1
|
Olendraite I, Brown K, Firth AE. Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets. Mol Biol Evol 2023; 40:msad060. [PMID: 37014783 PMCID: PMC10101049 DOI: 10.1093/molbev/msad060] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/15/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.
Collapse
Affiliation(s)
- Ingrida Olendraite
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
2
|
Madariaga-Mazón A, Naveja JJ, Becerra A, Alberto Campillo-Balderas J, Hernández-Morales R, Jácome R, Lazcano A, Martinez-Mayorga K. Subtle structural differences of nucleotide analogs may impact SARS-CoV-2 RNA-dependent RNA polymerase and exoribonuclease activity. Comput Struct Biotechnol J 2022; 20:5181-5192. [PMID: 36097553 PMCID: PMC9452397 DOI: 10.1016/j.csbj.2022.08.056] [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: 03/22/2022] [Revised: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
The rapid spread and public health impact of the novel SARS-CoV-2 variants that cause COVID-19 continue to produce major global impacts and social distress. Several vaccines were developed in record time to prevent and limit the spread of the infection, thus playing a pivotal role in controlling the pandemic. Although the repurposing of available drugs attempts to provide therapies of immediate access against COVID-19, there is still a need for developing specific treatments for this disease. Remdesivir, molnupiravir and Paxlovid remain the only evidence-supported antiviral drugs to treat COVID-19 patients, and only in severe cases. To contribute on the search of potential Covid-19 therapeutic agents, we targeted the viral RNA-dependent RNA polymerase (RdRp) and the exoribonuclease (ExoN) following two strategies. First, we modeled and analyzed nucleoside analogs sofosbuvir, remdesivir, favipiravir, ribavirin, and molnupiravir at three key binding sites on the RdRp-ExoN complex. Second, we curated and virtually screened a database containing 517 nucleotide analogs in the same binding sites. Finally, we characterized key interactions and pharmacophoric features presumably involved in viral replication halting at multiple sites. Our results highlight structural modifications that might lead to more potent SARS-CoV-2 inhibitors against an expansive range of variants and provide a collection of nucleotide analogs useful for screening campaigns.
Collapse
Affiliation(s)
- Abraham Madariaga-Mazón
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál Mérida, Yucatán 97302, Mexico
| | - José J Naveja
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Institute for Molecular Biology and University Cancer Center (UCT) Mainz, Germany
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico.,El Colegio Nacional, Mexico City, Mexico
| | - Karina Martinez-Mayorga
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál Mérida, Yucatán 97302, Mexico
| |
Collapse
|