Binding affinity and mechanisms of SARS-CoV-2 variants.

During the rapid worldwide spread of SARS-CoV-2, the viral genome has been undergoing numerous mutations, especially in the spike (S) glycoprotein gene that encode a type-I fusion protein, which plays an important role in the infectivity and transmissibility of the virus into the host cell. In this work, we studied the effect of S glycoprotein residue mutations on the binding affinity and mechanisms of SARS-CoV-2 using molecular dynamics simulations and sequence analysis. We quantitatively determined the degrees of binding affinity caused by different S glycoprotein mutations, and the result indicated that the 501Y.V1 variant yielded the highest enhancements in binding affinity (increased by 36.8%), followed by the N439K variant (increased by 29.5%) and the 501Y.V2 variant (increased by 19.6%). We further studied the structures, chemical bonds, binding free energies (enthalpy and entropy), and residue contribution decompositions of these variants to provide physical explanations for the changes in SARS-CoV-2 binding affinity caused by these residue mutations. This research identified the binding affinity differences of the SARS-CoV-2 variants and provides a basis for further surveillance, diagnosis, and evaluation of mutated viruses.

Immune persistence induced by two-dose BBIBP-CorV vaccine with different intervals, and immunogenicity and safety of a homologous booster dose in high-risk occupational population.

BACKGROUND: The immune persistence of neutralizing antibodies elicited by BBIBP-CorV vaccines on day 0-14, 0-21 and 0-28 schedule, and the immunogenicity and safety of a homologous booster dose after different priming vaccination regimens is scarcely reported. METHODS: : Responders (GMT≥16) at day 28, after priming with the two-dose vaccine, were followed up at 3, 6, and 10 months. Eligible participants received a homologous booster dose at month 10 and were followed-up 28 days post-booster. RESULTS: The GMT of neutralizing antibodies in 0-28d-10 m and 0-21d-10 m group were significantly higher than 0-14d-10 m group from month 3 (71.6 & 64.2 vs 46.4, p < 0.001) to month 10 (32.4 & 28.8 vs 20.3, p < 0.001) after the second dose. On day 28 post-booster, a remarkable rebound in neutralizing antibodies (246.2, 277.5, and 288.6, respectively) was observed in the three groups. All adverse reactions were mild after booster injection. CONCLUSIONS: The priming two-dose BBIBP-CorV vaccine with 0-28 days and 0-21 days schedule could lead to a longer persistence of neutralizing antibody than the 0-14 days schedule. Regardless of the priming vaccination regimens, a homologous booster dose led to a strong rebound in neutralizing antibodies and might persist for at least 18 months.

Safety and immunogenicity of inactivated SARS-CoV-2 vaccine in high-risk occupational population: a randomized, parallel, controlled clinical trial.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the resulting coronavirus disease 2019 (COVID-19) have a substantial burden on health-care systems around the world. This is a randomized parallel controlled trial for assessment of the immunogenicity and safety of an inactivated SARS-CoV-2 vaccine, aiming to determine an appropriate vaccination interval of the vaccine for high-risk occupational population. METHODS: In an ongoing randomized, parallel, controlled phase IV trial between January and May 2021 in Taiyuan City, Shanxi Province, China, we randomly assigned the airport ground staff and public security officers aged 18 to 59 years to receive two doses of inactivated SARS-CoV-2 vaccine at 14 days, 21 days, or 28 days. The serum neutralizing antibody to live SARS-CoV-2 was performed at baseline and 28 days after immunization. Long-term data are being collected. The primary immunogenicity endpoints were neutralization antibody seroconversion and geometric mean titer (GMT) at 28 days after the second dose. Analysis of variance (ANOVA), chi-square, and logistic regression analysis were used for data analysis. RESULTS: A total of 809 participants underwent randomization and received two doses of injections: 270, 270, 269 in the 0-14, 0-21, and 0-28 vaccination group, respectively. By day 28 after the second injection, SARS-CoV-2 neutralizing antibody of GMT was 98.4 (95% CI: 88.4-108.4) in the 0-14 group, which was significantly lower compared with 134.4 (95% CI: 123.1-145.7) in the 0-21 group (P < 0.001 vs 0-14 group) and 145.5 (95% CI: 131.3-159.6) in the 0-28 group (P < 0.001 vs 0-14 group), resulting in the seroconversion rates to neutralizing antibodies (GMT ≥ 16) of 100.0% for all three groups, respectively. The intention-to-treat (ITT) analysis yielded similar results. All reported adverse reactions were mild. CONCLUSIONS: Both a two-dose of inactivated SARS-CoV-2 vaccine at 0-21 days and 0-28 days regimens significantly improved SARS-CoV-2 neutralizing antibody level compared to the 0-14 days regimen in high-risk occupational population, with seroconversion rates of 100.0%. TRIAL REGISTRATION: Chinese Clinical Trial Registry, ChiCTR2100041705, ChiCTR2100041706. Registered 1 January 2021, www.chictr.org.cn .

Potential inhibitors for the novel coronavirus (SARS-CoV-2).

The lack of a vaccine or any effective treatment for the aggressive novel coronavirus disease (COVID-19) has created a sense of urgency for the discovery of effective drugs. Several repurposing pharmaceutical candidates have been reported or envisaged to inhibit the emerging infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but their binding sites, binding affinities and inhibitory mechanisms are still unavailable. In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. The results suggest that Chloroquine has the strongest binding affinity with 3CL hydrolase (Mpro) among clinically approved drugs, indicating its effective inhibitory ability for SARS-CoV-2. However, the newly designed inhibitor 13b shows potentially improved inhibition efficiency with larger binding energy compared with Chloroquine. We further calculate the important binding site residues at the active site and demonstrate that the MET 165 and HIE 163 contribute the most for 13b, while the MET 165 and GLN 189 for Chloroquine, based on residual energy decomposition analysis. The proposed work offers a higher research priority for 13b to treat the infection of SARS-CoV-2 and provides theoretical basis for further design of effective drug molecules with stronger inhibition.