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SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential
Open accessPreprint — published as 10.1016/j.bpj.2021.03.024 · Paper page
Abstract
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between twenty and thirty proteins to carry out their viral replication cycle including infection, immune evasion, and replication. Among these, nonstructural protein 16 (Nsp16), a 2’-O-methyltransferase, plays an essential role in immune evasion. Nsp16 achieves this by mimicking its human homolog, CMTr1, which methylates mRNA to enhance translation efficiency and distinguish self from other. Unlike human CMTr1, Nsp16 requires a binding partner, Nsp10, to activate its enzymatic activity. The requirement of this binding partner presents two questions that we investigate in this manuscript. First, how does Nsp10 activate Nsp16? While experimentally-derived structures of the active Nsp16/Nsp10 complex exist, structures of inactive, monomeric Nsp16 have yet to be solved. Therefore, it is unclear how Nsp10 activates Nsp16. Using over one millisecond of molecular dynamics simulations of both Nsp16 and its complex with Nsp10, we investigate how the presence of Nsp10 shifts Nsp16’s conformational ensemble in order to activate it. Second, guided by this activation mechanism and Markov state models (MSMs), we investigate if Nsp16 adopts inactive structures with cryptic pockets that, if targeted with a small molecule, could inhibit Nsp16 by stabilizing its inactive state. After identifying such a pocket in SARS-CoV-2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV-1 and MERS, but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket. Statement of Significance: Coronaviruses are a major threat to human health. These viruses employ molecular machines, called proteins, to infect host cells and replicate. Characterizing the structure and dynamics of these proteins could provide a basis for designing small molecule antivirals. In this work, we use computer simulations to understand the moving parts of an essential SARS-CoV-2 protein, understand how a binding partner turns it on and off, and identify a novel pocket that antivirals could target to shut this protein off. The pocket is also present in other coronaviruses but not in the related human protein, so it could be a valuable target for pan-coronavirus antivirals.
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Markov state models of biomolecular conformational dynamics
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Metadata
- Authors
- Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Bowman, Gregory R.
- ORCID
- Venue
- Biophysical Journal
- Publisher
- openRxiv
- Published
- 2020-12-10
- Volume
- 120
- Issue
- 14
- Pages
- 2880-2889
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC8007187
- OpenAlex
- W3140438776
- Cited by
- 84
- References
- 1
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 12 · 2023: 17 · 2022: 24 · 2021: 16
- FWCI
- 5.46
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation (R01 GM124007, 1552471, RF1AG067194, RAPID 58628, CAREER)
- David and Lucile Packard Foundation (R01 GM124007, RF1AG067194, RAPID 58628, MCB-1552471)
- Burroughs Wellcome Fund (MCB-1552471, R01 GM124007, RF1AG067194, RAPID 58628)
- National Institutes of Health (RAPID 58628, NIH-R01, MCB-1552471)
- National Institute on Aging (RF1AG067194)
- National Institute of General Medical Sciences (R01GM124007, T32GM007200)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, nsp16, nsp10, 2'-O-methyltransferase, cryptic pocket, enzyme activation mechanism, molecular dynamics simulation, Markov state models, SARS-CoV-1, MERS-CoV
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