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Davis DA, Nair A, Astter Y, Treco E, Peyser B, Gussio R, Nguyen T, Eaton B, Postnikova E, Murphy M, Shrestha P, Bulut H, Hattorri SI, Mitsuya H, Yarchoan R. Discovery of a nasal spray steroid, tixocortol, as an inhibitor of SARS-CoV-2 main protease and viral replication. RSC Med Chem 2024; 15:d4md00454j. [PMID: 39371432 PMCID: PMC11450544 DOI: 10.1039/d4md00454j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/15/2024] [Indexed: 10/08/2024] Open
Abstract
Coronaviruses rely on the viral-encoded chymotrypsin-like main protease (Mpro or 3CLpro) for replication and assembly. Our previous research on Mpro of SARS-CoV-2 identified cysteine 300 (Cys300) as a potential allosteric site of Mpro inhibition. Here, we identified tixocortol (TX) as a covalent modifier of Cys300 which inhibits Mpro activity in vitro as well as in a cell-based Mpro expression assay. Most importantly TX inhibited SARS-CoV-2 replication in ACE2 expressing HeLa cells. Biochemical analysis and kinetic assays were consistent with TX acting as a non-competitive inhibitor. By contrast, TX was a weaker inhibitor and modifier of C300S Mpro, confirming a role for Cys300 in inhibition of WT Mpro but also providing evidence for an additional Cys target. TX pivalate (TP), a prodrug for TX that was previously marketed as a nasal spray, also inhibited SARS-CoV-2 replication in HeLa-ACE2 cells at low micromolar IC50s. These studies suggest that TX and/or TP could possibly be repurposed for the prevention and/or treatment of SARS-CoV-2 infection.
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Affiliation(s)
- David A Davis
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Ashwin Nair
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Yana Astter
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Emma Treco
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Brian Peyser
- Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health USA
| | - Rick Gussio
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA
- Computational Institute for Health and Environmental Research, (CIFHER.ORG) Riverside 5, RM 4076, 8490 Progress Dr. Frederick MD 21701 USA
| | - Tam Nguyen
- Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health USA
| | - Brett Eaton
- Integrated Research Facility at Fort Detrick 8200 Research Plaza Frederick MD 21702 USA
| | - Elena Postnikova
- Integrated Research Facility at Fort Detrick 8200 Research Plaza Frederick MD 21702 USA
| | - Michael Murphy
- Integrated Research Facility at Fort Detrick 8200 Research Plaza Frederick MD 21702 USA
| | - Prabha Shrestha
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Haydar Bulut
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Shin-Ichiro Hattorri
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute 1-21-1 Toyama Shinjuku-ku Tokyo 162-8655 Japan
| | - Hiroaki Mitsuya
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute 1-21-1 Toyama Shinjuku-ku Tokyo 162-8655 Japan
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute Bethesda MD USA
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Youn KW, Lee S, Kim JH, Park YI, So J, Kim C, Cho CW, Park J. Amentoflavone from Selaginella tamariscina inhibits SARS-CoV-2 RNA-dependent RNA polymerase. Heliyon 2024; 10:e36568. [PMID: 39258186 PMCID: PMC11386279 DOI: 10.1016/j.heliyon.2024.e36568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
The SARS-CoV-2 pandemic caused millions of deaths due to its prominent infectivity and mortality. Although the vaccines and medicines for SARS-CoV-2 are on the market, new coronavirus variants like influenza are expected to reemerge continuously. Therefore, effective and inexpensive medicines will be required to respond to SARS-CoV-2 variants. Here, we used herbal plant extracts to search for effective compounds that can interfere with SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and found that Selaginella tamariscina extract (STE) can reduce SARS-CoV-2 RdRp activity. The HCoV-OC43 beta coronavirus model was used to examine whether STE treatment could inhibit coronavirus replication and reduce coronavirus-induced cytotoxicity. Next, we searched the active compound of STE and found that amentoflavone is the main active compound of STE. Finally, we demonstrated that amentoflavone inhibits SARS-CoV-2 RdRp and coronavirus replication. Our results collectively indicate that amentoflavone from STE is possibly beneficial in responding to coronavirus-related diseases, including SARS-CoV-2.
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Affiliation(s)
- Kyoung Won Youn
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Siyun Lee
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Jang Hoon Kim
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, 27709, Republic of Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Jaeyeon So
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Chansoo Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, 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, 26493, Republic of Korea
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3
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Grimes SL, Denison MR. The Coronavirus helicase in replication. Virus Res 2024; 346:199401. [PMID: 38796132 PMCID: PMC11177069 DOI: 10.1016/j.virusres.2024.199401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
The coronavirus nonstructural protein (nsp) 13 encodes an RNA helicase (nsp13-HEL) with multiple enzymatic functions, including unwinding and nucleoside phosphatase (NTPase) activities. Attempts for enzymatic inactivation have defined the nsp13-HEL as a critical enzyme for viral replication and a high-priority target for antiviral development. Helicases have been shown to play numerous roles beyond their canonical ATPase and unwinding activities, though these functions are just beginning to be explored in coronavirus biology. Recent genetic and biochemical studies, as well as work in structurally-related helicases, have provided evidence that supports new hypotheses for the helicase's potential role in coronavirus replication. Here, we review several aspects of the coronavirus nsp13-HEL, including its reported and proposed functions in viral replication and highlight fundamental areas of research that may aid the development of helicase inhibitors.
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Affiliation(s)
- Samantha L Grimes
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark R Denison
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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4
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So J, Kim JH, Lee S, Kim C, Park R, Park J. Arctigenin from Forsythia viridissima Fruit Inhibits the Replication of Human Coronavirus. Int J Mol Sci 2024; 25:7363. [PMID: 39000469 PMCID: PMC11242317 DOI: 10.3390/ijms25137363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Coronavirus can cause various diseases, from mild symptoms to the recent severe COVID-19. The coronavirus RNA genome is frequently mutated due to its RNA nature, resulting in many pathogenic and drug-resistant variants. Therefore, many medicines should be prepared to respond to the various coronavirus variants. In this report, we demonstrated that Forsythia viridissima fruit ethanol extract (FVFE) effectively reduces coronavirus replication. We attempted to identify the active compounds and found that actigenin from FVFE effectively reduces human coronavirus replication. Arctigenin treatment can reduce coronavirus protein expression and coronavirus-induced cytotoxicity. These results collectively suggest that arctigenin is a potent natural compound that prevents coronavirus replication.
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Affiliation(s)
- Jaeyeon So
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Jang Hoon Kim
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung 27709, Republic of Korea
| | - Siyun Lee
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Chansoo Kim
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Rackhyun Park
- Department of Life Science, Yong-In University, Yongin 17092, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
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5
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Sučec I, Pankratova Y, Parasar M, Hong M. Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63. Protein Sci 2024; 33:e4923. [PMID: 38501465 PMCID: PMC10949323 DOI: 10.1002/pro.4923] [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: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 03/20/2024]
Abstract
The envelope (E) proteins of coronaviruses (CoVs) form cation-conducting channels that are associated with the pathogenicity of these viruses. To date, high-resolution structural information about these viroporins is limited to the SARS-CoV E protein. To broaden our structural knowledge of other members of this family of viroporins, we now investigate the conformation of the E protein of the human coronavirus (hCoV), NL63. Using two- and three-dimensional magic-angle-spinning NMR, we have measured 13 C and 15 N chemical shifts of the transmembrane domain of E (ETM), which yielded backbone (ϕ, ψ) torsion angles. We further measured the water accessibility of NL63 ETM at neutral pH versus acidic pH in the presence of Ca2+ ions. These data show that NL63 ETM adopts a regular α-helical conformation that is unaffected by pH and the N-terminal ectodomain. Interestingly, the water accessibility of NL63 ETM increases only modestly at acidic pH in the presence of Ca2+ compared to neutral pH, in contrast to SARS ETM, which becomes much more hydrated at acidic pH. This difference suggests a structural basis for the weaker channel conductance of α-CoV compared to β-CoV E proteins. The weaker E channel activity may in turn contribute to the reduced virulence of hCoV-NL63 compared to SARS-CoV viruses.
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Affiliation(s)
- Iva Sučec
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Yanina Pankratova
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mriganka Parasar
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Li Y, Miyani B, Faust RA, David RE, Xagoraraki I. A broad wastewater screening and clinical data surveillance for virus-related diseases in the metropolitan Detroit area in Michigan. Hum Genomics 2024; 18:14. [PMID: 38321488 PMCID: PMC10845806 DOI: 10.1186/s40246-024-00581-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Periodic bioinformatics-based screening of wastewater for assessing the diversity of potential human viral pathogens circulating in a given community may help to identify novel or potentially emerging infectious diseases. Any identified contigs related to novel or emerging viruses should be confirmed with targeted wastewater and clinical testing. RESULTS During the COVID-19 pandemic, untreated wastewater samples were collected for a 1-year period from the Great Lakes Water Authority Wastewater Treatment Facility in Detroit, MI, USA, and viral population diversity from both centralized interceptor sites and localized neighborhood sewersheds was investigated. Clinical cases of the diseases caused by human viruses were tabulated and compared with data from viral wastewater monitoring. In addition to Betacoronavirus, comparison using assembled contigs against a custom Swiss-Prot human virus database indicated the potential prevalence of other pathogenic virus genera, including: Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Bocaparvovirus, Molluscipoxvirus, Parechovirus, Roseolovirus, Lymphocryptovirus, Alphavirus, Spumavirus, Lentivirus, Deltaretrovirus, Enterovirus, Kobuvirus, Gammaretrovirus, Cardiovirus, Erythroparvovirus, Salivirus, Rubivirus, Orthohepevirus, Cytomegalovirus, Norovirus, and Mamastrovirus. Four nearly complete genomes were recovered from the Astrovirus, Enterovirus, Norovirus and Betapolyomavirus genera and viral species were identified. CONCLUSIONS The presented findings in wastewater samples are primarily at the genus level and can serve as a preliminary "screening" tool that may serve as indication to initiate further testing for the confirmation of the presence of species that may be associated with human disease. Integrating innovative environmental microbiology technologies like metagenomic sequencing with viral epidemiology offers a significant opportunity to improve the monitoring of, and predictive intelligence for, pathogenic viruses, using wastewater.
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Affiliation(s)
- Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA
| | - Russell A Faust
- Oakland County Health Division, 1200 Telegraph Rd, Pontiac, MI, 48341, USA
| | - Randy E David
- School of Medicine, Wayne State University, Detroit, MI, 48282, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA.
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Najimi N, Tajount L, Regragui Z, Remz C, Ait-Lhaj-Mhand R, Kadi C, Belayachi L, Seghrouchni F, Nadia dakka, El Hassani RA, Elharti E, Oumzil H, Bakri Y. Pre-pandemic antibodies screening against SARS-CoV-2 and virus detection among children diagnosed with eruptive fevers. Int J Immunopathol Pharmacol 2024; 38:3946320241260633. [PMID: 38836458 PMCID: PMC11155355 DOI: 10.1177/03946320241260633] [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: 12/15/2023] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
OBJECTIVES This study aims to assess the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG antibodies against the spike (S) and nucleocapsid (NP) proteins, as well as neutralizing antibodies against the receptor-binding domain (RBD). Additionally, it aims to detect viral RNA of SARS-CoV-2 in pre-pandemic archival pediatric specimens collected before the announcement of the COVID-19 pandemic spread on March 20th, 2020, in Morocco. The objective is to investigate the existence of pre-pandemic immunity to SARS-CoV-2. METHODS We conducted a cross-sectional study, to analyze IgG antibody levels in a cohort of 106 pre-pandemic pediatric participants. Using an indirect enzyme-linked immunosorbent assay (ELISA), we measured the IgG levels against the S and NP proteins of SARS-CoV-2. Additionally, we staged a competitive ELISA assay to evaluate the neutralizing capability of these antibodies. We used reverse transcription polymerase chain reaction (rRT-PCR) to detect viral NP and ORF1ab genes of SARS-CoV-2 in oropharyngeal swabs. Moreover, we conducted on the same specimens a multiplexed RT-PCR to detect RNA of the most common 27 pathogens involved in lower respiratory tract infections. RESULTS Among the 106 serum samples, 13% (nn = =14) tested positive for SARS-CoV-2 IgG antibodies using ELISA. Temporal analysis indicated varying IgG positivity levels across 2019. Neutralizing antibodies were found in 21% of the 28 samples analyzed, including two with high inhibition rates (93%). The SARS-CoV-2 RNA was detected using rRT-PCR in 14 samples. None of the samples tested positive for the other 27 pathogens associated with lower respiratory tract infections, using multiplexed RT-PCR. CONCLUSION Our study addresses the possibility, that COVID-19 infections occurred in Morocco before the recognized outbreak. On the other hand, some of the cases might reflect cross-reactivity with other coronaviruses or be influenced by previous viral exposures or vaccinations. Understanding these factors is crucial to comprehending pediatric immune responses to newly emerging infectious diseases.
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Affiliation(s)
- Nouhaila Najimi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco and Mohammed VI University of Sciences and Health, Casablanca, Morocco
| | - Latifa Tajount
- Laboratory of Spectroscopy, Molecular Modeling, Materials, Nanomaterials, Water and Environment, Materials for Environment Team, ENSAM, Mohammed V University in Rabat, Rabat, Morocco
| | - Zakia Regragui
- Virology Department, Institut National d’Hygiène, Rabat, Morocco
| | - Chaimae Remz
- Virology Department, Institut National d’Hygiène, Rabat, Morocco
| | | | - Chaimae Kadi
- Mohammed VI Center for Research & Innovation, Rabat, Morocco and Mohammed VI University of Sciences and Health, Casablanca, Morocco
- Laboratory of Biology and Health, Faculty of Sciences of Tetouan, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Lamiae Belayachi
- International University of Rabat (UIR), Faculty of Medicine, Centre de Recherche en Sciences de la Santé (CreSS), Faculty of Medecine, Health Sciences Research Centre (CReSS), International University of Rabat (UIR), Rabat, Morocco
| | - Fouad Seghrouchni
- Mohammed VI Center for Research & Innovation, Rabat, Morocco and Mohammed VI University of Sciences and Health, Casablanca, Morocco
| | - Nadia dakka
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Center of Genomic of Human Pathologies Biology Faculty of Medicine, Mohammed V University in Rabat, Rabat, Morocco
| | - Rabii Ameziane El Hassani
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Center of Genomic of Human Pathologies Biology Faculty of Medicine, Mohammed V University in Rabat, Rabat, Morocco
| | - Elmir Elharti
- Virology Department, Institut National d’Hygiène, Rabat, Morocco
| | - Hicham Oumzil
- Center of Genomic of Human Pathologies Biology Faculty of Medicine, Mohammed V University in Rabat, Rabat, Morocco
- Medical Biotechnology Laboratory, Faculty of Medicine at Mohammed V University in Rabat, Rabat, Morocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Center of Genomic of Human Pathologies Biology Faculty of Medicine, Mohammed V University in Rabat, Rabat, Morocco
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8
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Townsend JP, Hassler HB, Lamb AD, Sah P, Alvarez Nishio A, Nguyen C, Tew AD, Galvani AP, Dornburg A. Seasonality of endemic COVID-19. mBio 2023; 14:e0142623. [PMID: 37937979 PMCID: PMC10746271 DOI: 10.1128/mbio.01426-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE The seasonality of COVID-19 is important for effective healthcare and public health decision-making. Previous waves of SARS-CoV-2 infections have indicated that the virus will likely persist as an endemic pathogen with distinct surges. However, the timing and patterns of potentially seasonal surges remain uncertain, rendering effective public health policies uninformed and in danger of poorly anticipating opportunities for intervention, such as well-timed booster vaccination drives. Applying an evolutionary approach to long-term data on closely related circulating coronaviruses, our research provides projections of seasonal surges that should be expected at major temperate population centers. These projections enable local public health efforts that are tailored to expected surges at specific locales or regions. This knowledge is crucial for enhancing medical preparedness and facilitating the implementation of targeted public health interventions.
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Affiliation(s)
- Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Program in Microbiology, Yale University, New Haven, USA
| | - Hayley B. Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
| | - April D. Lamb
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Pratha Sah
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | | | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alexandra D. Tew
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
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9
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Lokhande KB, Kale A, Shahakar B, Shrivastava A, Nawani N, Swamy KV, Singh A, Pawar SV. Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy. Comput Biol Chem 2023; 106:107912. [PMID: 37454399 DOI: 10.1016/j.compbiolchem.2023.107912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
COVID-19 shook the world during the pandemic, where the climax it reached was vaccine manufacturing at an unfathomable pace. Alternative promising solutions to prevent infection from SARS-CoV-2 and its variants will remain crucial in the years to come. Due to its key role in viral replication, the major protease (Mpro) enzyme of SARS-CoV-2 can be an attractive therapeutic target. In the present work, natural terpenoids from mangrove medicinal plant Xylocarpus moluccensis (Lam.) M. Roem. were screened using computational methods for inhibition of Mpro protein. Out of sixty-seven terpenoids, Angolensic acid methyl ester, Moluccensin V, Thaixylomolin F, Godavarin J, and Xylomexicanolide A were shortlisted based on their docking scores and interaction affinities (- 13.502 to - 15.52 kcal/mol). The efficacy was validated by the 100 ns molecular dynamics study. Lead terpenoids were within the acceptable range of RMSD and RMSF with a mean value of 2.5 Å and 1.5 Å, respectively indicating that they bound tightly within Mpro and there was minimal fluctuation and stability of Mpro upon binding of these terpenoids. The utmost favorable binding strengths as calculated by MM-GBSA, were of Angolensic acid methyl ester and Moluccensin V with binding free energies (ΔGbind) of - 39.084, and - 43.160 kcal/mol, respectively. The terpenoids showed no violations in terms of Drug Likeliness and ADMET predictions. Overall, the findings indicate that Angolensic acid methyl ester and Moluccensin V are effective terpenoids having strong binding interaction with Mpro protein, which must be tested in vitro as an effective anti-SARS-CoV-2 drug.
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Affiliation(s)
- Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India; Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Arti Kale
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India
| | - Bhagyashree Shahakar
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India
| | - Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Neelu Nawani
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India.
| | - K Venkateswara Swamy
- MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, Maharashtra, India
| | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Sarika Vishnu Pawar
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411033, Maharashtra, India.
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