Immune Escape Mechanisms of SARS-CoV-2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization

Impact of vaccination on SARS-CoV-2 evolution and immune escape variants

Vaccines and host genetic factors can influence the SARS-CoV-2 evolution and emergence of new variants. Even vaccinated cases get affected as virus continues to evolve, raising concerns about vaccine efficacy and the emergence of immune escape variants. Here, we have analyzed 2295 whole-genome sequences of SARS-CoV-2 collected from vaccinated and unvaccinated cases to evaluate the impact of vaccines on virus diversity within hosts. Our comparative analysis revealed a significant higher incidence of intra-host single nucleotides variants (iSNVs) in vaccinated cases compared to unvaccinated ones (p value<0.0001). Furthermore, we have found that specific mutational processes, including APOBEC (C > T) mediated and ADAR1 (A > G) mediated mutations, were found more prevalent in vaccinated cases. Vaccinated cases exhibited higher accumulation of nonsynonymous mutation than unvaccinated cases. Fixed iSNVs were predominantly located in the ORF1ab and spike genes, several key omicron defining immune escape variants S477N, Q493R, Q498R, Y505H, L452R, and N501Y were identified in the RBD domain of spike gene in vaccinated cases. Our findings suggest that vaccine plays an important role in the evolution of the virus genome. The virus genome acquires random mutations due to error-prone replication of the virus, host modification through APOBEC and ADAR1 mediated editing mechanism, and oxidative stress. These mutations become fixed in the viral population due to the selective pressure imposed by vaccination.

A Machine Learning Approach to Identify Key Residues Involved in Protein-Protein Interactions Exemplified with SARS-CoV-2 Variants

Human infection with the coronavirus disease 2019 (COVID-19) is mediated by the binding of the spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the human angiotensin-converting enzyme 2 (ACE2). The frequent mutations in the receptor-binding domain (RBD) of the spike protein induced the emergence of variants with increased contagion and can hinder vaccine efficiency. Hence, it is crucial to better understand the binding mechanisms of variant RBDs to human ACE2 and develop efficient methods to characterize this interaction. In this work, we present an approach that uses machine learning to analyze the molecular dynamics simulations of RBD variant trajectories bound to ACE2. Along with the binding free energy calculation, this method was used to characterize the major differences in ACE2-binding capacity of three SARS-CoV-2 RBD variants-namely the original Wuhan strain, Omicron BA.1, and the more recent Omicron BA.5 sublineages. Our analyses assessed the differences in binding free energy and shed light on how it affects the infectious rates of different variants. Furthermore, this approach successfully characterized key binding interactions and could be deployed as an efficient tool to predict different binding inhibitors to pave the way for new preventive and therapeutic strategies.

The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes

Point mutations play a vital role in the conformational transformation of HRAS. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by constructions of free energy landscapes (FELs) were adopted to explore the effect of mutations D33K, A59T and L120A on conformation states of the GDP-bound HRAS. The results from the post-processing analyses on GaMD trajectories suggest that mutations alter the flexibility and motion modes of the switch domains from HRAS. The analyses from FELs show that mutations induce more disordered states of the switch domains and affect interactions of GDP with HRAS, implying that mutations yield a vital effect on the binding of HRAS to effectors. The GDP-residue interaction network revealed by our current work indicates that salt bridges and hydrogen bonding interactions (HBIs) play key roles in the binding of GDP to HRAS. Furthermore, instability in the interactions of magnesium ions and GDP with the switch SI leads to the extreme disorder of the switch domains. This study is expected to provide the energetic basis and molecular mechanism for further understanding the function of HRAS.Communicated by Ramaswamy H. Sarma.

Advanced molecular mechanisms of modified DRV compounds in targeting HIV-1 protease mutations and interrupting monomer dimerization

HIV-1 protease (PR) plays a crucial role in the treatment of HIV as a key target. The global issue of emerging drug resistance is escalating, and PR mutations pose a substantial challenge to the effectiveness of inhibitors. HIV-1 PR is an ideal model for studying drug resistance to inhibitors. The inhibitor, darunavir (DRV), exhibits a high genetic barrier to viral resistance, but with mutations of residues in the PR, there is also some resistance to DRV. Inhibitors can impede PR in two ways: one involves binding to the active site of the dimerization protease, and the other involves binding to the PR monomer, thereby preventing dimerization. In this study, we aimed to investigate the inhibitory effect of DRV with a modified inhibitor on PR, comparing the differences between wild-type and mutated PR, using molecular dynamics simulations. The inhibitory effect of the inhibitors on PR monomers was subsequently investigated. And molecular mechanics Poisson-Boltzmann surface area evaluated the binding free energy. The energy contribution of individual residues in the complex was accurately calculated by the alanine scanning binding interaction entropy method. The results showed that these inhibitors had strong inhibitory effects against PR mutations, with GRL-142 exhibiting potent inhibition of both the PR monomer and dimer. Improved inhibitors could strengthen hydrogen bonds and interactions with PR, thereby boosting inhibition efficacy. The binding of the inhibitor and mutation of the PR affected the distance between D25 and I50, preventing their dimerization and the development of drug resistance. This study could accelerate research targeting HIV-1 PR inhibitors and help to further facilitate drug design targeting both mechanisms.

Effectiveness of VSV vectored SARS-CoV-2 spike when administered through intranasal, intramuscular or a combination of both

A critical feature of the VSV vector platform is the ability to pseudotype the virus with different glycoproteins from other viruses, thus altering cellular tropism of the recombinant virus. The route of administration is critical in triggering local and systemic immune response and protection. Most of the vaccine platforms used at the forefront are administered by intramuscular injection. However, it is not known at what level ACE2 is expressed on the surface of skeletal muscle cells, which will have a significant impact on the efficiency of a VSV-SARS-CoV-2 spike vaccine to mount a protective immune response when administered intramuscularly. In this study, we investigate the immunogenicity and efficacy of a prime-boost immunization regimen administered intranasally (IN), intramuscularly (IM), or combinations of the two. We determined that the prime-boost combinations of IM followed by IN immunization (IM + IN) or IN followed by IN immunization (IN + IN) exhibited strong spike-specific IgG, IgA and T cell response in vaccinated K18 knock-in mice. Hamsters vaccinated with two doses of VSV expressing SARS-CoV-2 spike, both delivered by IN or IM + IN, showed strong protection against SARS-CoV-2 variants of concern Alpha and Delta. This protection was also observed in aged hamsters. Our study underscores the highly crucial role immunization routes have with the VSV vector platform to elicit a strong and protective immune response.

Developing magnetic barcode bead fluorescence assay for high throughput analyzing humoral responses against multiple SARS-CoV-2 variants

The continuous mutation of SARS-CoV-2 highlights the need for rapid, cost-effective, and high-throughput detection methods. To better analyze the antibody levels against SARS-CoV-2 and its variants in vaccinated or infected subjects, we developed a multiplex detection named Barcode Bead Fluorescence (BBF) assay. These barcode beads were magnetic, characterized by 2-dimensional edges, highly multiplexed, and could be decrypted with visible light. We conjugated 12 magnetic barcode beads with corresponding nine spike proteins (wild-type, alpha, beta, gamma, delta, and current omicrons), two nucleocapsid proteins (wild-type and omicron), and one negative control. First, the conjugated beads underwent serial quality controls via fluorescence labeling, e.g., reproducibility (R square = 0.99) and detection limits (119 pg via anti-spike antibody). Next, we investigated serums from vaccinated subjects and COVID-19 patients for clinical applications. A significant reduction of antibody levels against all variant beads was observed in both vaccinated and COVID-19 studies. Subjects with two doses of mRNA-1273 exhibited the highest level of antibodies against all spike variants compared to two doses of AZD1222 and unvaccinated. We also found that COVID-19 patients showed higher antibody levels against spike beads from wild-type, alpha, beta, and delta. Finally, the nucleocapsid beads served as markers to distinguish infections from vaccinated subjects. Overall, this study developed the BBF assay for analyzing humoral immune responses, which has the advantages of robustness, automation, scalability, and cost-effectiveness.

Identification of key mutations responsible for the enhancement of receptor-binding affinity and immune escape of SARS-CoV-2 Omicron variant

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised concerns worldwide due to its enhanced transmissibility and immune escapability. The first dominant Omicron BA.1 subvariant harbors more than 30 mutations in the spike protein from the prototype virus, of which 15 mutations are located at the receptor binding domain (RBD). These mutations in the RBD region attracted significant attention, which potentially enhance the binding of the receptor human angiotensin-converting enzyme 2 (hACE2) and decrease the potency of neutralizing antibodies/nanobodies. This study applied the molecular dynamics simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method, to investigate the molecular mechanism behind the impact of the mutations acquired by Omicron on the binding affinity between RBD and hACE2. Our results indicate that five key mutations, i.e., N440K, T478K, E484A, Q493R, and G496S, contributed significantly to the enhancement of the binding affinity by increasing the electrostatic interactions of the RBD-hACE2 complex. Moreover, fourteen neutralizing antibodies/nanobodies complexed with RBD were used to explore the effects of the mutations in Omicron RBD on their binding affinities. The calculation results indicate that the key mutations E484A and Y505H reduce the binding affinities to RBD for most of the studied neutralizing antibodies/nanobodies, mainly attributed to the elimination of the original favorable gas-phase electrostatic and hydrophobic interactions between them, respectively. Our results provide valuable information for developing effective vaccines and antibody/nanobody drugs.

Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease

Papain-like protease (PLpro), a non-structural protein encoded by SARS-CoV-2, is an important therapeutic target. Regions 1 and 5 of an existing drug, GRL0617, can be optimized to produce cooperativity with PLpro binding, resulting in stronger binding affinity. This work investigated the origin of the cooperativity using molecular dynamics simulations combined with the interaction entropy (IE) method. The regions' improvement exhibits cooperativity by calculating the binding free energies between the complex of PLpro-inhibitor. The thermodynamic integration method further verified the cooperativity generated in the drug improvement. To further determine the specific source of cooperativity, enthalpy and entropy in the complexes were calculated using molecular mechanics/generalized Born surface area and IE. The results show that the entropic change is an important contributor to the cooperativity. Our study also identified residues P248, Q269, and T301 that play a significant role in cooperativity. The optimization of the inhibitor stabilizes these residues and minimizes the entropic loss, and the cooperativity observed in the binding free energy can be attributed to the change in the entropic contribution of these residues. Based on our research, the application of cooperativity can facilitate drug optimization, and provide theoretical ideas for drug development that leverage cooperativity by reducing the contribution of entropy through multi-locus binding.

Comprehensive analysis unveils altered binding kinetics of 5-/6-methylCytosine/adenine modifications in R2R3-DNA system

Recent studies have shown that DNA methylation is an important epigenetic marker. Two prominent forms are methylation of the C5 position of cytosine and methylation of the C6 position of adenine. Given the vital significance of DNA methylation, investigating the mechanisms that influence protein binding remains a compelling pursuit. This study used molecular dynamics simulations to investigate the binding patterns of R2R3 protein and four differentially methylated DNAs. The alanine scanning combined with interaction entropy method was used to identify key residues that respond to different methylation patterns. The order of protein binding ability to DNA is as follows: unmethylated DNA > A11 methylation (5'-A6mAC-3') (6m2A system) > A10 methylation (5'-6mAAC-3') (6m1A system) > both A10 and A11 methylation (5'-6mA6mAC-3') (6mAA system) > C12 methylation (5'-AA5mC-3') (5mC system). All methylation systems lead to the sixth α helix (H6) (residues D105 to L116) moving away from the binding interface, and in the 5mC and 6m1A systems, the third α helix (H3) (residues G54 to L65) exhibits a similar trend. When the positively charged amino acids in H3 and H6 move away from the binding interface, their electrostatic and van der Waals interactions with the negatively charged DNA are weakened. Structural changes induced by methylation contributed to the destabilization of the hydrogen bond network near the original binding site, except for the 6m2A system. Moreover, there is a positive correlation between the number of methylated sites and the probability of distorting the DNA structure. Our study explores how different methylation patterns affect binding and structural adaptability, and have implications for drug discovery and understanding diseases related to abnormal methylation.

Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation

The Omicron lineage of SARS-CoV-2, which was first reported in November 2021, has spread globally and become dominant, splitting into several sublineages. Experiments have shown that Omicron lineage has escaped or reduced the activity of existing monoclonal antibodies, but the origin of escape mechanism caused by mutation is still unknown. This work uses molecular dynamics and umbrella sampling methods to reveal the escape mechanism of BA.1.1 to monoclonal antibody (mAb) Tixagevimab (AZD1061) and BA.5 to mAb Cilgavimab (AZD8895), both mAbs were combined to form antibody cocktail, Evusheld (AZD7442). The binding free energy of BA.1.1-AZD1061 and BA.5-AZD8895 has been severely reduced due to multiple-site mutated Omicron variants. Our results show that the two Omicron variants, which introduce a substantial number of positively charged residues, can weaken the electrostatic attraction between the receptor binding domain (RBD) and AZD7442, thus leading to a decrease in affinity. Additionally, using umbrella sampling along dissociation pathway, we found that the two Omicron variants severely impaired the interaction between the RBD of SARS-CoV-2's spike glycoprotein (S protein) and complementary determining regions (CDRs) of mAbs, especially in CDR3H. Although mAbs AZD8895 and AZD1061 are knocked out by BA.5 and BA.1.1, respectively, our results confirm that the antibody cocktail AZD7442 retains activity against BA.1.1 and BA.5 because another antibody is still on guard. The study provides theoretical insights for mAbs interacting with BA.1.1 and BA.5 from both energetic and dynamic perspectives, and we hope this will help in developing new monoclonals and combinations to protect those unable to mount adequate vaccine responses.

Dual mechanism: Epigenetic inhibitor apabetalone reduces SARS-CoV-2 Delta and Omicron variant spike binding and attenuates SARS-CoV-2 RNA induced inflammation

The SARS-CoV-2 virus initiates infection via interactions between the viral spike protein and the ACE2 receptors on host cells. Variants of concern have mutations in the spike protein that enhance ACE2 binding affinity, leading to increased virulence and transmission. Viral RNAs released after entry into host cells trigger interferon-I (IFN-I) mediated inflammatory responses for viral clearance and resolution of infection. However, overreactive host IFN-I responses and pro-inflammatory signals drive COVID-19 pathophysiology and disease severity during acute infection. These immune abnormalities also lead to the development of post-COVID syndrome if persistent. Novel therapeutics are urgently required to reduce short- and long-term pathologic consequences associated with SARS-CoV-2 infection. Apabetalone, an inhibitor of epigenetic regulators of the BET protein family, is a candidate for COVID-19 treatment via a dual mechanism of action. In vitro, apabetalone downregulates ACE2 gene expression to limit SARS-CoV-2 entry and propagation. In pre-clinical models and patients treated for cardiovascular disease, apabetalone inhibits expression of inflammatory mediators involved in the pathologic cytokine storm (CS) stimulated by various cytokines. Here we show apabetalone treatment of human lung epithelial cells reduces binding of viral spike protein regardless of mutations found in the highly contagious Delta variant and heavily mutated Omicron. Additionally, we demonstrate that apabetalone counters expression of pro-inflammatory factors with roles in CS and IFN-I signaling in lung cells stimulated with SARS-CoV-2 RNA. Our results support clinical evaluation of apabetalone to treat COVID-19 and post-COVID syndrome regardless of the SARS-CoV-2 variant.

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus 2 variants toward the host cell. Diversity of these variants challenges the development of effective general therapies, their transmissibility relying either on an increased affinity toward their dedicated human receptor, the angiotensin-converting enzyme 2 (ACE2), or on escaping the immune response. Now that robust structural data are available, we have determined with utmost accuracy the standard binding free energy of the receptor-binding domain to the most widespread variants, namely, Alpha, Beta, Delta, and Omicron BA.2, as well as the wild type (WT) in complex either with ACE2 or with antibodies, namely, S2E12 and H11-D4, using a rigorous theoretical framework that combines molecular dynamics and potential-of-mean-force calculations. Our results show that an appropriate starting structure is crucial to ensure appropriate reproduction of the binding affinity, allowing the variants to be compared. They also emphasize the necessity to apply the relevant methodology, bereft of any shortcut, to account for all the contributions to the standard binding free energy. Our estimates of the binding affinities support the view that while the Alpha and Beta variants lean on an increased affinity toward the host cell, the Delta and Omicron BA.2 variants choose immune escape. Moreover, the S2E12 antibody, already known to be active against the WT (Starr et al., 2021; Mlcochova et al., 2021), proved to be equally effective against the Delta variant. In stark contrast, H11-D4 retains a low affinity toward the WT compared to that of ACE2 for the latter. Assuming robust structural information, the methodology employed herein successfully addresses the challenging protein-protein binding problem in the context of coronavirus disease 2019 while offering promising perspectives for predictive studies of ever-emerging variants.

Epistatic Variations in the Omicron Receptor Binding Domain Can Enhance Host Recognition: An In Silico Assessment and Prediction

The hypermutated receptor binding domain (RBD) of the Omicron (B.1.1.529) lineage exhibits a different binding interface with human angiotensin-converting enzyme 2 (ACE2) relative to that of the wild-type Wuhan Hu-1, yet how the altered interaction will affect viral evolution is largely unknown. Here, we used molecular dynamics simulation to characterize the binding features of the Omicron BA.1/hACE2 complex and used free energy perturbation calculations to assess the ongoing and putative variations. The complex reveals a substantial rearrangement of the interfacial hydrogen-bond network: R493 of RBD forms a dynamic electrostatic interaction with both E35 and D38 of hACE2, which prohibits the hydrogen bonds of R498-D38 and Y449-D38. Whereas most circulating mutations minimally affect RBD binding to hACE2, the charge-altering mutation R493Q attenuates the affinity by abolishing the electrostatic interaction. However, the potential variants H505Y or N417K/R493Q could restore and gain even greater binding affinities than BA.1 as a result of their optimized interaction network and epistasis effects.

Molecular Mechanism of the Non-Covalent Orally Targeted SARS-CoV-2 Mpro Inhibitor S-217622 and Computational Assessment of Its Effectiveness against Mainstream Variants

Convenient and efficient therapeutic agents are urgently needed to block the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, the mechanism for the novel orally targeted SARS-CoV-2 main protease (M^pro) inhibitor S-217622 is revealed through a molecular dynamics simulation. The difference in the movement modes of the S-217622-M^pro complex and apo-M^pro suggested S-217622 could inhibit the motility intensity of M^pro, thus maintaining their stable binding. Subsequent energy calculations showed that the P2 pharmacophore possessed the highest energy contribution among the three pharmacophores of S-217622. Additionally, hot-spot residues H41, M165, C145, E166, and H163 have strong interactions with S-217622. To further investigate the resistance of S-217622 to six mainstream variants, the binding modes of S-217622 with these variants were elucidated. The subtle differences in energy compared to that of the wild type implied that the binding patterns of these systems were similar, and S-217622 still inhibited these variants. We hope this work will provide theoretical insights for optimizing novel targeted M^pro drugs.

A comprehensive analysis of the efficacy and effectiveness of COVID-19 vaccines

It is urgently needed to update the comprehensive analysis about the efficacy or effectiveness of COVID-19 vaccines especially during the COVID-19 pandemic caused by SARS-CoV-2 Delta and Omicron variants. In general, the current COVID-19 vaccines showed a cumulative efficacy of 66.4%, 79.7%, and 93.6% to prevent SARS-CoV-2 infection, symptomatic COVID-19, and severe COVID-19, respectively, but could not prevent the asymptomatic infection of SARS-CoV-2. Furthermore, the current COVID-19 vaccines could effectively prevent COVID-19 caused by the Delta variant although the incidence of breakthrough infection of the SARS-CoV-2 Delta variant increased when the intervals post full vaccination extended, suggesting the waning effectiveness of COVID-19 vaccines. In addition, one-dose booster immunization showed an effectiveness of 74.5% to prevent COVID-19 caused by the Delta variant. However, current COVID-19 vaccines could not prevent the infection of Omicron sub-lineage BA.1.1.529 and had about 50% effectiveness to prevent COVID-19 caused by Omicron sub-lineage BA.1.1.529. Furthermore, the effectiveness was 87.6% and 90.1% to prevent severe COVID-19 and COVID-19-related death caused by Omicron sub-lineage BA.2, respectively, while one-dose booster immunization could enhance the effectiveness of COVID-19 vaccines to prevent the infection and COVID-19 caused by Omicron sub-lineage BA.1.1.529 and sub-lineage BA.2. Two-dose booster immunization showed an increased effectiveness of 81.8% against severe COVID-19 caused by the Omicron sub-lineage BA.1.1.529 variant compared with one-dose booster immunization. The effectiveness of the booster immunization with RNA-based vaccine BNT162b2 or mRNA-1273 was over 75% against severe COVID-19 more than 17 weeks after booster immunization whereas the heterogenous booster immunization showed better effectiveness than homologous booster immunization. In summary, the current COVID-19 vaccines could effectively protect COVID-19 caused by Delta and Omicron variants but was less effective against Omicron variant infection. One-dose booster immunization could enhance protection capability, and two-dose booster immunization could provide additional protection against severe COVID-19.

In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins

The SARS-CoV-2 variant Omicron is characterized, among others, by more than 30 amino acid changes occurring on the spike glycoprotein with respect to the original SARS-CoV-2 spike protein. We report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human antibodies, obtained by modeling them into selected publicly available resolved 3D structures of spike–antibody complexes and investigating the effects of these mutations at structural level. We predict that the interactions of Omicron spike with human antibodies can be either negatively or positively affected by amino acid changes, with a predicted total loss of interactions only in a few complexes. Moreover, our analysis applied also to the spike-ACE2 interaction predicts that these amino acid changes may increase Omicron transmissibility. Our approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology and represents a model to be adopted also in the case of other variants.