SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential

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-CoV2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV1 and MERS, but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket.

Activation of the SARS-CoV-2 NSP14 3′–5′ exoribonuclease by NSP10 and response to antiviral inhibitors

“…NSP16 promotes the cap-1 structure adding a methyl group onto the cap-0 structure and is completely inactive in the absence of NSP10 in SARS-CoV-1 ( 30 ). It is proposed that NSP10 allosterically activates NSP16 and helps to assemble the MTase active site ( 32 ). Here, we observe that while NSP14 is capable of exoribonuclease activity, the activity is orders of magnitude lower than the activity of the NSP10/14 complex.…”

Cellular miR-150-5p may have a crucial role to play in the biology of SARS-CoV-2 infection by regulating nsp10 gene

“…Further analysis determined a possible interaction between cellular miR-150-5p and a unique miRNA recognition element (MRE) on the SARS-CoV-2 encoded non-structural protein 10 ( nsp10 ) gene. The nsp10 gene product has a crucial role to play in viral replication and in evading host immune response [ 21 ]. The nsp10 protein binds to nsp14 and nsp16 to activate their 3ʹ to 5ʹ exoribonuclease (ExoN) and methylation activity, respectively [ 22 ]; both of which aid in translation efficiency, immune evasion, and SARS-CoV-2 replication.…”

SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

“…Can regulate the effects of IL-6 action by inhibiting STAT3 and STAT5 [177]. Promotes lysosomal degradation of the α-chain of the IFN-I receptor (IFNAR1) and induces ER stress (shown in SARS-CoV-1) [185,186]. Forms transmembrane ionic potassium-specific channels that facilitate the release of the virus from the cell [187].…”