Abstract:Non-structural proteins (nsp) constitute the SARS-CoV-2 replication and transcription complex (RTC) to play a pivotal role in the virus life cycle. Here we determine the atomic structure of a SARS-CoV-2 mini RTC, assembled by viral RNA-dependent RNA polymerase (RdRp, nsp12) with a template-primer RNA, nsp7 and nsp8, and two helicase molecules (nsp13-1 and nsp13-2), by cryo-electron microscopy. Two groups of mini RTCs with different conformations of nsp13-1 are identified. In both of them, nsp13-1 stabilizes ov… Show more
“…The figure that follows (Fig. 13 ) shows the NSP13 in complex with the RNA-dependent RNA polymerase complex (RdRp complex: NSP12–NSP7–NSP8) with a strand of RNA embedded in the NSP13′ unit (PDB ID: 7XCM) [ 37 ], which presumably corresponds to the RNA template that the helicase is “unwinding” for replication to occur. Fig.…”
Section: Discussionmentioning
confidence: 99%
“…(There are two NSP13 units (NSP13 and NSP13′), two NSP8 units (NSP8 and NSP8′), one NSP12 unit, and one NSP7 unit) (Color figure online) Fig. 13 Structure of NSP13 (grey, helicase) in complex with NSP12 (red), NSP7 (blue), NSP8 (green), and RNA (PDB ID: 7XCM) [ 37 ]. (There are two NSP13 units (NSP13 and NSP13′), two NSP8 units (NSP8 and NSP8′), one NSP12 unit, and one NSP7 unit).…”
The global pandemic that shut down the world in 2020 was caused by the virus, SARS CoV-2. The chemistry of the various nonstructural proteins (NSP3, NSP5, NSP12, NSP13, NSP14, NSP15, NSP16) of SARS CoV-2 is discussed. Secondly, a recent major focus of this pandemic is the variant strains of SARS CoV-2 that are increasingly occurring and more transmissible. One strain, called “D614G”, possesses a glycine (G) instead of an aspartate (D) at position 614 of the spike protein. Additionally, other emerging strains called “501Y.V1” and “501Y.V2” have several differences in the receptor binding domain of the spike protein (N501Y) as well as other locations. These structural changes may enhance the interaction between the spike protein and the ACE2 receptor of the host, increasing infectivity. The global pandemic caused by SARS CoV-2 is a rapidly evolving situation, emphasizing the importance of continuing the efforts to interrogate and understand this virus.
Supplementary Information
The online version contains supplementary material available at 10.1007/s10930-021-09967-8.
“…The figure that follows (Fig. 13 ) shows the NSP13 in complex with the RNA-dependent RNA polymerase complex (RdRp complex: NSP12–NSP7–NSP8) with a strand of RNA embedded in the NSP13′ unit (PDB ID: 7XCM) [ 37 ], which presumably corresponds to the RNA template that the helicase is “unwinding” for replication to occur. Fig.…”
Section: Discussionmentioning
confidence: 99%
“…(There are two NSP13 units (NSP13 and NSP13′), two NSP8 units (NSP8 and NSP8′), one NSP12 unit, and one NSP7 unit) (Color figure online) Fig. 13 Structure of NSP13 (grey, helicase) in complex with NSP12 (red), NSP7 (blue), NSP8 (green), and RNA (PDB ID: 7XCM) [ 37 ]. (There are two NSP13 units (NSP13 and NSP13′), two NSP8 units (NSP8 and NSP8′), one NSP12 unit, and one NSP7 unit).…”
The global pandemic that shut down the world in 2020 was caused by the virus, SARS CoV-2. The chemistry of the various nonstructural proteins (NSP3, NSP5, NSP12, NSP13, NSP14, NSP15, NSP16) of SARS CoV-2 is discussed. Secondly, a recent major focus of this pandemic is the variant strains of SARS CoV-2 that are increasingly occurring and more transmissible. One strain, called “D614G”, possesses a glycine (G) instead of an aspartate (D) at position 614 of the spike protein. Additionally, other emerging strains called “501Y.V1” and “501Y.V2” have several differences in the receptor binding domain of the spike protein (N501Y) as well as other locations. These structural changes may enhance the interaction between the spike protein and the ACE2 receptor of the host, increasing infectivity. The global pandemic caused by SARS CoV-2 is a rapidly evolving situation, emphasizing the importance of continuing the efforts to interrogate and understand this virus.
Supplementary Information
The online version contains supplementary material available at 10.1007/s10930-021-09967-8.
“…At the early sensing phase, HCoV encoded proteins are committed to escape innate response by PRRs, particularly those related to viral RNA recognition. SARS-CoV and other HCoV such as SARS-CoV-2, replicate in the interior of double-membrane vesicles to prevent RIG-I activation by dsRNA replication intermediates [ 60 ]. SARS-CoV can evade RIG-I and MDA5 recognition of the viral RNA by using its nonstructural protein 14 (nsp14).…”
Section: Modulation Of Innate Antiviral Response By Hcovmentioning
SARS-CoV-2 is a recently identified coronavirus accountable for the current pandemic disease known as COVID-19. Different patterns of disease progression infer a diverse host immune response, with interferon (IFN) being pivotal. IFN-I and III are produced and released by virus-infected cells during the interplay with SARS-CoV-2, thus establishing an antiviral state in target cells. However, the efficacy of IFN and its role in the possible outcomes of the disease are not yet defined, as it is influenced both by factors inherent to the virus and to the host. The virus exhibits multiple strategies to counteract the innate immune response, including those shared by SARS-CoV and MERS-CoV and other novel ones. Inborn errors in the host may affect IFN-related effector proteins or decrease its levels in plasma upon neutralization by preexistent autoantibodies. This battle between the IFN response triggered upon SARS-CoV-2 infection, its magnitude and timing, and the efficacy of its antiviral tools in dispute against the viral evasion strategies together with the genetic factors of the host, generate a scenario whose fate contributes to defining the severity of COVID-19.
“…Nsp12 requires nsp7 and nsp8 for processivity in vitro ( 9 ) and likely other nsps, such as nsp9 and nsp13, for processivity in vivo . The structures of nsp12/7/8 and nsp8/9/12/13 complexes from SARS-CoV and SARS-CoV-2 have been solved by cryo-EM ( 10 – 12 ).…”
Pandemic SARS-CoV-2 causes a mild to severe respiratory disease called Coronavirus Disease 2019 (COVID-19). Control of SARS-CoV-2 spread will depend on vaccine-induced or naturally acquired protective herd immunity. Until then, antiviral strategies are needed to manage COVID-19, but approved antiviral treatments, such as remdesivir, can only be delivered intravenously. Enisamium (laboratory code FAV00A, trade name Amizon®) is an orally active inhibitor of influenza A and B viruses in cell culture and clinically approved in countries of the Commonwealth of Independent States. Here we show that enisamium can inhibit SARS-CoV-2 infections in NHBE and Caco-2 cells. In vitro, the previously identified enisamium metabolite VR17-04 directly inhibits the activity of the SARS-CoV-2 RNA polymerase. Docking and molecular dynamics simulations suggest that VR17-04 prevents GTP and UTP incorporation. To confirm enisamium’s antiviral properties, we conducted a double-blind, randomized, placebo-controlled trial in adult, hospitalized COVID-19 patients, which needed medical care either with or without supplementary oxygen. Patients received either enisamium (500 mg per dose) or placebo for 7 days. A pre-planned interim analysis showed in the subgroup of patients needing supplementary oxygen (n = 77) in the enisamium group a mean recovery time of 11.1 days, compared to 13.9 days for the placebo group (log-rank test; p=0.0259). No significant difference was found for all patients (n = 373) or those only needing medical care (n = 296). These results thus suggest that enisamium is an inhibitor of SARS-CoV-2 RNA synthesis and that enisamium treatment shortens the time to recovery for COVID-19 patients needing oxygen.Significance statementSARS-CoV-2 is the causative agent of COVID-19. Although vaccines are now becoming available to prevent SARS-CoV-2 spread, the development of antivirals remains necessary for treating current COVID-19 patients and combating future coronavirus outbreaks. Here, we report that enisamium, which can be administered orally, can prevent SARS-CoV-2 replication and that its metabolite VR17-04 can inhibit the SARS-CoV-2 RNA polymerase in vitro. Moreover, we find that COVID-19 patients requiring supplementary oxygen, recover more quickly than patients treated with a placebo. Enisamium may therefore be an accessible treatment for COVID-19 patients.
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