1
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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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2
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Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 PMCID: PMC11131022 DOI: 10.1093/procel/pwae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
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Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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3
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Mesaros EF, Dugan BJ, Gao M, Sheraz M, McGovern-Gooch K, Xu F, Fan KY, Nguyen D, Kultgen SG, Lindstrom A, Stever K, Tercero B, Binder RJ, Liu F, Micolochick Steuer HM, Mani N, Harasym TO, Thi EP, Cuconati A, Dorsey BD, Cole AG, Lam AM, Sofia MJ. Discovery of C-Linked Nucleoside Analogues with Antiviral Activity against SARS-CoV-2. ACS Infect Dis 2024; 10:1780-1792. [PMID: 38651692 DOI: 10.1021/acsinfecdis.4c00122] [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] [Indexed: 04/25/2024]
Abstract
The recent COVID-19 pandemic underscored the limitations of currently available direct-acting antiviral treatments against acute respiratory RNA-viral infections and stimulated major research initiatives targeting anticoronavirus agents. Two novel nsp5 protease (MPro) inhibitors have been approved, nirmatrelvir and ensitrelvir, along with two existing nucleos(t)ide analogues repurposed as nsp12 polymerase inhibitors, remdesivir and molnupiravir, but a need still exists for therapies with improved potency and systemic exposure with oral dosing, better metabolic stability, and reduced resistance and toxicity risks. Herein, we summarize our research toward identifying nsp12 inhibitors that led to nucleoside analogues 10e and 10n, which showed favorable pan-coronavirus activity in cell-infection screens, were metabolized to active triphosphate nucleotides in cell-incubation studies, and demonstrated target (nsp12) engagement in biochemical assays.
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Affiliation(s)
- Eugen F Mesaros
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Benjamin J Dugan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Min Gao
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Muhammad Sheraz
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | | | - Fran Xu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Kristi Yi Fan
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Duyan Nguyen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Steven G Kultgen
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Aaron Lindstrom
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Kim Stever
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Breanna Tercero
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Randall J Binder
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Fei Liu
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | | | - Nagraj Mani
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Troy O Harasym
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Emily P Thi
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Andrea Cuconati
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Bruce D Dorsey
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Andrew G Cole
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Angela M Lam
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
| | - Michael J Sofia
- Arbutus Biopharma, Inc., 701 Veterans Circle, Warminster, Pennsylvania 18974, United States
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4
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Bradley CC, Wang C, Gordon AJE, Wen AX, Luna PN, Cooke MB, Kohrn BF, Kennedy SR, Avadhanula V, Piedra PA, Lichtarge O, Shaw CA, Ronca SE, Herman C. Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence. Nat Microbiol 2024; 9:1382-1392. [PMID: 38649410 DOI: 10.1038/s41564-024-01655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
RNA viruses, like SARS-CoV-2, depend on their RNA-dependent RNA polymerases (RdRp) for replication, which is error prone. Monitoring replication errors is crucial for understanding the virus's evolution. Current methods lack the precision to detect rare de novo RNA mutations, particularly in low-input samples such as those from patients. Here we introduce a targeted accurate RNA consensus sequencing method (tARC-seq) to accurately determine the mutation frequency and types in SARS-CoV-2, both in cell culture and clinical samples. Our findings show an average of 2.68 × 10-5 de novo errors per cycle with a C > T bias that cannot be solely attributed to APOBEC editing. We identified hotspots and cold spots throughout the genome, correlating with high or low GC content, and pinpointed transcription regulatory sites as regions more susceptible to errors. tARC-seq captured template switching events including insertions, deletions and complex mutations. These insights shed light on the genetic diversity generation and evolutionary dynamics of SARS-CoV-2.
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Affiliation(s)
- Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alice X Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Cooke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shannon E Ronca
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Feigin Biosafety Level 3 Facility, Texas Children's Hospital, Houston, TX, USA
- National School of Tropical Medicine, Department of Pediatrics Tropical Medicine, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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5
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Pérez-Vargas J, Lemieux G, Thompson CAH, Désilets A, Ennis S, Gao G, Gordon DG, Schulz AL, Niikura M, Nabi IR, Krajden M, Boudreault PL, Leduc R, Jean F. Nanomolar anti-SARS-CoV-2 Omicron activity of the host-directed TMPRSS2 inhibitor N-0385 and synergistic action with direct-acting antivirals. Antiviral Res 2024; 225:105869. [PMID: 38548023 DOI: 10.1016/j.antiviral.2024.105869] [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: 02/05/2024] [Revised: 03/10/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
SARS-CoV-2 Omicron subvariants with increased transmissibility and immune evasion are spreading globally with alarming persistence. Whether the mutations and evolution of spike (S) Omicron subvariants alter the viral hijacking of human TMPRSS2 for viral entry remains to be elucidated. This is particularly important to investigate because of the large number and diversity of mutations of S Omicron subvariants reported since the emergence of BA.1. Here we report that human TMPRSS2 is a molecular determinant of viral entry for all the Omicron clinical isolates tested in human lung cells, including ancestral Omicron subvariants (BA.1, BA.2, BA.5), contemporary Omicron subvariants (BQ.1.1, XBB.1.5, EG.5.1) and currently circulating Omicron BA.2.86. First, we used a co-transfection assay to demonstrate the endoproteolytic cleavage by TMPRSS2 of spike Omicron subvariants. Second, we found that N-0385, a highly potent TMPRSS2 inhibitor, is a robust entry inhibitor of virus-like particles harbouring the S protein of Omicron subvariants. Third, we show that N-0385 exhibits nanomolar broad-spectrum antiviral activity against live Omicron subvariants in human Calu-3 lung cells and primary patient-derived bronchial epithelial cells. Interestingly, we found that N-0385 is 10-20 times more potent than the repositioned TMPRSS2 inhibitor, camostat, against BA.5, EG.5.1, and BA.2.86. We further found that N-0385 shows broad synergistic activity with clinically approved direct-acting antivirals (DAAs), i.e., remdesivir and nirmatrelvir, against Omicron subvariants, demonstrating the potential therapeutic benefits of a multi-targeted treatment based on N-0385 and DAAs.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Gabriel Lemieux
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Connor A H Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Antoine Désilets
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Guang Gao
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada; Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Danielle G Gordon
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Annika Lea Schulz
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
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6
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Thomas J, Ghosh A, Ranjan S, Satija J. Cheminformatics approach to identify andrographolide derivatives as dual inhibitors of methyltransferases (nsp14 and nsp16) of SARS-CoV-2. Sci Rep 2024; 14:9801. [PMID: 38684706 PMCID: PMC11058777 DOI: 10.1038/s41598-024-58532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
The Covid-19 pandemic outbreak has accelerated tremendous efforts to discover a therapeutic strategy that targets severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to control viral infection. Various viral proteins have been identified as potential drug targets, however, to date, no specific therapeutic cure is available against the SARS-CoV-2. To address this issue, the present work reports a systematic cheminformatic approach to identify the potent andrographolide derivatives that can target methyltransferases of SARS-CoV-2, i.e. nsp14 and nsp16 which are crucial for the replication of the virus and host immune evasion. A consensus of cheminformatics methodologies including virtual screening, molecular docking, ADMET profiling, molecular dynamics simulations, free-energy landscape analysis, molecular mechanics generalized born surface area (MM-GBSA), and density functional theory (DFT) was utilized. Our study reveals two new andrographolide derivatives (PubChem CID: 2734589 and 138968421) as natural bioactive molecules that can form stable complexes with both proteins via hydrophobic interactions, hydrogen bonds and electrostatic interactions. The toxicity analysis predicts class four toxicity for both compounds with LD50 value in the range of 500-700 mg/kg. MD simulation reveals the stable formation of the complex for both the compounds and their average trajectory values were found to be lower than the control inhibitor and protein alone. MMGBSA analysis corroborates the MD simulation result and showed the lowest energy for the compounds 2734589 and 138968421. The DFT and MEP analysis also predicts the better reactivity and stability of both the hit compounds. Overall, both andrographolide derivatives exhibit good potential as potent inhibitors for both nsp14 and nsp16 proteins, however, in-vitro and in vivo assessment would be required to prove their efficacy and safety in clinical settings. Moreover, the drug discovery strategy aiming at the dual target approach might serve as a useful model for inventing novel drug molecules for various other diseases.
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Affiliation(s)
- Jobin Thomas
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Anupam Ghosh
- NanoBio Research Lab, School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721301, India
| | - Shivendu Ranjan
- NanoBio Research Lab, School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721301, India
| | - Jitendra Satija
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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7
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Rabie AM, Eltayb WA. Potent Dual Polymerase/Exonuclease Inhibitory Activities of Antioxidant Aminothiadiazoles Against the COVID-19 Omicron Virus: A Promising In Silico/In Vitro Repositioning Research Study. Mol Biotechnol 2024; 66:592-611. [PMID: 36690820 PMCID: PMC9870775 DOI: 10.1007/s12033-022-00551-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 01/25/2023]
Abstract
Recently, natural and synthetic nitrogenous heterocyclic antivirals topped the scene as first choices for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying disease, the coronavirus disease 2019 (COVID-19). Meanwhile, the mysterious evolution of a new strain of SARS-CoV-2, the Omicron variant and its sublineages, caused a new defiance in the continual COVID-19 battle. Hitting the two principal coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) synchronously using the same ligand is a highly effective novel dual pathway to hinder SARS-CoV-2 reproduction and stop COVID-19 progression irrespective of the SARS-CoV-2 variant type since RdRps and ExoNs are widely conserved among all SARS-CoV-2 strains. Herein, the present computational/biological study screened our previous small libraries of nitrogenous heterocyclic compounds, searching for the most ideal drug candidates predictably able to efficiently act through this double approach. Theoretical filtration gave rise to three promising antioxidant nitrogenous heterocyclic compounds of the 1,3,4-thiadiazole type, which are CoViTris2022, Taroxaz-26, and ChloViD2022. Further experimental evaluation proved for the first time, utilizing the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that ChloViD2022, CoViTris2022, and Taroxaz-26 could effectively inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 0.17 and 0.41 μM for ChloViD2022, 0.21 and 0.69 μM for CoViTris2022, and 0.23 and 0.73 μM for Taroxaz-26, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico outcomes greatly supported these biochemical results, proposing that the three molecules potently strike the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's vital active sites. Moreover, the idealistic pharmacophoric hallmarks of CoViTris2022, Taroxaz-26, and ChloViD2022 molecules relatively make them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their highly flexible structures open for various kinds of chemical derivatization. To cut it short, the present pivotal findings of this comprehensive work disclosed the promising repositioning potentials of the three 2-aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, to successfully interfere with the crucial biological interactions of the coronaviral-2 polymerase/exoribonuclease with the four principal RNA nucleotides, and, as a result, cure COVID-19 infection, encouraging us to rapidly start the three drugs' broad preclinical/clinical anti-COVID-19 evaluations.
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Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City, Mansoura, 35511, Dakahlia Governorate, Egypt.
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City, Dikernis, 35744, Dakahlia Governorate, Egypt.
| | - Wafa A Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan.
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8
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Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones AN, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz GM, Pyrć K, Czarna A. Despite the odds: formation of the SARS-CoV-2 methylation complex. Nucleic Acids Res 2024:gkae165. [PMID: 38499483 DOI: 10.1093/nar/gkae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14's exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.
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Affiliation(s)
- Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-387 Kraków, Poland
| | - Jacek Plewka
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Michał Rawski
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - André Mourão
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Leanid Kresik
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Kinga Lis
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemical Engineering and Technology, Kraków University of Technology, 31-155 Kraków, Poland
| | - Alisha N Jones
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Magdalena Pachota
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Abdulkarim Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, 44002 Erbil, Kurdistan Region, Iraq
- Department of Community Health, College of Health Technology, Cihan University-Erbil, 44001 Erbil, Kurdistan Region, Iraq
| | - Kinga Hartman
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Ravi Sonani
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Igor Minia
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Markus Landthaler
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Michael Sattler
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Piotr Suder
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Grzegorz M Popowicz
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Krzysztof Pyrć
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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9
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Majchrzak M, Madej Ł, Łysek-Gładysińska M, Zarębska-Michaluk D, Zegadło K, Dziuba A, Nogal-Nowak K, Kondziołka W, Sufin I, Myszona-Tarnowska M, Jaśkowski M, Kędzierski M, Maciukajć J, Matykiewicz J, Głuszek S, Adamus-Białek W. The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19. BMC Infect Dis 2024; 24:281. [PMID: 38439047 PMCID: PMC10913261 DOI: 10.1186/s12879-024-09146-x] [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: 09/15/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The evolution of SARS-CoV-2 has been observed from the very beginning of the fight against COVID-19, some mutations are indicators of potentially dangerous variants of the virus. However, there is no clear association between the genetic variants of SARS-CoV-2 and the severity of COVID-19. We aimed to analyze the genetic variability of RdRp in correlation with different courses of COVID-19. RESULTS The prospective study included 77 samples of SARS-CoV-2 isolated from outpatients (1st degree of severity) and hospitalized patients (2nd, 3rd and 4th degree of severity). The retrospective analyses included 15,898,266 cases of SARS-CoV-2 genome sequences deposited in the GISAID repository. Single-nucleotide variants were identified based on the four sequenced amplified fragments of SARS-CoV-2. The analysis of the results was performed using appropriate statistical methods, with p < 0.05, considered statistically significant. Additionally, logistic regression analysis was performed to predict the strongest determinants of the observed relationships. The number of mutations was positively correlated with the severity of the COVID-19, and older male patients. We detected four mutations that significantly increased the risk of hospitalization of COVID-19 patients (14676C > T, 14697C > T, 15096 T > C, and 15279C > T), while the 15240C > T mutation was common among strains isolated from outpatients. The selected mutations were searched worldwide in the GISAID database, their presence was correlated with the severity of COVID-19. CONCLUSION Identified mutations have the potential to be used to assess the increased risk of hospitalization in COVID-19 positive patients. Experimental studies and extensive epidemiological data are needed to investigate the association between individual mutations and the severity of COVID-19.
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Affiliation(s)
- Michał Majchrzak
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Łukasz Madej
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | | | | | - Katarzyna Zegadło
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Anna Dziuba
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | | | | | | | | | | | | | | | | | - Stanisław Głuszek
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
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10
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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11
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Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [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: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
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Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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12
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Abdelnabi R, Lassaunière R, Maes P, Weynand B, Neyts J. Comparing the Infectivity of Recent SARS-CoV-2 Omicron Sub-Variants in Syrian Hamsters. Viruses 2024; 16:122. [PMID: 38257822 PMCID: PMC10819014 DOI: 10.3390/v16010122] [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: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Since the emergence of the first omicron SARS-CoV-2 variant at the end of 2021, several sub-variants have evolved and become predominant in the human population, showing enhanced transmissibility and ability to (partly) escape the adaptive immune response. The XBB sub-variants (e.g., EG.5.1) have become globally dominant. Besides the XBB sub-variants, a phylogenetically distinct variant, i.e., BA.2.86, is also circulating; it carries several mutations in the spike protein as compared to its parental BA.2 variant. Here, we explored the infectivity of the BA.2.86 and EG.5.1 sub-variants compared to the preceding BA.5 sub-variant in Syrian hamsters. Such preclinical models are important for the evaluation of updated vaccine candidates and novel therapeutic modalities. Following intranasal infection with either variant, throat swabs and lung samples were collected on days 3 and 4 post infection. No significant differences in viral RNA loads in throat swabs were observed between these sub-variants. However, the infectious virus titers in the lungs of EG.5.1- and BA.2.86-infected animals were significantly lower compared to the BA.5-infected ones. The lung pathology scores of animals infected with EG.5.1 and BA.2.86 were also markedly lower than that of BA.5 sub-variant. Together, we show that EG.5.1 and BA.2.86 sub-variants exhibit an attenuated replication in hamsters' lungs as compared to the BA.5 sub-variant.
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Affiliation(s)
- Rana Abdelnabi
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Department of Microbiology, Immunology and Transplantation, VirusBank Platform, KU Leuven, B-3001 Leuven, Belgium
| | | | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, KU Leuven, B-3000 Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, Division of Translational Cell and Tissue Research, KU Leuven, B-3000 Leuven, Belgium;
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, B-3000 Leuven, Belgium;
- Department of Microbiology, Immunology and Transplantation, VirusBank Platform, KU Leuven, B-3001 Leuven, Belgium
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13
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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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van Breemen RB, Muchiri RN. Affinity selection-mass spectrometry in the discovery of anti-SARS-CoV-2 compounds. MASS SPECTROMETRY REVIEWS 2024; 43:39-46. [PMID: 35929396 PMCID: PMC9538385 DOI: 10.1002/mas.21800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Small molecule therapeutic agents are needed to treat or prevent infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is the cause of the COVID-19 pandemic. To expedite the discovery of lead compounds for development, assays have been developed based on affinity selection-mass spectrometry (AS-MS), which enables the rapid screening of mixtures such as combinatorial libraries and extracts of botanicals or other sources of natural products. AS-MS assays have been used to find ligands to the SARS-CoV-2 spike protein for inhibition of cell entry as well as to the 3-chymotrypsin-like cysteine protease (3CLpro) and the RNA-dependent RNA polymerase complex constituent Nsp9, which are targets for inhibition of viral replication. The AS-MS approach of magnetic microbead affinity selection screening has been used to discover high-affinity peptide ligands to the spike protein as well as the hemp cannabinoids cannabidiolic acid and cannabigerolic acid, which can prevent cell infection by SARS-CoV-2. Another AS-MS method, native mass spectrometry, has been used to discover that the flavonoids baicalein, scutellarein, and ganhuangenin, can inhibit the SARS-CoV-2 protease 3CLpro. Native mass spectrometry has also been used to find an ent-kaurane natural product, oridonin, that can bind to the viral protein Nsp9 and interfere with RNA replication. These natural lead compounds are under investigation for the development of therapeutic agents to prevent or treat SARS-CoV-2 infection.
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Affiliation(s)
- Richard B. van Breemen
- Department of Pharmaceutical Sciences, Linus Pauling Institute, College of PharmacyOregon State UniversityCorvallisOregonUSA
| | - Ruth N. Muchiri
- Department of Pharmaceutical Sciences, Linus Pauling Institute, College of PharmacyOregon State UniversityCorvallisOregonUSA
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15
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Formentin M, Chignola R, Favretti M. Optimal entropic properties of SARS-CoV-2 RNA sequences. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231369. [PMID: 38298394 PMCID: PMC10827432 DOI: 10.1098/rsos.231369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
The reaction of the scientific community against the COVID-19 pandemic has generated a huge (approx. 106 entries) dataset of genome sequences collected worldwide and spanning a relatively short time window. These unprecedented conditions together with the certain identification of the reference viral genome sequence allow for an original statistical study of mutations in the virus genome. In this paper, we compute the Shannon entropy of every sequence in the dataset as well as the relative entropy and the mutual information between the reference sequence and the mutated ones. These functions, originally developed in information theory, measure the information content of a sequence and allows us to study the random character of mutation mechanism in terms of its entropy and information gain or loss. We show that this approach allows us to set in new format known features of the SARS-CoV-2 mutation mechanism like the CT bias, but also to discover new optimal entropic properties of the mutation process in the sense that the virus mutation mechanism track closely theoretically computable lower bounds for the entropy decrease and the information transfer.
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Affiliation(s)
- Marco Formentin
- Department of Mathematics Tullio Levi-Civita, University of Padova, via Trieste 63 35131 Padova, Italy
| | - Roberto Chignola
- Department of Biotechnology, University of Verona, Strada le Grazie 15-CV1, 37134 Verona, Italy
| | - Marco Favretti
- Department of Mathematics Tullio Levi-Civita, University of Padova, via Trieste 63 35131 Padova, Italy
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16
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Wang H, Rizvi SRA, Dong D, Lou J, Wang Q, Sopipong W, Su Y, Najar F, Agarwal PK, Kozielski F, Haider S. Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16. eLife 2023; 12:RP87884. [PMID: 38127066 PMCID: PMC10735223 DOI: 10.7554/elife.87884] [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] [Indexed: 12/23/2023] Open
Abstract
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5' end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2'-O-methyltransferase and NSP14 through its N7 methyltransferase activity, which are essential for the replication of the viral genome as well as evading the host's innate immunity. NSP10 acts as a crucial cofactor and stimulator of NSP14 and NSP16. To further understand the role of NSP10, we carried out a comprehensive analysis of >13 million globally collected whole-genome sequences (WGS) of SARS-CoV-2 obtained from the Global Initiative Sharing All Influenza Data (GISAID) and compared it with the reference genome Wuhan/WIV04/2019 to identify all currently known variants in NSP10. T12I, T102I, and A104V in NSP10 have been identified as the three most frequent variants and characterized using X-ray crystallography, biophysical assays, and enhanced sampling simulations. In contrast to other proteins such as spike and NSP6, NSP10 is significantly less prone to mutation due to its crucial role in replication. The functional effects of the variants were examined for their impact on the binding affinity and stability of both NSP14-NSP10 and NSP16-NSP10 complexes. These results highlight the limited changes induced by variant evolution in NSP10 and reflect on the critical roles NSP10 plays during the SARS-CoV-2 life cycle. These results also indicate that there is limited capacity for the virus to overcome inhibitors targeting NSP10 via the generation of variants in inhibitor binding pockets.
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Affiliation(s)
- Huan Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Syed RA Rizvi
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Danni Dong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Jiaqi Lou
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Qian Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Watanyoo Sopipong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Yufeng Su
- College of Engineering, Design and Physical Sciences, Brunel University LondonUxbridgeUnited Kingdom
| | - Fares Najar
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Pratul K Agarwal
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
- UCL Centre for Advanced Research Computing, University College LondonLondonUnited Kingdom
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17
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Samrat SK, Bashir Q, Zhang R, Huang Y, Liu Y, Wu X, Brown T, Wang W, Zheng YG, Zhang QY, Chen Y, Li Z, Li H. A universal fluorescence polarization high throughput screening assay to target the SAM-binding sites of SARS-CoV-2 and other viral methyltransferases. Emerg Microbes Infect 2023; 12:2204164. [PMID: 37060263 PMCID: PMC10165934 DOI: 10.1080/22221751.2023.2204164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/16/2023]
Abstract
SARS-CoV-2 has caused a global pandemic with significant humanity and economic loss since 2020. Currently, only limited options are available to treat SARS-CoV-2 infections for vulnerable populations. In this study, we report a universal fluorescence polarization (FP)-based high throughput screening (HTS) assay for SAM-dependent viral methyltransferases (MTases), using a fluorescent SAM-analogue, FL-NAH. We performed the assay against a reference MTase, NSP14, an essential enzyme for SARS-CoV-2 to methylate the N7 position of viral 5'-RNA guanine cap. The assay is universal and suitable for any SAM-dependent viral MTases such as the SARS-CoV-2 NSP16/NSP10 MTase complex and the NS5 MTase of Zika virus (ZIKV). Pilot screening demonstrated that the HTS assay was very robust and identified two candidate inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the NSP14 MTase with low micromolar IC50. We used three functional MTase assays to unambiguously verified the inhibitory potency of these molecules for the NSP14 N7-MTase function. Binding studies indicated that these molecules are bound directly to the NSP14 MTase with similar low micromolar affinity. Moreover, we further demonstrated that these molecules significantly inhibited the SARS-CoV-2 replication in cell-based assays at concentrations not causing cytotoxicity. Furthermore, NSC111552 significantly synergized with known SARS-CoV-2 drugs including nirmatrelvir and remdesivir. Finally, docking suggested that these molecules bind specifically to the SAM-binding site on the NSP14 MTase. Overall, these molecules represent novel and promising candidates to further develop broad-spectrum inhibitors for the management of viral infections.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Wei Wang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yin Chen
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ, USA
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18
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Rabie AM, Abdel-Dayem MA, Abdalla M. Promising Experimental Anti-SARS-CoV-2 Agent "SLL-0197800": The Prospective Universal Inhibitory Properties against the Coming Versions of the Coronavirus. ACS OMEGA 2023; 8:35538-35554. [PMID: 37810715 PMCID: PMC10552502 DOI: 10.1021/acsomega.2c08073] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/22/2023] [Indexed: 10/10/2023]
Abstract
Isoquinoline derivatives having some nucleosidic structural features are considered as candidate choices for effective remediation of the different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their following disease, the coronavirus disease 2019 (COVID-19). SLL-0197800 is a recently discovered isoquinoline compound with potential strong universal anticoronaviral activities against SARS-CoV-2 and its previous strains. SLL-0197800 nonspecifically hits the main protease (Mpro) enzyme of the different coronaviruses. Herein in the present study, we tested the probability of the previous findings of this experimental agent to be extended to comprise any coronavirus through concurrently disrupting the mutable-less replication enzymes like the RNA-dependent RNA polymerase (RdRp) protein as well as the 3'-to-5' exoribonuclease (ExoN) protein. The in vitro anti-RdRp/ExoN assay revealed the potent inhibitory activities of SLL-0197800 on the coronaviral replication with minute values of anti-RdRp and anti-RdRp/ExoN EC50 (about 0.16 and 0.27 μM, respectively). The preliminary in silico outcomes significantly supported these biochemical findings. To put it simply, the present important results of these extension efforts greatly reinforce and extend the SLL-0197800's preceding findings, showing that the restraining/blocking actions (i.e., inhibitory activities) of this novel investigational anti-SARS-CoV-2 agent against the Mpro protein could be significantly extended against other copying and multiplication enzymes such as RdRp and ExoN, highlighting the potential use of SLL-0197800 against the coming versions of the homicidal coronavirus (if any), i.e., revealing the probable nonspecific anticoronaviral features and qualities of this golden experimental drug against nearly any coronaviral strain, for instance, SARS-CoV-3.
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Affiliation(s)
- Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Head
of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia
Governorate, Egypt
| | - Marwa A. Abdel-Dayem
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Horus University—Egypt (HUE), New Damietta 34518, Damietta Governorate, Egypt
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province 250012, PR China
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19
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Xu T, Zhang L. Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase. Comput Struct Biotechnol J 2023; 21:4385-4394. [PMID: 37711189 PMCID: PMC10498173 DOI: 10.1016/j.csbj.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Since the outbreak of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has become a main target for antiviral therapeutics due to its essential role in viral replication and transcription. Thus, nucleoside analogs structurally resemble the natural RdRp substrate and hold great potential as inhibitors. Until now, extensive experimental investigations have been performed to explore nucleoside analogs to inhibit the RdRp, and concerted efforts have been made to elucidate the underlying molecular mechanisms further. This review begins by discussing the nucleoside analogs that have demonstrated inhibition in the experiments. Second, we examine the current understanding of the molecular mechanisms underlying the action of nucleoside analogs on the SARS-CoV-2 RdRp. Recent findings in structural biology and computational research are presented through the classification of inhibitory mechanisms. This review summarizes previous experimental findings and mechanistic investigations of nucleoside analogs inhibiting SARS-CoV-2 RdRp. It would guide the rational design of antiviral medications and research into viral transcriptional mechanisms.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fujian 361005, China
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20
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Lista F, Peragallo MS, Biselli R, De Santis R, Mariotti S, Nisini R, D'Amelio R. Have Diagnostics, Therapies, and Vaccines Made the Difference in the Pandemic Evolution of COVID-19 in Comparison with "Spanish Flu"? Pathogens 2023; 12:868. [PMID: 37513715 PMCID: PMC10384375 DOI: 10.3390/pathogens12070868] [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: 04/26/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
In 1918 many countries, but not Spain, were fighting World War I. Spanish press could report about the diffusion and severity of a new infection without censorship for the first-time, so that this pandemic is commonly defined as "Spanish flu", even though Spain was not its place of origin. "Spanish flu" was one of the deadliest pandemics in history and has been frequently compared with the coronavirus disease (COVID)-19 pandemic. These pandemics share similarities, being both caused by highly variable and transmissible respiratory RNA viruses, and diversity, represented by diagnostics, therapies, and especially vaccines, which were made rapidly available for COVID-19, but not for "Spanish flu". Most comparison studies have been carried out in the first period of COVID-19, when these resources were either not yet available or their use had not long started. Conversely, we wanted to analyze the role that the advanced diagnostics, anti-viral agents, including monoclonal antibodies, and innovative COVID-19 vaccines, may have had in the pandemic containment. Early diagnosis, therapies, and anti-COVID-19 vaccines have markedly reduced the pandemic severity and mortality, thus preventing the collapse of the public health services. However, their influence on the reduction of infections and re-infections, thus on the transition from pandemic to endemic condition, appears to be of minor relevance. The high viral variability of influenza and coronavirus may probably be contained by the development of universal vaccines, which are not easy to be obtained. The only effective weapon still remains the disease prevention, to be achieved with the reduction of promiscuity between the animal reservoirs of these zoonotic diseases and humans.
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Affiliation(s)
- Florigio Lista
- Istituto di Scienze Biomediche della Difesa, Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, 00184 Roma, Italy
| | - Mario Stefano Peragallo
- Centro Studi e Ricerche di Sanità e Veterinaria, Comando Logistico dell'Esercito, 00184 Roma, Italy
| | - Roberto Biselli
- Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, 00184 Roma, Italy
| | - Riccardo De Santis
- Istituto di Scienze Biomediche della Difesa, Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, 00184 Roma, Italy
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza, Università di Roma, 00161 Roma, Italy
| | - Sabrina Mariotti
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Roberto Nisini
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Raffaele D'Amelio
- Dipartimento di Medicina Clinica e Molecolare, Sapienza, Università di Roma, 00198 Roma, Italy
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21
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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22
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Nowill AE, Caruso M, de Campos-Lima PO. T-cell immunity to SARS-CoV-2: what if the known best is not the optimal course for the long run? Adapting to evolving targets. Front Immunol 2023; 14:1133225. [PMID: 37388738 PMCID: PMC10303130 DOI: 10.3389/fimmu.2023.1133225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/11/2023] [Indexed: 07/01/2023] Open
Abstract
Humanity did surprisingly well so far, considering how unprepared it was to respond to the coronavirus disease 2019 (COVID-19) threat. By blending old and ingenious new technology in the context of the accumulated knowledge on other human coronaviruses, several vaccine candidates were produced and tested in clinical trials in record time. Today, five vaccines account for the bulk of the more than 13 billion doses administered worldwide. The ability to elicit biding and neutralizing antibodies most often against the spike protein is a major component of the protection conferred by immunization but alone it is not enough to limit virus transmission. Thus, the surge in numbers of infected individuals by newer variants of concern (VOCs) was not accompanied by a proportional increase in severe disease and death rate. This is likely due to antiviral T-cell responses, whose evasion is more difficult to achieve. The present review helps navigating the very large literature on T cell immunity induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination. We examine the successes and shortcomings of the vaccinal protection in the light of the emergence of VOCs with breakthrough potential. SARS-CoV-2 and human beings will likely coexist for a long while: it will be necessary to update existing vaccines to improve T-cell responses and attain better protection against COVID-19.
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Affiliation(s)
- Alexandre E. Nowill
- Integrated Center for Pediatric OncoHaematological Research, State University of Campinas, Campinas, SP, Brazil
| | - Manuel Caruso
- CHU de Québec-Université Laval Research Center (Oncology Division), Université Laval Cancer Research Center, Québec, QC, Canada
| | - Pedro O. de Campos-Lima
- Boldrini Children’s Center, Campinas, SP, Brazil
- Molecular and Morphofunctional Biology Graduate Program, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
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23
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Synthesis and anti-SARS-CoV-2 evaluation of lipid prodrugs of β-D- N4-hydroxycytidine (NHC) and a 3′-fluoro-substituted analogue of NHC. Bioorg Chem 2023; 135:106527. [PMID: 37031504 PMCID: PMC10076076 DOI: 10.1016/j.bioorg.2023.106527] [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: 02/09/2023] [Revised: 03/12/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
β-D-N4-hydroxycytidine (NHC, EIDD-1931) is a nucleoside analogue that exhibits broad spectrum antiviral activity against a variety of RNA viruses. Herein, we report the synthesis of a series of lipid prodrugs of NHC and a novel 3′-fluoro modified NHC analogue, and evaluation of their antiviral activity against five variants of SARS-CoV-2. All lipid prodrugs showed potent antiviral activity against the tested SARS-CoV-2 variants with EC50 values in the range of 0.31–3.51 μM, which were comparable to those of NHC or higher than those of remdesivir and molnupiravir. An increase in the cytostatic activity of the lipid prodrugs was found, but prodrug 2d proved equally selective as molnupinavir. The 3′-F analogue of NHC (6) only displayed minor antiviral activity against the SARS-CoV-2 Omicron variant (EC50 = 29.91 μM), while no activity was found for other variants at the highest concentration tested. The promising antiviral data of the lipid prodrugs of NHC suggest that they deserve further investigation as new anti-SARS-CoV-2 drugs.
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24
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Abdalla M, Rabie AM. Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant. Comput Biol Chem 2023; 104:107768. [PMID: 36842392 PMCID: PMC9450471 DOI: 10.1016/j.compbiolchem.2022.107768] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 09/04/2022] [Indexed: 01/18/2023]
Abstract
Nucleoside analogs/derivatives (NAs/NDs) with potent antiviral activities are now deemed very convenient choices for the treatment of coronavirus disease 2019 (COVID-19) arisen by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. At the same time, the appearance of a new strain of SARS-CoV-2, the Omicron variant, necessitates multiplied efforts in fighting COVID-19. Counteracting the crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) jointly altogether using the same inhibitor is a quite successful new plan to demultiplicate SARS-CoV-2 particles and eliminate COVID-19 whatever the SARS-CoV-2 subtype is (due to the significant conservation nature of RdRps and ExoNs in the different SARS-CoV-2 strains). Successive in silico screening of known NAs finally disclosed six different promising NAs, which are riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir, respectively, that predictably can act through the planned dual-action mode. Further in vitro evaluations affirmed the anti-SARS-CoV-2/anti-COVID-19 potentials of these NAs, with riboprine and forodesine being at the top. The two NAs are able to effectively antagonize the replication of the new virulent SARS-CoV-2 strains with considerably minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 189 and 408 nM for riboprine and 207 and 657 nM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. Furthermore, the favorable structural characteristics of the two molecules qualify them for varied types of isosteric and analogistic chemical derivatization. In one word, the present important outcomes of this comprehensive dual study revealed the anticipating repurposing potentials of some known nucleosides, led by the two NAs riboprine and forodesine, to successfully discontinue the coronaviral-2 polymerase/exoribonuclease interactions with RNA nucleotides in the SARS-CoV-2 Omicron variant (BA.5 sublineage) and accordingly alleviate COVID-19 infections, motivating us to initiate the two drugs' diverse anti-COVID-19 pharmacological evaluations to add both of them betimes in the COVID-19 therapeutic protocols.
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Affiliation(s)
- Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, PR China.
| | - Amgad M. Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt,Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt,Correspondence to: 16 Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt
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25
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Sayan M, Arikan A, Sanlidag E. Molecular Epidemiology of SARS-CoV-2 Omicron Sub-Lineages Isolated from Turkish Patients Infected with COVID-19. Viruses 2023; 15:v15051066. [PMID: 37243152 DOI: 10.3390/v15051066] [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: 03/24/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford University Coronavirus Antiviral & Resistance Database online tool was used for variant analyses of the strains uploaded to GISAID as Omicron (n = 20.959) between January 2021 and February,2023. Out of 288 different Omicron subvariants, B.1, BA.1, BA.2, BA.4, BE.1, BF.1, BM.1, BN.1, BQ.1, CK.1, CL.1, and XBB.1 were the main determined subvariants, and BA.1 (34.7%), BA.2 (30.8%), and BA.5 (23.6%) were reported most frequently. RdRp and 3CLPro-related resistance mutations were determined in n = 150, 0.72% sequences, while the rates of resistance against RdRp and 3CLpro inhibitors were reported at 0.1% and 0.6%, respectively. Mutations that were previously associated with a reduced susceptibility to remdesivir, nirmatrelvir/r, and ensitrelvir were most frequently detected in BA.2 (51.3%). The mutations detected at the highest rate were A449A/D/G/V (10.5%), T21I (10%), and L50L/F/I/V (6%). Our findings suggest that continuous monitoring of variants, due to the diversity of Omicron lineages, is necessary for global risk assessment. Although drug-resistant mutations do not pose a threat, the tracking of drug mutations will be necessary due to variant heterogenicity.
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Affiliation(s)
- Murat Sayan
- PCR Unit, Research, and Education Hospital, Faculty of Medicine, Kocaeli University, Kocaeli 41380, Turkey
- DESAM Research Institute, Near East University, Nicosia 99138, Cyprus
| | - Ayse Arikan
- DESAM Research Institute, Near East University, Nicosia 99138, Cyprus
- Department of Medical Microbiology and Clinical Microbiology, Near East University, Nicosia 99138, Cyprus
- Department of Medical Microbiology and Clinical Microbiology, Kyrenia University, Kyrenia 99320, Cyprus
| | - Erdal Sanlidag
- DESAM Research Institute, Near East University, Nicosia 99138, Cyprus
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26
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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27
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Miropolskaya N, Kozlov M, Petushkov I, Prostova M, Pupov D, Esyunina D, Kochetkov S, Kulbachinskiy A. Effects of natural polymorphisms in SARS-CoV-2 RNA-dependent RNA polymerase on its activity and sensitivity to inhibitors in vitro. Biochimie 2023; 206:81-88. [PMID: 36252889 PMCID: PMC9568283 DOI: 10.1016/j.biochi.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2022]
Abstract
SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is the key enzyme required for viral replication and mRNA synthesis. RdRp is one of the most conserved viral proteins and a promising target for antiviral drugs and inhibitors. At the same time, analysis of public databases reveals multiple variants of SARS-CoV-2 genomes with substitutions in the catalytic RdRp subunit nsp12. Structural mapping of these mutations suggests that some of them may affect the interactions of nsp12 with its cofactors nsp7/nsp8 as well as with RNA substrates. We have obtained several mutations of these types and demonstrated that some of them decrease specific activity of RdRp in vitro, possibly by changing RdRp assembly and/or its interactions with RNA. Therefore, natural polymorphisms in RdRp may potentially affect viral replication. Furthermore, we have synthesized a series of polyphenol and diketoacid derivatives based on previously studied inhibitors of hepatitis C virus RdRp and found that several of them can inhibit SARS-CoV-2 RdRp. Tested mutations in RdRp do not have strong effects on the efficiency of inhibition. Further development of more efficient non-nucleoside inhibitors of SARS-CoV-2 RdRp should take into account the existence of multiple polymorphic variants of RdRp.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Maxim Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Maria Prostova
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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28
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Fidelity of Ribonucleotide Incorporation by the SARS-CoV-2 Replication Complex. J Mol Biol 2023; 435:167973. [PMID: 36690070 PMCID: PMC9854147 DOI: 10.1016/j.jmb.2023.167973] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 coronavirus has caused a global pandemic. Despite the initial success of vaccines at preventing infection, genomic variation has led to the proliferation of variants capable of higher infectivity. Mutations in the SARS-CoV-2 genome are the consequence of replication errors, highlighting the importance of understanding the determinants of SARS-CoV-2 replication fidelity. The RNA-dependent RNA polymerase (RdRp) is the central catalytic subunit for SARS-CoV-2 RNA replication and genome transcription. Here, we report the fidelity of ribonucleotide incorporation by SARS-CoV-2 RdRp (nsp12), along with its co-factors nsp7/nsp8, using steady-state kinetic analysis. Our analysis suggests that in the absence of the proofreading subunit (nsp14), the nsp12/7/8 complex has a surprisingly low base substitution fidelity (10-1-10-3). This is orders of magnitude lower than the fidelity reported for other coronaviruses (10-6-10-7), highlighting the importance of proofreading for faithful SARS-CoV-2 replication. We performed a mutational analysis of all reported SARS-CoV-2 genomes and identified mutations in both nsp12 and nsp14 that appear likely to lower viral replication fidelity through mechanisms that include impairing the nsp14 exonuclease activity or its association with the RdRp. Our observations provide novel insight into the mechanistic basis of replication fidelity in SARS-CoV-2 and the potential effect of nsp12 and nsp14 mutations on replication fidelity, informing the development of future antiviral agents and SARS-CoV-2 vaccines.
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Fumagalli SE, Padhiar NH, Meyer D, Katneni U, Bar H, DiCuccio M, Komar AA, Kimchi-Sarfaty C. Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies. Virol J 2023; 20:31. [PMID: 36812119 PMCID: PMC9936480 DOI: 10.1186/s12985-023-01982-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Since the onset of the SARS-CoV-2 pandemic, bioinformatic analyses have been performed to understand the nucleotide and synonymous codon usage features and mutational patterns of the virus. However, comparatively few have attempted to perform such analyses on a considerably large cohort of viral genomes while organizing the plethora of available sequence data for a month-by-month analysis to observe changes over time. Here, we aimed to perform sequence composition and mutation analysis of SARS-CoV-2, separating sequences by gene, clade, and timepoints, and contrast the mutational profile of SARS-CoV-2 to other comparable RNA viruses. METHODS Using a cleaned, filtered, and pre-aligned dataset of over 3.5 million sequences downloaded from the GISAID database, we computed nucleotide and codon usage statistics, including calculation of relative synonymous codon usage values. We then calculated codon adaptation index (CAI) changes and a nonsynonymous/synonymous mutation ratio (dN/dS) over time for our dataset. Finally, we compiled information on the types of mutations occurring for SARS-CoV-2 and other comparable RNA viruses, and generated heatmaps showing codon and nucleotide composition at high entropy positions along the Spike sequence. RESULTS We show that nucleotide and codon usage metrics remain relatively consistent over the 32-month span, though there are significant differences between clades within each gene at various timepoints. CAI and dN/dS values vary substantially between different timepoints and different genes, with Spike gene on average showing both the highest CAI and dN/dS values. Mutational analysis showed that SARS-CoV-2 Spike has a higher proportion of nonsynonymous mutations than analogous genes in other RNA viruses, with nonsynonymous mutations outnumbering synonymous ones by up to 20:1. However, at several specific positions, synonymous mutations were overwhelmingly predominant. CONCLUSIONS Our multifaceted analysis covering both the composition and mutation signature of SARS-CoV-2 gives valuable insight into the nucleotide frequency and codon usage heterogeneity of SARS-CoV-2 over time, and its unique mutational profile compared to other RNA viruses.
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Affiliation(s)
- Sarah E Fumagalli
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Nigam H Padhiar
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT, USA
| | | | - Anton A Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.
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Eltayb WA, Abdalla M, Rabie AM. Novel Investigational Anti-SARS-CoV-2 Agent Ensitrelvir "S-217622": A Very Promising Potential Universal Broad-Spectrum Antiviral at the Therapeutic Frontline of Coronavirus Species. ACS OMEGA 2023; 8:5234-5246. [PMID: 36798145 PMCID: PMC9897045 DOI: 10.1021/acsomega.2c03881] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/05/2022] [Indexed: 06/06/2023]
Abstract
Lately, nitrogenous heterocyclic antivirals, such as nucleoside-like compounds, oxadiazoles, thiadiazoles, triazoles, quinolines, and isoquinolines, topped the therapeutic scene as promising agents of choice for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying ailment, the coronavirus disease 2019 (COVID-19). At the same time, the continuous emergence of new strains of SARS-CoV-2, like the Omicron variant and its multiple sublineages, resulted in a new defiance in the enduring COVID-19 battle. Ensitrelvir (S-217622) is a newly discovered orally active noncovalent nonpeptidic agent with potential strong broad-spectrum anticoronaviral activities, exhibiting promising nanomolar potencies against the different SARS-CoV-2 variants. S-217622 effectively and nonspecifically hits the main protease (Mpro) enzyme of a broad scope of coronaviruses. Herein, in the present computational/biological study, we tried to extend these previous findings to prove the universal activities of this investigational agent against any coronavirus, irrespective of its type, through synchronously acting on most of its main unchanged replication enzymes/proteins, including (in addition to the Mpro), e.g., the highly conserved RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN). Biochemical evaluation proved, using the in vitro anti-RdRp/ExoN bioassay, that S-217622 can potently inhibit the replication of coronaviruses, including the new virulent strains of SARS-CoV-2, with extremely minute in vitro anti-RdRp and anti-RdRp/ExoN half-maximal effective concentration (EC50) values of 0.17 and 0.27 μM, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico results greatly supported these biochemical results, proposing that the S-217622 molecule strongly and stabilizingly strikes the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's principal active sites predictably via the nucleoside analogism mode of anti-RNA action (since the S-217622 molecule can be considered as a uridine analog). Moreover, the idealistic druglikeness and pharmacokinetic characteristics of S-217622 make it ready for pharmaceutical formulation with the expected very good clinical behavior as a drug for the infections caused by coronaviruses, e.g., COVID-19. To cut it short, the current critical findings of this extension work significantly potentiate and extend the S-217622's previous in vitro/in vivo (preclinical) results since they showed that the striking inhibitory activities of this novel anti-SARS-CoV-2 agent on the Mpro could be extended to other replication enzymes like RdRp and ExoN, unveiling the possible universal use of the compound against the next versions of the virus (i.e., disclosing the nonspecific anticoronaviral properties of this compound against almost any coronavirus strain), e.g., SARS-CoV-3, and encouraging us to rapidly start the compound's vast clinical anti-COVID-19 evaluations.
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Affiliation(s)
- Wafa A. Eltayb
- Biotechnology
Department, Faculty of Science and Technology, Shendi University, Shendi 11111, River Nile State, Sudan
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province 250012, P. R. China
| | - Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Drug
Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia
Governorate, Egypt
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Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Rabie AM, Eltayb WA. Strong Dual Antipolymerase/Antiexonuclease Actions of Some Aminothiadiazole Antioxidants: A Promising In-Silico/ In-Vitro Repurposing Research Study against the COVID-19 Omicron Virus (B.1.1.529.3 Lineage). ADVANCES IN REDOX RESEARCH 2023:100064. [PMID: 36776420 PMCID: PMC9907022 DOI: 10.1016/j.arres.2023.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/03/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
Currently, nitrogen-containing heterocyclic virucides take the lead as top options for treating the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their escorting disease, the coronavirus disease 2019 (COVID-19). But unfortunately, the sudden emergence of a new strain of SARS-CoV-2, the Omicron variant and its lineages, complicated matters in the incessant COVID-19 battle. Goaling the two paramount coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) at synchronous times using single ligand is a quite effective new binary avenue to restrain SARS-CoV-2 reproduction and cease COVID-19 progression irrespective of the SARS-CoV-2 strain type, as RdRps and ExoNs are vastly conserved in all SARS-CoV-2 strains. The presented in-silico/in-vitro research winnowed our own small libraries of antioxidant nitrogenous heterocyclic compounds, inspecting for the utmost convenient drug candidates expectedly capable of effectively working through this dual tactic. Computational screening afforded three promising compounds of the antioxidant 1,3,4-thiadiazole class, which were named ChloViD2022, Taroxaz-26, and CoViTris2022. Subsequent biological examination, employing the in-vitro anti-RdRp/anti-ExoN and anti-SARS-CoV-2 assays, exclusively demonstrated that ChloViD2022, CoViTris2022, and Taroxaz-26 could efficiently block the replication of the new lineages of SARS-CoV-2 with considerably minute anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.18 and 0.44 μM for ChloViD2022, 0.22 and 0.72 μM for CoViTris2022, and 0.25 and 0.78 μM for Taroxaz-26, in the order, overtaking the standard anti-SARS-CoV-2 drug molnupiravir. These biochemical findings were optimally presupported by the results of the prior in-silico screening, suggesting that the three compounds might potently hit the catalytic active sites of the virus's RdRp and ExoN enzymes. Furthermore, the perfect pharmacophoric features of ChloViD2022, Taroxaz-26, and CoViTris2022 molecules make them typical dual inhibitors of SARS-CoV-2 replication and proofreading, with their relatively flexible structures eligible for diverse forms of chemical modification. In sum, the current important results of this thorough research work exposed the interesting repurposing potential of the three 2-amino-1,3,4-thiadiazole ligands, ChloViD2022, Taroxaz-26, and CoViTris2022, to effectively conflict with the vital biointeractions between the coronavirus's polymerase/exoribonuclease and the four essential RNA nucleotides, and, accordingly, arrest COVID-19 disease, persuading the relevant investigators to quickly begin the three agents' comprehensive preclinical and clinical anti-COVID-19 assessments.
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Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt
| | - Wafa A Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi 11111, River Nile State, Sudan
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Hogan JI, Duerr R, Dimartino D, Marier C, Hochman SE, Mehta S, Wang G, Heguy A. Remdesivir Resistance in Transplant Recipients With Persistent Coronavirus Disease 2019. Clin Infect Dis 2023; 76:342-345. [PMID: 36156117 PMCID: PMC9619446 DOI: 10.1093/cid/ciac769] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 01/18/2023] Open
Abstract
New mutations conferring resistance to SARS-CoV-2 therapeutics have important clinical implications. We describe the first cases of an independently acquired V792I RNA-dependent RNA polymerase mutation developing in renal transplant recipients after remdesivir exposure. Our work underscores the need for augmented efforts to identify concerning mutations and address their clinical implications.
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Affiliation(s)
- John I Hogan
- Department of Medicine, NYU Long Island School of Medicine, Mineola, New York, USA
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Dacia Dimartino
- Genome Technology Center, NYU Langone Health, New York, New York, USA
| | - Christian Marier
- Genome Technology Center, NYU Langone Health, New York, New York, USA
| | - Sarah E Hochman
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Sapna Mehta
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Adriana Heguy
- Genome Technology Center, NYU Langone Health, New York, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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Imprachim N, Yosaatmadja Y, Newman JA. Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development. Nucleic Acids Res 2023; 51:475-487. [PMID: 36546776 PMCID: PMC9841433 DOI: 10.1093/nar/gkac1207] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 11/23/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
NSP14 is a dual function enzyme containing an N-terminal exonuclease domain (ExoN) and C-terminal Guanine-N7-methyltransferase (N7-MTase) domain. Both activities are essential for the viral life cycle and may be targeted for anti-viral therapeutics. NSP14 forms a complex with NSP10, and this interaction enhances the nuclease but not the methyltransferase activity. We have determined the structure of SARS-CoV-2 NSP14 in the absence of NSP10 to 1.7 Å resolution. Comparisons with NSP14/NSP10 complexes reveal significant conformational changes that occur within the NSP14 ExoN domain upon binding of NSP10, including helix to coil transitions that facilitate the formation of the ExoN active site and provide an explanation of the stimulation of nuclease activity by NSP10. We have determined the structure of NSP14 in complex with cap analogue 7MeGpppG, and observe conformational changes within a SAM/SAH interacting loop that plays a key role in viral mRNA capping offering new insights into MTase activity. We perform an X-ray fragment screen on NSP14, revealing 72 hits bound to sites of inhibition in the ExoN and MTase domains. These fragments serve as excellent starting point tools for structure guided development of NSP14 inhibitors that may be used to treat COVID-19 and potentially other future viral threats.
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Affiliation(s)
- Nergis Imprachim
- Centre for Medicines Discovery, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Yuliana Yosaatmadja
- Centre for Medicines Discovery, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
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Vidyasagar GVC, Reddy PVJ, Kumar S, Polipalli SK, Jaiswal RM, Venkateswarulu TC, Kishor PBK, Suravajhala P, Polavarapu R. Perspectives on Rapid Antigen Tests for Downstream Validation and Development of Theranostics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:285-310. [PMID: 37378774 DOI: 10.1007/978-3-031-28012-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Point-of-care SARS-CoV-2 rapid antigen tests have proven to be useful over the years and have become more apparent to the public eye during COVID-19 pandemic due to their ease of use, rapid processing and result times, and low cost. Here, we have assessed the effectiveness and accuracy of rapid antigen tests in comparison to the standard real-time polymerase chain reaction analyses of the same samples.
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Affiliation(s)
- G Vinaya Chandu Vidyasagar
- Genomix CARL Pvt. Ltd., Pulivendula, AP, India
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Guntur, AP, India
| | | | - Somesh Kumar
- Genome Sequencing Laboratory, Lok Nayak Hospital, Jawaharlal Nehru Marg, New Delhi, India
- Bioclues.org, Hyderabad, Telangana, India
| | - Sunil Kumar Polipalli
- Genome Sequencing Laboratory, Lok Nayak Hospital, Jawaharlal Nehru Marg, New Delhi, India
- Bioclues.org, Hyderabad, Telangana, India
| | - Ram Mohan Jaiswal
- Blood Centre and Transplantation Immunology Lab, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur, Rajasthan, India
| | - T C Venkateswarulu
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Guntur, AP, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, Telangana, India.
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, Kerala, India.
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Evaluation of a series of nucleoside analogs as effective anticoronaviral-2 drugs against the Omicron-B.1.1.529/BA.2 subvariant: A repurposing research study. Med Chem Res 2023; 32:326-341. [PMID: 36593869 PMCID: PMC9797896 DOI: 10.1007/s00044-022-02970-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/06/2022] [Indexed: 12/30/2022]
Abstract
Mysterious evolution of a new strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the Omicron variant, led to a new challenge in the persistent coronavirus disease 2019 (COVID-19) battle. Objecting the conserved SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) together using one ligand is a successful new tactic to stop SARS-CoV-2 multiplication and COVID-19 progression. The current comprehensive study investigated most nucleoside analogs (NAs) libraries, searching for the most ideal drug candidates expectedly able to act through this double tactic. Gradual computational filtration afforded six different promising NAs, riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir. Further biological assessment proved that riboprine and forodesine are able to powerfully inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.21 and 0.45 μM for riboprine and about 0.23 and 0.70 μM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. These biochemical findings were supported by the prior in silico data. Additionally, the ideal pharmacophoric features of riboprine and forodesine molecules render them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading. These findings suggest that riboprine and forodesine could serve as prospective lead compounds against COVID-19. Graphical abstract.
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Dangerfield T, Johnson KA. Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease. ACS BIO & MED CHEM AU 2022; 2:600-606. [PMID: 36570070 PMCID: PMC9718090 DOI: 10.1021/acsbiomedchemau.2c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus that causes COVID-19, continues to evolve resistance to vaccines and existing antiviral therapies at an alarming rate, increasing the need for new direct-acting antiviral drugs. Despite significant advances in our fundamental understanding of the kinetics and mechanism of viral RNA replication, there are still open questions regarding how the proofreading exonuclease (NSP10/NSP14 complex) contributes to replication fidelity and resistance to nucleoside analogs. Through single turnover kinetic analysis, we show that the preferred substrate for the exonuclease is double-stranded RNA without any mismatches. Double-stranded RNA containing a 3'-terminal remdesivir was hydrolyzed at a rate similar to a correctly base-paired cognate nucleotide. Surprisingly, single-stranded RNA or duplex RNA containing a 3'-terminal mismatch was hydrolyzed at rates 125- and 45-fold slower, respectively, compared to the correctly base-paired double-stranded RNA. These results define the substrate specificity and rate of removal of remdesivir for the exonuclease and outline rigorous kinetic assays that could help in finding next-generation exonuclease inhibitors or nucleoside analogs that are able to evade excision. These results also raise important questions about the role of the polymerase/exonuclease complex in proofreading during viral replication. Addressing these questions through rigorous kinetic analysis will facilitate the search for desperately needed antiviral drugs to combat COVID-19.
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Rabie AM, Abdalla M. Forodesine and Riboprine Exhibit Strong Anti-SARS-CoV-2 Repurposing Potential: In Silico and In Vitro Studies. ACS BIO & MED CHEM AU 2022; 2:565-585. [PMID: 37582236 PMCID: PMC9631343 DOI: 10.1021/acsbiomedchemau.2c00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 11/07/2022]
Abstract
Lately, nucleos(t)ide antivirals topped the scene as top options for the treatment of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Targeting the two broadly conserved SARS-CoV-2 enzymes, RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN), together using only one shot is a very successful new tactic to stop SARS-CoV-2 multiplication irrespective of the SARS-CoV-2 variant type. Herein, the current studies investigated most nucleoside analogue (NA) libraries, searching for the ideal drug candidates expectedly able to act through this double tactic. Gradual computational filtration gave rise to six different promising NAs along with their corresponding triphosphate (TP) nucleotides. The subsequent biological assessment proved for the first time that, among the six NAs, riboprine and forodesine are able to hyperpotently inhibit the replication of the Omicron strain of SARS-CoV-2 with extremely low in vitro anti-RdRp, anti-ExoN, and anti-SARS-CoV-2 EC50 values of about 0.18, 0.28, and 0.40 μM for riboprine and about 0.20, 0.31, and 0.65 μM for forodesine, respectively, surpassing remdesivir and molnupiravir. The significant probability that both compounds may also act as prodrugs for their final TP nucleotides in vivo pushed us to examine the same activities for forodesine-TP and riboprine-TP. Both nucleotides similarly displayed very promising results, respectively, which are much better than those for the two reference TP nucleotides, GS-443902 and β-d-N4-hydroxycytidine 5'-TP (NHC-TP). The prior in silico data supported these biochemical findings, suggesting that riboprine and forodesine molecules and their expected active TP metabolites strongly hit the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's main active sites. In brief, the current important results of this comprehensive study revealed the interesting repurposing potentials of, mainly, the two bioactive nucleosides forodesine and riboprine and their TP nucleotides to effectively shut down the polymerase/exoribonuclease-RNA nucleotide interactions of SARS-CoV-2 and consequently treat COVID-19 infections.
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Affiliation(s)
- Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City35511,Mansoura, Dakahlia Governorate, Egypt
- Head
of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City35744,Dikernis, Dakahlia Governorate, Egypt
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province250012, P. R. China
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Rabie AM, Abdalla M. A Series of Adenosine Analogs as the First Efficacious Anti-SARS-CoV-2 Drugs against the B.1.1.529.4 Lineage: A Preclinical Repurposing Research Study. ChemistrySelect 2022; 7:e202201912. [PMID: 36718467 PMCID: PMC9877610 DOI: 10.1002/slct.202201912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/30/2022] [Indexed: 12/13/2022]
Abstract
Given the rapid progression of the coronavirus disease 2019 (COVID-19) pandemic, an ultrafast response was urgently required to handle this major public crisis. To contain the pandemic, investments are required to develop diagnostic tests, prophylactic vaccines, and novel therapies. Lately, nucleoside analog (NA) antivirals topped the scene as top options for the treatment of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Meanwhile, the continuous generation of new lineages of the SARS-CoV-2 Omicron variant caused a new challenge in the persistent COVID-19 battle. Hitting the two crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) collectively together using only one single ligand is a very successful new approach to stop SARS-CoV-2 multiplication and combat COVID-19 irrespective of the SARS-CoV-2 variant type because RdRps and ExoNs are broadly conserved among all SARS-CoV-2 strains. Herein, the current comprehensive study investigated most NAs libraries, searching for the most ideal drug candidates expectedly able to perfectly act through this double tactic. Gradual computational filtration gave rise to six different promising NAs, which are riboprine, forodesine, tecadenoson, nelarabine, vidarabine, and maribavir, respectively. Further biological assessment proved for the first time, using the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that riboprine and forodesine, among all the six tested NAs, are able to powerfully inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.22 and 0.49 μM for riboprine and about 0.25 and 0.73 μM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. The prior in silico data supported these biochemical findings, suggesting that riboprine and forodesine molecules strongly hit the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's main active sites. Additionally, the ideal pharmacophoric features of riboprine and forodesine molecules render them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their relatively flexible structures open for diverse types of chemical derivatization. In Brief, the current important results of this comprehensive study revealed the interesting repurposing potentials of, mainly, the two nucleosides riboprine and forodesine to effectively shut down the polymerase/exoribonuclease-RNA nucleotides interactions of the SARS-CoV-2 Omicron variant and consequently treat COVID-19 infections, motivating us to rapidly begin the two drugs' broad preclinical/clinical anti-COVID-19 bioevaluations, hoping to combine both drugs soon in the COVID-19 treatment protocols.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD)35511MansouraDakahlia GovernorateEgypt,Head of Drug Discovery & Clinical Research Department Dikernis General Hospital (DGH)Magliss El-Madina Street Dikernis35744DikernisDakahlia GovernorateEgypt
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education)Department of PharmaceuticsSchool of Pharmaceutical SciencesCheeloo College of MedicineShandong University44 Cultural West RoadShandong Province250012PR China
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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Xiong D, Zhang X, Yu J, Wei H. Distribution of intra‐host variations and mutations in the genomes of SARS‐CoV‐2 and their implications on detection and therapeutics. MedComm (Beijing) 2022; 3:e186. [DOI: 10.1002/mco2.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
- CAS Key Laboratory of Special Pathogens and Biosafety University of Chinese Academy of Sciences Beijing China
| | - Xiaoxu Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
- CAS Key Laboratory of Special Pathogens and Biosafety University of Chinese Academy of Sciences Beijing China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety Center for Biosafety Mega‐Science Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China
- CAS Key Laboratory of Special Pathogens and Biosafety University of Chinese Academy of Sciences Beijing China
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43
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Kodchakorn K, Kongtawelert P. Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity. PLoS One 2022; 17:e0277745. [PMID: 36395151 PMCID: PMC9671323 DOI: 10.1371/journal.pone.0277745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic caused by a virus that can be transmitted from human to human via air droplets has changed the quality of life and economic systems all over the world. The viral DNA has mutated naturally over time leading to the diversity of coronavirus victims which has posed a serious threat to human security on a massive scale. The current variants have developed in a dominant way and are considered "Variants of Concern" by the World Health Organization (WHO). In this work, Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants were obtained to evaluate whether naturally occurring mutations have strengthened viral infectivity. We apply reliable in silico structural dynamics and energetic frameworks of the mutated S-RBD protein for ACE2-binding to analyze and compare the structural information related to the wild-type. In particular, the hotspot residues at Q493, Q498, and N501 on the S-RBD protein were determined as contributing factors to the employment stability of the relevant binding interface. The L452R mutation induces an increment of the hydrogen bonds formed by changing the Q493 environment for ACE2 binding. Moreover, the Q493K exchange in Omicron enables the formation of two additional salt bridges, leading to a strong binding affinity by increased electrostatic interaction energy. These results could be used in proposing concrete informative data for a structure-based design engaged in finding better therapeutics against novel variants.
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Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
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44
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Akarapipad P, Bertelson E, Pessell A, Wang TH, Hsieh K. Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19. BIOSENSORS 2022; 12:bios12110978. [PMID: 36354487 PMCID: PMC9688249 DOI: 10.3390/bios12110978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 05/29/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.
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Affiliation(s)
- Patarajarin Akarapipad
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Bertelson
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander Pessell
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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45
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Sarkar MS, Madabhavi I. SARS-CoV-2 variants of concern: a review. Monaldi Arch Chest Dis 2022. [DOI: 10.4081/monaldi.2022.2337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The virus that causes severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family Coronaviridae. The SARS-CoV-2 virus is a positive sense, non-segmented single-strand RNA virus that causes coronavirus disease 2019 (COVID-19), which was first reported in December 2019 in Wuhan, China. COVID-19 is now a worldwide pandemic. Globally, several newer variants have been identified; however, only a few of them are of concern (VOCs). VOCs differ in terms of infectivity, transmissibility, disease severity, drug efficacy, and neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. VOCs reported from various parts of the world include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron). These VOCs are the result of mutations, with some based on spike proteins. Mutations may also cause molecular diagnostic tests to fail to detect the few VOCs, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, Stanford variants database, and CINAHL from December 2019 to February 2022 using the following search terms: Variant of Concern, SARS-CoV-2, Omicron, etc. All types of research were chosen. All research methods were considered. This review discusses the various VOCs, as well as their mutations, infectivity, transmissibility, and neutralization efficacy.
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46
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Lee SJ, Kim YJ, Ahn DG. Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2. J Microbiol Biotechnol 2022; 32:1073-1085. [PMID: 36039385 PMCID: PMC9628960 DOI: 10.4014/jmb.2206.06064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.
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Affiliation(s)
- Su Jin Lee
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Yu-Jin Kim
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Dae-Gyun Ahn
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
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47
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Lueking R, Clark AE, Narasimhan M, Mahimainathan L, Muthukumar A, Larsen CP, SoRelle JA. SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis. Front Genet 2022; 13:942713. [PMID: 36226173 PMCID: PMC9549124 DOI: 10.3389/fgene.2022.942713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Immunocompromised patients can experience prolonged SARS-CoV-2 infections in the setting of a lack of protectivity immunity despite vaccination. As circulating SARS-CoV-2 strains become more heterogeneous, concomitant infection with multiple SARS-CoV-2 variants has become an increasing concern. Immunocompromised patient populations represent potential reservoirs for the emergence of novel SARS-CoV-2 variants through mutagenic change or coinfection followed by recombinatory events. Identification of SARS-CoV-2 coinfections is challenging using traditional next generation sequencing pipelines; however, targeted genotyping approaches can facilitate detection. Here we describe five COVID-19 cases caused by coinfection with different SARS-CoV-2 variants (Delta/Omicron BA.1 and Omicron BA.1/BA.2) as identified by multiplex fragment analysis.
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Affiliation(s)
- Richard Lueking
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Andrew E. Clark
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Madhusudhanan Narasimhan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lenin Mahimainathan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Alagarraju Muthukumar
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Christian P. Larsen
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jeffrey A. SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- *Correspondence: Jeffrey A. SoRelle,
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A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation. Biomolecules 2022; 12:biom12101353. [PMID: 36291562 PMCID: PMC9599796 DOI: 10.3390/biom12101353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID—percentage of intrinsic disorder—of the membrane protein M, PIDM) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PIDN) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations. The first observation demonstrated lesser and greater presence of the Omicron particles in the lungs and bronchial tissues, respectively, as there is a greater level of mucus in the bronchi. The other observation revealed that there are lower viral loads in 2017-pangolin-CoV, which is predicted to have similarly low PIDN as Omicron. The abnormally hard M, which is very rarely seen in coronaviruses, arose from the fecal–oral behaviors of pangolins via exposure to buried feces. Pangolins provide an environment for coronavirus (CoV) attenuation, which is seen in Omicron. Phylogenetic study using M shows that COVID-19-related bat-CoVs from Laos and Omicron are clustered in close proximity to pangolin-CoVs, which suggests the recurrence of interspecies transmissions. Hard M may have implications for long COVID-19, with immune systems having difficulty degrading viral proteins/particles.
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49
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Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors. Eur J Med Chem 2022; 243:114760. [PMID: 36152387 DOI: 10.1016/j.ejmech.2022.114760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
Abstract
During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.
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50
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The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron. Viruses 2022; 14:v14092009. [PMID: 36146815 PMCID: PMC9505243 DOI: 10.3390/v14092009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 12/12/2022] Open
Abstract
In late December of 2019, high-throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we provide a short retrospective analysis of SARS-CoV-2 variants by analyzing a subset (n = 97,437) of all publicly available SARS-CoV-2 genomes (n = ~11.9 million) that were randomly selected but equally distributed over the course of the pandemic. We plot the appearance of new variants of concern (VOCs) over time and show that the mutation rates in Omicron (BA.1) and Omicron sub-lineages (BA.2–BA.5) are significantly elevated compared to previously identified SARS-CoV-2 variants. Mutations in Omicron are primarily restricted to the spike and nucleocapsid proteins, while 24 other viral proteins—including those involved in SARS-CoV-2 replication—are generally conserved. Collectively, this suggests that the genetic distinction of Omicron primarily arose from selective pressures on the spike, and that the fidelity of replication of this variant has not been altered.
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