Volante
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - Roberta Cavalli
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10100, Torino, Italy.
| | - Ali M Mougharbel
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany.
| | - Ulrich Kortz
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany.
| | - Manuela Donalisio
- Department of Clinical and Biological Sciences, Laboratory of Molecular Virology and Antiviral Research, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - David Lembo
- Department of Clinical and Biological Sciences, Laboratory of Molecular Virology and Antiviral Research, University of Turin, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
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2
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Doijen J, Heo I, Temmerman K, Vermeulen P, Diels A, Jaensch S, Burcin M, Van den Broeck N, Raeymaekers V, Peremans J, Konings K, Clement M, Peeters D, Van Loock M, Koul A, Buyck C, Van Gool M, Van Damme E. A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects. Antiviral Res 2024; 222:105789. [PMID: 38158129 DOI: 10.1016/j.antiviral.2023.105789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a major threat to global health. Although the World Health Organization ended the public health emergency status, antiviral drugs are needed to address new variants of SARS-CoV-2 and future pandemics. To identify novel broad-spectrum coronavirus drugs, we developed a high-content imaging platform compatible with high-throughput screening. The platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. We demonstrated that the antiviral activity of compounds against SARS-CoV-2 variants (Omicron BA.5 and Omicron XBB.1.5), SARS-CoV, and human coronavirus 229E could easily be assessed. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled us to identify compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity. With the platform, we screened ∼900K compounds and triaged hits, thereby identifying potential candidate compounds carrying broad-spectrum activity with limited off-target effects. The flexibility and early-stage identification of compounds with limited host cell effects provided by this high-content imaging platform can facilitate coronavirus drug discovery. We anticipate that its rapid deployability and fast turnaround can also be applied to combat future pandemics.
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Affiliation(s)
- Jordi Doijen
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Inha Heo
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Koen Temmerman
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Peter Vermeulen
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Annick Diels
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Steffen Jaensch
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Mark Burcin
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | | | - Joren Peremans
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Katrien Konings
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Maxime Clement
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Danielle Peeters
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Marnix Van Loock
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Anil Koul
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Christophe Buyck
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michiel Van Gool
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ellen Van Damme
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
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3
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Kim JH, Park YI, Hur M, Park WT, Moon YH, Huh YC, Kim TIL, Kang MH, Kang JS, Cho CW, Park J. Inhibition by components of Glycyrrhiza uralensis of 3CLpro and HCoV-OC43 proliferation. J Enzyme Inhib Med Chem 2023; 38:2242704. [PMID: 37537881 PMCID: PMC10405751 DOI: 10.1080/14756366.2023.2242704] [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: 05/26/2023] [Revised: 07/06/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). 3CLpro is a key enzyme in coronavirus proliferation and a treatment target for COVID-19. In vitro and in silico, compounds 1-3 from Glycyrrhiza uralensis had inhibitory activity and binding affinity for 3CLpro. These compounds decreased HCoV-OC43 cytotoxicity in RD cells. Moreover, they inhibited viral growth by reducing the amounts of the necessary proteins (M, N, and RDRP). Therefore, compounds 1-3 are inhibitors of 3CLpro and HCoV-OC43 proliferation.
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Affiliation(s)
- Jang Hoon Kim
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Mok Hur
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Woo Tae Park
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Youn-Ho Moon
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Yun-Chan Huh
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Tae IL Kim
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Min Hye Kang
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Jong Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Chong Woon Cho
- College of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
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4
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Stagnoli S, Macari G, Corsi P, Capone B, Vidaurrazaga A, Ereño-Orbea J, Ardá A, Polticelli F, Jiménez-Barbero J, Abrescia NGA, Coluzza I. Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection. ACS OMEGA 2023; 8:43490-43499. [PMID: 38027314 PMCID: PMC10666140 DOI: 10.1021/acsomega.3c02921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023]
Abstract
The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening of the Receptor Binding Domain (RBD) of the spike protein of SARS-CoV-2 with small compounds. Through in silico screening, we identified two potential candidates that would lock the Receptor Binding Domain (RBD) in a closed configuration, preventing the virus from infecting the host cells. We show that two drugs already approved by the FDA, mithramycin and dihydroergotamine, can block infection using concentrations in the μM range in cell-based assays. Further STD-NMR experiments support dihydroergotamine's direct interaction with the spike protein. Overall, our results indicate that repurposing of these compounds might lead to potential clinical drug candidates for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Soledad Stagnoli
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Gabriele Macari
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Pietro Corsi
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Barbara Capone
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Ander Vidaurrazaga
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - June Ereño-Orbea
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ana Ardá
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
| | - Fabio Polticelli
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
- National
Institute of Nuclear Physics, Roma Tre Section, 00154 Rome, Italy
| | - Jesús Jiménez-Barbero
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de
Investigación Biomédica En Red de Enfermedades Respiratorias.
(CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department
of Organic & Inorganic Chemistry, Faculty
of Science and Technology University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
| | - Nicola GA Abrescia
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, 28029 Madrid, Spain
| | - Ivan Coluzza
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Computational
Soft Matter and Biophysics Lab, Basque Center
for Materials, Applications and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque
Científico UPV/EHU Barrio Sarriena, 48940 Leioa, Spain
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5
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Abreu C, Ortega C, Olivero-Deibe N, Carrión F, Gaete-Argel A, Valiente-Echeverría F, Soto-Rifo R, Milan Bonotto R, Marcello A, Pantano S. Customizably designed multibodies neutralize SARS-CoV-2 in a variant-insensitive manner. Front Immunol 2023; 14:1226880. [PMID: 37638023 PMCID: PMC10447908 DOI: 10.3389/fimmu.2023.1226880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
The COVID-19 pandemic evolves constantly, requiring adaptable solutions to combat emerging SARS-CoV-2 variants. To address this, we created a pentameric scaffold based on a mammalian protein, which can be customized with up to 10 protein binding modules. This molecular scaffold spans roughly 20 nm and can simultaneously neutralize SARS-CoV-2 Spike proteins from one or multiple viral particles. Using only two different modules targeting the Spike's RBD domain, this construct outcompetes human antibodies from vaccinated individuals' serum and blocks in vitro cell attachment and pseudotyped virus entry. Additionally, the multibodies inhibit viral replication at low picomolar concentrations, regardless of the variant. This customizable multibody can be easily produced in procaryote systems, providing a new avenue for therapeutic development and detection devices, and contributing to preparedness against rapidly evolving pathogens.
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Affiliation(s)
| | | | | | | | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Rafaela Milan Bonotto
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Alessandro Marcello
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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6
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Milan Bonotto R, Mitrović A, Sosič I, Martinez-Orellana P, Dattola F, Gobec S, Kos J, Marcello A. Cathepsin inhibitors nitroxoline and its derivatives inhibit SARS-CoV-2 infection. Antiviral Res 2023:105655. [PMID: 37355023 PMCID: PMC10287183 DOI: 10.1016/j.antiviral.2023.105655] [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: 01/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
The severity of the SARS-CoV-2 pandemic and the recurring (re)emergence of viruses prompted the development of new therapeutic approaches that target viral and host factors crucial for viral infection. Among them, host peptidases cathepsins B and L have been described as essential enzymes during SARS-CoV-2 entry. In this study, we evaluated the effect of potent selective cathepsin inhibitors as antiviral agents. We demonstrated that selective cathepsin B inhibitors, such as the antimicrobial agent nitroxoline and its derivatives, impair SARS-CoV-2 infection in vitro. Antiviral activity observed at early stage of virus entry was cell-type dependent and correlated well with the intracellular content and enzymatic function of cathepsins B or L. Furthermore, tested inhibitors were effective against the ancestral SARS-CoV-2 D614 as well as against the more recent BA.1_4 (Omicron). Taken together, our results highlight the important role of host cysteine cathepsin B in SARS-CoV-2 virus entry and show that cathepsin-specific inhibitors, such as nitroxoline and its derivatives, could be used to treat COVID-19. Finally, these results also suggest that nitroxoline has potential to be further explored as repurposed drug in antiviral therapy.
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Affiliation(s)
- Rafaela Milan Bonotto
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Ana Mitrović
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Pamela Martinez-Orellana
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Federica Dattola
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia.
| | - Alessandro Marcello
- Laboratory of Molecular Virology, The International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano, 99, 34149, Trieste, Italy.
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7
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Ulinici M, Suljič A, Poggianella M, Milan Bonotto R, Resman Rus K, Paraschiv A, Bonetti AM, Todiras M, Corlateanu A, Groppa S, Ceban E, Petrovec M, Marcello A. Characterisation of the Antibody Response in Sinopharm (BBIBP-CorV) Recipients and COVID-19 Convalescent Sera from the Republic of Moldova. Vaccines (Basel) 2023; 11:vaccines11030637. [PMID: 36992221 DOI: 10.3390/vaccines11030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
The early availability of effective vaccines against SARS-CoV-2, the aetiologic cause of COVID-19, has been at the cornerstone of the global recovery from the pandemic. This study aimed to assess the antispike RBD IgG antibody titres and neutralisation potential of COVID-19 convalescent plasma and the sera of Moldovan adults vaccinated with the Sinopharm BBIBP-CorV vaccine. An IgG ELISA with recombinant SARS-CoV-2 spike RBD and two pseudovirus-based neutralisation assays have been developed to evaluate neutralising antibodies against SARS-CoV-2 in biosafety level 2 containment facilities. A significant moderate correlation was observed between IgG titres and the overall neutralising levels for each neutralisation assay (ρ = 0.64, p < 0.001; ρ = 0.52, p < 0.001). A separate analysis of convalescent and vaccinated individuals showed a higher correlation of neutralising and IgG titres in convalescent individuals (ρ = 0.68, p < 0.001, ρ = 0.45, p < 0.001) compared with vaccinated individuals (ρ = 0.58, p < 0.001; ρ = 0.53, p < 0.001). It can be concluded that individuals who recovered from infection developed higher levels of antispike RBD IgG antibodies. In comparison, the Sinopharm-vaccinated individuals produced higher levels of neutralising antibodies than convalescent plasma.
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Affiliation(s)
- Mariana Ulinici
- National Institute for Health and Medical Research, Faculty of Medicine, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova
- Alfa Diagnostica Laboratory, 2021 Chisinau, Moldova
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Monica Poggianella
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Rafaela Milan Bonotto
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Katarina Resman Rus
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Angela Paraschiv
- National Institute for Health and Medical Research, Faculty of Medicine, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova
| | - Amedeo Marco Bonetti
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Mihail Todiras
- National Institute for Health and Medical Research, Faculty of Medicine, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova
| | - Alexandru Corlateanu
- National Institute for Health and Medical Research, Faculty of Medicine, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova
| | - Stanislav Groppa
- National Institute for Health and Medical Research, Faculty of Medicine, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova
| | - Emil Ceban
- National Institute for Health and Medical Research, Faculty of Medicine, Nicolae Testemitanu State University of Medicine and Pharmacy, 2004 Chisinau, Moldova
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
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8
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Piplani S, Singh P, Petrovsky N, Winkler DA. Identifying SARS-CoV-2 Drugs Binding to the Spike Fatty Acid Binding Pocket Using In Silico Docking and Molecular Dynamics. Int J Mol Sci 2023; 24:ijms24044192. [PMID: 36835602 PMCID: PMC9966092 DOI: 10.3390/ijms24044192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Drugs against novel targets are needed to treat COVID-19 patients, especially as SARS-CoV-2 is capable of rapid mutation. Structure-based de novo drug design and repurposing of drugs and natural products is a rational approach to discovering potentially effective therapies. These in silico simulations can quickly identify existing drugs with known safety profiles that can be repurposed for COVID-19 treatment. Here, we employ the newly identified spike protein free fatty acid binding pocket structure to identify repurposing candidates as potential SARS-CoV-2 therapies. Using a validated docking and molecular dynamics protocol effective at identifying repurposing candidates inhibiting other SARS-CoV-2 molecular targets, this study provides novel insights into the SARS-CoV-2 spike protein and its potential regulation by endogenous hormones and drugs. Some of the predicted repurposing candidates have already been demonstrated experimentally to inhibit SARS-CoV-2 activity, but most of the candidate drugs have yet to be tested for activity against the virus. We also elucidated a rationale for the effects of steroid and sex hormones and some vitamins on SARS-CoV-2 infection and COVID-19 recovery.
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Affiliation(s)
- Sakshi Piplani
- College of Medicine and Public Health, Flinders University, Bedford Park 5046, Australia
- Vaxine Pty Ltd., 11 Walkley Avenue, Warradale 5046, Australia
| | - Puneet Singh
- College of Medicine and Public Health, Flinders University, Bedford Park 5046, Australia
- Vaxine Pty Ltd., 11 Walkley Avenue, Warradale 5046, Australia
| | - Nikolai Petrovsky
- College of Medicine and Public Health, Flinders University, Bedford Park 5046, Australia
- Vaxine Pty Ltd., 11 Walkley Avenue, Warradale 5046, Australia
- Correspondence:
| | - David A. Winkler
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
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9
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Cunha AES, Loureiro RJS, Simões CJV, Brito RMM. Unveiling New Druggable Pockets in Influenza Non-Structural Protein 1: NS1-Host Interactions as Antiviral Targets for Flu. Int J Mol Sci 2023; 24:ijms24032977. [PMID: 36769298 PMCID: PMC9918223 DOI: 10.3390/ijms24032977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Influenza viruses are responsible for significant morbidity and mortality worldwide in winter seasonal outbreaks and in flu pandemics. Influenza viruses have a high rate of evolution, requiring annual vaccine updates and severely diminishing the effectiveness of the available antivirals. Identifying novel viral targets and developing new effective antivirals is an urgent need. One of the most promising new targets for influenza antiviral therapy is non-structural protein 1 (NS1), a highly conserved protein exclusively expressed in virus-infected cells that mediates essential functions in virus replication and pathogenesis. Interaction of NS1 with the host proteins PI3K and TRIM25 is paramount for NS1's role in infection and pathogenesis by promoting viral replication through the inhibition of apoptosis and suppressing interferon production, respectively. We, therefore, conducted an analysis of the druggability of this viral protein by performing molecular dynamics simulations on full-length NS1 coupled with ligand pocket detection. We identified several druggable pockets that are partially conserved throughout most of the simulation time. Moreover, we found out that some of these druggable pockets co-localize with the most stable binding regions of the protein-protein interaction (PPI) sites of NS1 with PI3K and TRIM25, which suggests that these NS1 druggable pockets are promising new targets for antiviral development.
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Affiliation(s)
- Andreia E. S. Cunha
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui J. S. Loureiro
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence: (R.J.S.L.); (R.M.M.B.)
| | - Carlos J. V. Simões
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- BSIM Therapeutics, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Rui M. M. Brito
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- BSIM Therapeutics, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
- Correspondence: (R.J.S.L.); (R.M.M.B.)
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Kullappan M, Mary U, Ambrose JM, Veeraraghavan VP, Surapaneni KM. Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. J Biomol Struct Dyn 2023; 41:912-929. [PMID: 34904526 DOI: 10.1080/07391102.2021.2014973] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
COVID-19 has become a public health concern around the world. The frequency of N440K variant was higher during the second wave in South India. The mutation was observed in the Receptor Binding Domain region (RBD) of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) spike (S) protein. The binding affinity of SARS-CoV-2-Angiotensin-Converting Enzyme-2 (ACE-2) plays a major role in the transmission and severity of the disease. To understand the binding affinity of the wild and mutant SARS-CoV-2 S with ACE2, molecular modeling studies were carried out. We discovered that the wild SARS-CoV-2 S RBD-ACE-2 complex has a high binding affinity and stability than that of the mutant. The N440K strain escapes from antibody neutralization, which might increase reinfection and decrease vaccine efficiency. To find a potential inhibitor against mutant N440K SARS-CoV-2, a virtual screening process was carried out and found ZINC169293961, ZINC409421825 and ZINC22060839 as the best binding energy compounds. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India
| | - Usha Mary
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai, India
| | - Jenifer M Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India
| | - Vishnu Priya Veeraraghavan
- Department of Biochemistry, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Velappanchavadi, Chennai, Tamil Nadu, India
| | - Krishna Mohan Surapaneni
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India.,Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India.,Department of Molecular Virology, Clinical Skills & Simulation, Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India.,Department of Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, India
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11
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Zhao L, Qin X, Lin T, Xie F, Yao L, Li Y, Xiong B, Xu Z, Ye Y, Chen H, Qiu SX. Multi-target mechanisms against coronaviruses of constituents from Chinese Dagang Tea revealed by experimental and docking studies. JOURNAL OF ETHNOPHARMACOLOGY 2022; 297:115528. [PMID: 35835344 PMCID: PMC9273292 DOI: 10.1016/j.jep.2022.115528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 06/01/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The leaves of Eurya chinensis(Chinese Dagang Tea)have been consumed as herbal tea for centuries in Guangdong, China, and have also been used to prevent influenza and treat colds and fevers in traditional Chinese medicine. However, there are no reports on the chemical profile and efficacy of its leaves for the treatment of fever and viral infections. MATERIALS AND METHODS The chemical constituents of Eurya chinensis leaves were isolated and identified by phytochemical study and spectroscopic data, E. chinensis extracts and compounds were evaluated for their antiviral activities by cytopathic effect (CPE) reduction and antibody-based EC50 assay. The antiviral effect of the main component was confirmed by immunofluorescence and transmission electron microscopy. Virtual screening and docking enzyme inhibition experiments were performed to analyze the anti-coronavirus mechanisms of the compounds from E. chinensis leaves. RESULTS In this study, we found for the first time that E. chinensis leaf extract exhibited inhibitory effects against coronaviruses HCoV-OC43 in vitro. Among 23 monomer compounds isolated from E. chinensis leaf extract, the triterpenoids (betulinic acid, α-amyrin) and the flavonoids (naringenin, eriodictyol and quercetin) showed marked antiviral activity. Microscopic optical analyses further demonstrated that betulinic acid can remove virus particles from HCoV-OC43 infected cells. Virtual screening and docking analysis towards the coronavirus in vogue revealed that betulinic acid was able to bind well to PLpro and Nsp14N7-MTase, and that the flavonoids prefer to bind with PLpro, Nsp3MES, NspP14N7-MTase, Nsp16GTA, and Nsp16SAM. The enzyme inhibition experiments demonstrated that betulinic acid (1) exhibited significant inhibition of PLpro and N7-MTase activity of SARS-CoV-2. CONCLUSION This study proposes E. chinensis and its triterpenoids and flavonoids as promising potential treatments for coronaviruses.
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Affiliation(s)
- Liyun Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Xubing Qin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Tingting Lin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Fuda Xie
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Liyuan Yao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yulin Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Binhong Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Zhifang Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Yongchang Ye
- Dongguan Natural Reserve Service Center of Guangdong Province, Dongguan, 523000, PR China
| | - Hongfeng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China
| | - Sheng-Xiang Qiu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, PR China.
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12
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Mahdian S, Arab SS. Effectiveness of Remdesivir in Comparison with Five Approved Antiviral Drugs for Inhibition of RdRp in Combat with SARS-CoV-2. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2022; 46:1359-1367. [PMID: 36187298 PMCID: PMC9510211 DOI: 10.1007/s40995-022-01364-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/16/2022] [Indexed: 01/18/2023]
Abstract
The treatment of COVID-19 disease has been one of the most critical essential concerns of researchers in recent years. One of the most exciting and potential therapeutic targets for SARS-CoV-2 therapy progression is RNA-dependent RNA polymerase (RdRP), a viral enzyme for viral RNA replication throughout host cells. According to some research, Remdesivir suppresses RdRp. The nucleoside medication remdesivir has been authorized under an Emergency Use Authorization to treat COVID-19. Given the role of this enzyme in virus replication, our scientific question is whether Remdesivir is the most appropriate antiviral drug to inhibit this enzyme or not. Accordingly, this study aimed to repurpose antiviral drugs to inhibition of RdRp using virtual screening and Molecular Dynamics simulation methods. Five FDA-approved antiviral medications, including Elbasvir, Glecaprevir, Ledipasvir, Paritaprevir, and Simeprevir, had good interaction potential with RdRp. Also, the results show that the number of H-bonds and contacts and ∆G interactions between the protein and ligand in the Remdesivir complex is less than those of other complexes. According to the given data which shows the tendency of binding with RdRp for Paritaprevir, Simeprevir, Glecaprevir, and Ledipasvir and Elbasvir is more than Remdesivir and due to the fact that these five drugs have a high tendency to bind to other targets in the SARS-CoV-2, the use of Remdesivir as an antiviral drug in the treatment of COVID-19 should be considered more sensitively.
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13
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, 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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14
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Piplani S, Singh P, Winkler DA, Petrovsky N. Potential COVID-19 Therapies from Computational Repurposing of Drugs and Natural Products against the SARS-CoV-2 Helicase. Int J Mol Sci 2022; 23:7704. [PMID: 35887049 PMCID: PMC9322913 DOI: 10.3390/ijms23147704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
Repurposing of existing drugs is a rapid way to find potential new treatments for SARS-CoV-2. Here, we applied a virtual screening approach using Autodock Vina and molecular dynamic simulation in tandem to screen and calculate binding energies of repurposed drugs against the SARS-CoV-2 helicase protein (non-structural protein nsp13). Amongst the top hits from our study were antivirals, antihistamines, and antipsychotics, plus a range of other drugs. Approximately 30% of our top 87 hits had published evidence indicating in vivo or in vitro SARS-CoV-2 activity. Top hits not previously reported to have SARS-CoV-2 activity included the antiviral agents, cabotegravir and RSV-604; the NK1 antagonist, aprepitant; the trypanocidal drug, aminoquinuride; the analgesic, antrafenine; the anticancer intercalator, epirubicin; the antihistamine, fexofenadine; and the anticoagulant, dicoumarol. These hits from our in silico SARS-CoV-2 helicase screen warrant further testing as potential COVID-19 treatments.
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Affiliation(s)
- Sakshi Piplani
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
| | - Puneet Singh
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
| | - David A. Winkler
- Biochemistry and Chemistry Department, La Trobe University, Kingsbury Drive, Melbourne 3086, Australia;
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Nikolai Petrovsky
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
- Department of Diabetes and Endocrinology, Flinders Medical Centre, Flinders University, 1 Flinders Drive, Adelaide 5042, Australia
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Chen CC, Zhuang ZJ, Wu CW, Tan YL, Huang CH, Hsu CY, Tsai EM, Hsieh TH. Venetoclax Decreases the Expression of the Spike Protein through Amino Acids Q493 and S494 in SARS-CoV-2. Cells 2022; 11:cells11121924. [PMID: 35741053 PMCID: PMC9221610 DOI: 10.3390/cells11121924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
The new coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) has been reported and spread globally. There is an urgent need to take urgent measures to treat and prevent further infection of this virus. Here, we use virtual drug screening to establish pharmacophore groups and analyze the ACE2 binding site of the spike protein with the ZINC drug database and DrugBank database by molecular docking and molecular dynamics simulations. Screening results showed that Venetoclax, a treatment drug for chronic lymphocytic leukemia, has a potential ability to bind to the spike protein of SARS-CoV-2. In addition, our in vitro study found that Venetoclax degraded the expression of the spike protein of SARS-CoV-2 through amino acids Q493 and S494 and blocked the interaction with the ACE2 receptor. Our results suggest that Venetoclax is a candidate for clinical prevention and treatment and deserves further research.
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Affiliation(s)
- Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Zhi-Jie Zhuang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
| | - Chia-Wei Wu
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
| | - Yi-Ling Tan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
| | - Chen-Hsiu Huang
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
| | - Chia-Yi Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan; (C.-Y.H.); (E.-M.T.)
| | - Eing-Mei Tsai
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan; (C.-Y.H.); (E.-M.T.)
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Tsung-Hua Hsieh
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
- Correspondence: ; Tel.: +886-7615-1100 (ext. 5072)
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16
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Kumari R, Kumar V, Dhankhar P, Dalal V. Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA. J Biomol Struct Dyn 2022:1-17. [PMID: 35510600 DOI: 10.1080/07391102.2022.2071340] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The recent pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) is a viral respiratory disease that has been spread all over the globe. Therefore, it is an urgent requirement to identify and develop drugs for this contagious infection. The papain-like protease (PLpro) of SARS-CoV-2 performs critical functions in virus replication and immune evasion, making it an enticing therapeutic target. SARS-CoV-2 and SARS-CoV PLpro proteases have significant similarities, and an inhibitor discovered for SARS-CoV PLpro is an exciting first step toward therapeutic development. Here, a set of antiviral molecules were screened at the catalytic and S-binding allosteric sites of papain-like protease (PLpro). Molecular docking results suggested that five molecules (44560613, 136277567, S5652, SC75741, and S3833) had good binding affinities at both sites of PLpro. Molecular dynamics analysis like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond results showed that identified molecules with PLpro tend to form stable PLpro-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis confirmed that antiviral molecules bound PLpro complex had lower energy (-184.72 ± 7.81 to -215.67 ± 6.73 kJ/mol) complexes. Noticeably, computational approaches revealed promising antivirals candidates for PLpro, which may be further tested by biochemical and cell-based assays to assess their potential for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Viney Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, India
| | - Poonam Dhankhar
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis MO, USA
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A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. PATTERNS (NEW YORK, N.Y.) 2022; 3:100433. [PMID: 35510183 PMCID: PMC9058900 DOI: 10.1016/j.patter.2021.100433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/30/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023]
Abstract
The high number of failed pre-clinical and clinical studies for compounds targeting Alzheimer disease (AD) has demonstrated that there is a need to reassess existing strategies. Here, we pursue a holistic, mechanism-centric drug repurposing approach combining computational analytics and experimental screening data. Based on this integrative workflow, we identified 77 druggable modifiers of tau phosphorylation (pTau). One of the upstream modulators of pTau, HDAC6, was screened with 5,632 drugs in a tau-specific assay, resulting in the identification of 20 repurposing candidates. Four compounds and their known targets were found to have a link to AD-specific genes. Our approach can be applied to a variety of AD-associated pathophysiological mechanisms to identify more repurposing candidates. Drug-repurposing approach that combines in silico analyses and in vitro screenings A drug- and mechanism-oriented model, the Human Brain Pharmacome (HBP) was created The HBP was used to mine data related to drugs and targets to generate a hypothesis Experimental evidence validated predicted drug-target combinations
Owing to current setbacks in the discovery and development of novel treatments tackling Alzheimer disease (AD), a re-evaluation of research and development (R&D) strategies is underway. Here, we present a holistic pharmacological approach that combines drug-target information with knowledge graphs that represent essential pathophysiology mechanisms. The resulting Human Brain Pharmacome (HBP) embeds hundreds of relevant drug-target interactions in the context of disease mechanisms governing AD. We demonstrate how such a tool can be used to aid AD research by identifying already-approved drugs that have the potential to treat the disease, thereby bypassing the expensive and time-consuming task of researching and developing a new drug. In our study, we identified new drug-target combinations and provided mechanistic explanations that help to improve our understanding of AD pathology and support future development of effective therapeutic strategies.
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Pasquero S, Gugliesi F, Griffante G, Dell’Oste V, Biolatti M, Albano C, Bajetto G, Delbue S, Signorini L, Dolci M, Landolfo S, De Andrea M. Novel antiviral activity of PAD inhibitors against human beta-coronaviruses HCoV-OC43 and SARS-CoV-2. Antiviral Res 2022; 200:105278. [PMID: 35288208 PMCID: PMC8915624 DOI: 10.1016/j.antiviral.2022.105278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/25/2022]
Abstract
The current SARS-CoV-2 pandemic, along with the likelihood that new coronavirus strains will appear in the nearby future, highlights the urgent need to develop new effective antiviral agents. In this scenario, emerging host-targeting antivirals (HTAs), which act on host-cell factors essential for viral replication, are a promising class of antiviral compounds. Here we show that a new class of HTAs targeting peptidylarginine deiminases (PADs), a family of calcium-dependent enzymes catalyzing protein citrullination, is endowed with a potent inhibitory activity against human beta-coronaviruses (HCoVs). Specifically, we show that infection of human fetal lung fibroblasts with HCoV-OC43 leads to enhanced protein citrullination through transcriptional activation of PAD4, and that inhibition of PAD4-mediated citrullination with either of the two pan-PAD inhibitors Cl-A and BB-Cl or the PAD4-specific inhibitor GSK199 curbs HCoV-OC43 replication. Furthermore, we show that either Cl-A or BB-Cl treatment of African green monkey kidney Vero-E6 cells, a widely used cell system to study beta-CoV replication, potently suppresses HCoV-OC43 and SARS-CoV-2 replication. Overall, our results demonstrate the potential efficacy of PAD inhibitors, in suppressing HCoV infection, which may provide the rationale for the repurposing of this class of inhibitors for the treatment of COVID-19 patients.
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19
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De March M, Terdoslavich M, Polez S, Guarnaccia C, Poggianella M, Marcello A, Skoko N, de Marco A. Expression, purification and characterization of SARS-CoV-2 spike RBD in ExpiCHO cells. Protein Expr Purif 2022; 194:106071. [PMID: 35172194 PMCID: PMC8841003 DOI: 10.1016/j.pep.2022.106071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/02/2022] [Accepted: 02/11/2022] [Indexed: 11/14/2022]
Abstract
Reliable diagnosis is critical to identify infections of SARS-CoV-2 as well as to evaluate the immune response to virus and vaccines. Consequently, it becomes crucial the isolation of sensitive antibodies to use as immunocapture elements of diagnostic tools. The final bottleneck to achieve these results is the availability of enough antigen of good quality. We have established a robust pipeline for the production of recombinant, functional SARS-CoV-2 Spike receptor binding domain (RBD) at high yield and low cost in culture flasks. RBD was expressed in transiently transfected ExpiCHO cells at 32 °C and 5% CO2 and purified up to 40 mg/L. The progressive protein accumulation in the culture medium was monitored with an immunobinding assay in order to identify the optimal collection time. Successively, a two-step chromatographic protocol enabled its selective purification in the monomeric state. RBD quality assessment was positively evaluated by SDS-PAGE, Western Blotting and Mass Spectrometry, while Bio-Layer Interferometry, flow cytometer and ELISA tests confirmed its functionality. This effective protocol for the RBD production in transient eukaryotic system can be immediately extended to the production of RBD mutants.
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20
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Mueller JK, Riederer P, Müller WE. Neuropsychiatric Drugs Against COVID-19: What is the Clinical
Evidence? PHARMACOPSYCHIATRY 2022; 55:7-15. [DOI: 10.1055/a-1717-2381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AbstractSince the beginning of the coronavirus disease (COVID)-19 pandemic, the need for
effective treatments for COVID-19 led to the idea of
“repurposing” drugs for antiviral treatment. Several
antipsychotics and antidepressants have been tested for in vitro activity
against the severe acute respiratory syndrome coronavirus 2. Chlorpromazine,
other phenothiazine antipsychotics, and the antidepressant fluoxetine were found
to be rather potent in these studies. However, whether effective plasma
concentrations can be obtained with clinically accepted doses of these drugs is
not clear. Data of COVID-19 patients are not yet available but several clinical
studies are currently underway.The specific serotonin reuptake inhibitor fluvoxamine is a potent Sigma-1
receptor agonist and reduces inflammation in animal models of cytokine-stress.
Accordingly, fluvoxamine treatment was superior to placebo in reducing impaired
respiratory function and other symptoms of inflammation in COVID-19 patients in
a placebo-controlled clinical study and another open clinical trial. The
beneficial effects of fluvoxamine on the course of COVID-19 were recently
confirmed in a large placebo-controlled double-blind trial with several hundred
patients.Inflammation represents a major risk factor for many psychiatric disorders which
explains the high susceptibilitiy of COVID-19 patients for psychiatric diseases.
Many antidepressants and antipsychotics possess anti-inflammatory properties
independent of sigma-1 activity which might be important to reduce psychiatric
symptoms of COVID-19 patients and to improve respiratory dysfunction and other
consequences of inflammation. This might explain the rather unspecific benefit
which has been reported for several cohorts of COVID-19 patients treated with
different psychotropic drugs.
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Affiliation(s)
- Juliane K. Mueller
- Department of Psychiatry, Psychosomatic Medicine, and Psychotherapy,
University Hospital Frankfurt, Frankfurt/M, Germany
| | - Peter Riederer
- Clinic and Policlinic for Psychiatry, Psychosomatics and Psychotherapy,
University Hospital Würzburg, Würzburg, Germany
- University of Southern Denmark Odense, J.B. Winslows Vey Odense,
Denmark
| | - Walter E. Müller
- Department of Pharmacology und Clinical Pharmacy, University Frankfurt,
Frankfurt/M, Germany
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21
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Sureram S, Arduino I, Ueoka R, Rittà M, Francese R, Srivibool R, Darshana D, Piel J, Ruchirawat S, Muratori L, Lembo D, Kittakoop P, Donalisio M. The Peptide A-3302-B Isolated from a Marine Bacterium Micromonospora sp. Inhibits HSV-2 Infection by Preventing the Viral Egress from Host Cells. Int J Mol Sci 2022; 23:947. [PMID: 35055133 PMCID: PMC8778767 DOI: 10.3390/ijms23020947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Herpesviruses are highly prevalent in the human population, and frequent reactivations occur throughout life. Despite antiviral drugs against herpetic infections, the increasing appearance of drug-resistant viral strains and their adverse effects prompt the research of novel antiherpetic drugs for treating lesions. Peptides obtained from natural sources have recently become of particular interest for antiviral therapy applications. In this work, we investigated the antiviral activity of the peptide A-3302-B, isolated from a marine bacterium, Micromonospora sp., strain MAG 9-7, against herpes simplex virus type 1, type 2, and human cytomegalovirus. Results showed that the peptide exerted a specific inhibitory activity against HSV-2 with an EC50 value of 14 μM. Specific antiviral assays were performed to investigate the mechanism of action of A-3302-B. We demonstrated that the peptide did not affect the expression of viral proteins, but it inhibited the late events of the HSV-2 replicative cycle. In detail, it reduced the cell-to-cell virus spread and the transmission of the extracellular free virus by preventing the egress of HSV-2 progeny from the infected cells. The dual antiviral and previously reported anti-inflammatory activities of A-3302-B, and its effect against an acyclovir-resistant HSV-2 strain are attractive features for developing a therapeutic to reduce the transmission of HSV-2 infections.
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Affiliation(s)
- Sanya Sureram
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
| | - Irene Arduino
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Reiko Ueoka
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; (R.U.); (J.P.)
| | - Massimo Rittà
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Rachele Francese
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | | | - Dhanushka Darshana
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; (R.U.); (J.P.)
| | - Somsak Ruchirawat
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Luisa Muratori
- Department of Clinical and Biological Sciences, Neuroscience Institute of the “Cavalieri Ottolenghi” Foundation (NICO), University of Turin, 10043 Orbassano, Italy;
| | - David Lembo
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Manuela Donalisio
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
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22
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Ray AK, Sen Gupta PS, Panda SK, Biswal S, Bhattacharya U, Rana MK. Repurposing of FDA-approved drugs as potential inhibitors of the SARS-CoV-2 main protease: Molecular insights into improved therapeutic discovery. Comput Biol Med 2021; 142:105183. [PMID: 34986429 PMCID: PMC8714248 DOI: 10.1016/j.compbiomed.2021.105183] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/26/2021] [Accepted: 12/26/2021] [Indexed: 12/22/2022]
Abstract
With numerous infections and fatalities, COVID-19 has wreaked havoc around the globe. The main protease (Mpro), which cleaves the polyprotein to form non-structural proteins, thereby helping in the replication of SARS-CoV-2, appears as an attractive target for antiviral therapeutics. As FDA-approved drugs have shown effectiveness in targeting Mpro in previous SARS-CoV(s), molecular docking and virtual screening of existing antiviral, antimalarial, and protease inhibitor drugs were carried out against SARS-CoV-2 Mpro. Among 53 shortlisted drugs with binding energies lower than that of the crystal-bound inhibitor α-ketoamide 13 b (−6.7 kcal/mol), velpatasvir, glecaprevir, grazoprevir, baloxavir marboxil, danoprevir, nelfinavir, and indinavir (−9.1 to −7.5 kcal/mol) were the most significant on the list (hereafter referred to as the 53-list). Molecular dynamics (MD) simulations confirmed the stability of their Mpro complexes, with the MMPBSA binding free energy (ΔGbind) ranging between −124 kJ/mol (glecaprevir) and −28.2 kJ/mol (velpatasvir). Despite having the lowest initial binding energy, velpatasvir exhibited the highest ΔGbind value for escaping the catalytic site during the MD simulations, indicating its reduced efficacy, as observed experimentally. Available inhibition assay data adequately substantiated the computational forecast. Glecaprevir and nelfinavir (ΔGbind = −95.4 kJ/mol) appear to be the most effective antiviral drugs against Mpro. Furthermore, the remaining FDA drugs on the 53-list can be worth considering, since some have already demonstrated antiviral activity against SARS-CoV-2. Hence, theoretical pKi (Ki = inhibitor constant) values for all 53 drugs were provided. Notably, ΔGbind directly correlates with the average distance of the drugs from the His41–Cys145 catalytic dyad of Mpro, providing a roadmap for rapid screening and improving the inhibitor design against SARS-CoV-2 Mpro.
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Affiliation(s)
- Abhik Kumar Ray
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Satyaranjan Biswal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Uddipan Bhattacharya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India.
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23
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Piplani S, Singh PK, Winkler DA, Petrovsky N. Computationally repurposed drugs and natural products against RNA dependent RNA polymerase as potential COVID-19 therapies. MOLECULAR BIOMEDICINE 2021; 2:28. [PMID: 34766004 PMCID: PMC8450033 DOI: 10.1186/s43556-021-00050-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022] Open
Abstract
Repurposing of existing drugs and drug candidates is an ideal approach to identify new potential therapies for SARS-CoV-2 that can be tested without delay in human trials of infected patients. Here we applied a virtual screening approach using Autodock Vina and molecular dynamics simulation in tandem to calculate binding energies for repurposed drugs against the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). We thereby identified 80 promising compounds with potential activity against SARS-Cov2, consisting of a mixture of antiviral drugs, natural products and drugs with diverse modes of action. A substantial proportion of the top 80 compounds identified in this study had been shown by others to have SARS-CoV-2 antiviral effects in vitro or in vivo, thereby validating our approach. Amongst our top hits not previously reported to have SARS-CoV-2 activity, were eribulin, a macrocyclic ketone analogue of the marine compound halichondrin B and an anticancer drug, the AXL receptor tyrosine kinase inhibitor bemcentinib. Our top hits from our RdRp drug screen may not only have utility in treating COVID-19 but may provide a useful starting point for therapeutics against other coronaviruses. Hence, our modelling approach successfully identified multiple drugs with potential activity against SARS-CoV-2 RdRp. Supplementary Information The online version contains supplementary material available at 10.1186/s43556-021-00050-3.
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Affiliation(s)
- Sakshi Piplani
- College of Medicine and Public Health, Flinders University, Bedford Park, 5046 Australia
- Vaxine Pty Ltd, 11 Walkley Avenue, Warradale, 5046 Australia
| | | | - David A. Winkler
- School of Biochemistry and Genetics, La Trobe University, Bundoora, 3086 Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052 Australia
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD UK
| | - Nikolai Petrovsky
- College of Medicine and Public Health, Flinders University, Bedford Park, 5046 Australia
- Vaxine Pty Ltd, 11 Walkley Avenue, Warradale, 5046 Australia
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24
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Inhibitors of Protein Glycosylation Are Active against the Coronavirus Severe Acute Respiratory Syndrome Coronavirus SARS-CoV-2. Viruses 2021; 13:v13050808. [PMID: 33946304 PMCID: PMC8144969 DOI: 10.3390/v13050808] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 12/23/2022] Open
Abstract
Repurposing clinically available drugs to treat the new coronavirus disease 2019 (COVID-19) is an urgent need in the course of the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2) pandemic, as very few treatment options are available. The iminosugar Miglustat is a well-characterized drug for the treatment of rare genetic lysosome storage diseases, such as Gaucher and Niemann-Pick type C, and has also been described to be active against a variety of enveloped viruses. The activity of Miglustat is here demonstrated in the micromolar range for SARS-CoV-2 in vitro. The drug acts at the post-entry level and leads to a marked decrease of viral proteins and release of infectious viruses. The mechanism resides in the inhibitory activity toward α-glucosidases that are involved in the early stages of glycoprotein N-linked oligosaccharide processing in the endoplasmic reticulum, leading to a marked decrease of the viral Spike protein. Indeed, the antiviral potential of protein glycosylation inhibitors against SARS-CoV-2 is further highlighted by the low-micromolar activity of the investigational drug Celgosivir. These data point to a relevant role of this approach for the treatment of COVID-19.
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25
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Fouedjou RT, Chtita S, Bakhouch M, Belaidi S, Ouassaf M, Djoumbissie LA, Tapondjou LA, Abul Qais F. Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors. J Biomol Struct Dyn 2021; 40:8615-8629. [PMID: 33908318 DOI: 10.1080/07391102.2021.1914170] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic instigated by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) which changed the daily train of the world's population and cause several dead. Despite the significant efforts made in developing vaccines and therapeutic drugs, there is currently no available effective treatment against this new coronavirus infection, hence the need to continue research which is aimed at limiting the progression of this virus. The present study which has as objective to carry out in silico studies on the metabolites of some Cameroonian medicinal plants of the Asteraceae family with a view to propose potential molecules to fight against COVID-19. The selected plants are commonly used to treat respiratory infectious diseases, and for this reason they may contain some constituents which could exhibit an antiviral activity against SARS-CoV-2. In this work, a set of 74 naturally occurring compounds are computed with SARS-CoV-2 main protease protein (PDB ID: 6lu7) and spike protein (PDB ID: 6m0j) for their affinity and stability using binding energy analysis and molecular docking. Chrysoeriol-7-O-β-D-glucuronopyranoside (compound 16) has showed promising results including excellent Absorption, Distribution, Metabolism and Excretion (ADME) parameters as well as insignificant toxicity. Finally, the stability of this compound is complex with the two proteins validated through molecular dynamics (MD) simulation, they displayed stable trajectory and molecular properties with consistent interaction profile in molecular dynamics simulations. These findings call for further in vitro and in vivo challenges of phytoconstituents against the COVID-19 as a potential agent to fight the spread of this dramatic pandemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Romuald Tematio Fouedjou
- Research Unit of Environmental and Applied Chemistry, Department of Chemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Samir Chtita
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohamed Bakhouch
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - Salah Belaidi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria.,Centre de Recherche en Sciences Pharmaceutiques - CRSP-la nouvelle ville Ali Mendjeli, Constantine, Algérie
| | - Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra, Algeria
| | - Loris Alvine Djoumbissie
- Research Unit of Noxious Chemistry and Environmental Engineering, Department of Chemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Léon Azefack Tapondjou
- Research Unit of Environmental and Applied Chemistry, Department of Chemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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