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The ongoing evolution of the Omicron lineage of SARS-CoV-2 has led to the emergence of subvariants that pose challenges to antibody neutralization. Understanding the binding dynamics between the receptor-binding domains (RBD) of these subvariants spike and monoclonal antibodies (mAbs) is pivotal for elucidating the mechanisms of immune escape and for advancing the development of therapeutic antibodies. This study focused on the RBD regions of Omicron subvariants BA.2, BA.5, BF.7, and XBB.1.5, employing molecular dynamics simulations to unravel their binding mechanisms with a panel of six mAbs, and subsequently analyzing the origins of immune escape from energetic and structural perspectives. Our results indicated that the antibody LY-COV1404 maintained binding affinities across all studied systems, suggesting the resilience of certain antibodies against variant-induced immune escape, as seen with the mAb 1D1-Fab. The newly identified mAb 002-S21F2 showed a similar efficacy profile to LY-COV1404, though with a slightly reduced binding to BF.7. In parallel, mAb REGN-10933 emerged as a potential therapeutic candidate against BF.7 and XBB.1.5, reflecting the importance of identifying variant-specific antibody interactions, akin to the binding optimization observed in BA.4/5 and XBB.1.5. And key residues that facilitate RBD-mAb binding were identified (T345, L441, K444, V445, and T500), alongside residues that hinder protein–protein interactions (D420, L455, K440, and S446). Particularly noteworthy was the inhibited binding of V445 and R509 with mAbs in the presence of mAb 002-S21F2, suggesting a mechanism for immune escape, especially through the reduction of V445 hydrophobicity. These findings enhance our comprehension of the binding interactions between mAbs and RBDs, contributing to the understanding of immune escape mechanisms. They also lay the groundwork for the design and optimization of antiviral drugs and have significant implications for the development of treatments against current and future coronaviruses. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Inhibitors that competitively bind MDM2/MDMX can block the inhibition of P53 by MDM2/MDMX and restart its tumor-suppressive effect. Molecular studies targeting MDM2/MDMX inhibitors have always been a hot topic in anticancer drug design. Although numerous inhibitors have been designed previously against MDM2/MDMX, their dual inhibition efficacy has not been demonstrated, and few studies assessed the general causes affecting the dual inhibition of MDM2/MDMX by these inhibitors. Here, molecular dynamics simulations and alanine scanning combined with the interaction entropy method were employed to precisely investigate whether 16 inhibitors could dually inhibit MDM2/MDMX and the similarities and differences in the interaction modes. Thereby addressing the key residue sites affecting dual inhibition. Residues L54/M53, I61/60, M62/61, Y67/66, and V93/92 of MDM2/MDMX, which are in corresponding positions in both protein structures, provide significant conditions for these inhibitors to bind to MDM2/MDMX tightly. In addition, most of these inhibitors prefer to bind MDM2 than MDMX, and residues H96 and I99 in MDM2 are attractive targets for inhibitors, resulting in inhibitors binding to MDM2/MDMX with different affinity. These key residues should be considered in the development of dual inhibitors. For these 16 inhibitors, most have dual inhibitory potential for MDM2/MDMX based on the binding affinity of the complexes. Still, it is questionable whether they can exert excellent dual inhibition considering the assessment of the hot-spots. At least their binding affinity for MDMX is not superior to that for MDM2 due to the difference in energy of the van der Waals interactions at the key sites. Furthermore, based on the analysis of three representative inhibitors (TUZ/HRH and HRQ with different binding preferences for MDM2/MDMX), 3-chloropyridine in TUZ leads to the differential binding affinity between the inhibitor and MDM2/MDMX. It readily forms hydrophobic interactions with the surrounding residues H96 and I99. But this phenomenon does not occur in the TUZ–MDMX system, implying the critical role of residues H96/P95 and I99/L98. And the completely different binding mechanism of HRQ binding to MDM2/MDMX explains its inability to inhibit MDM2 well. Thus, we are cautious about its dual inhibitory ability. Besides, HRH is more prone to strong van der Waals interactions with MDM2 than MDMX whereas its 2-chlorofluorobenzene is detrimental to this. We hope that these findings will provide reliable molecular insights for the screening and optimization of targeting MDM2/MDMX dual inhibitors. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 Delta (B.1.617.2) variant was identified in India in October 2020, and it has quickly become the mainstream strain with strong toxicity and spread, posing great challenges to epidemic control. However, the molecular mechanism of its powerful infectivity remains unclear. It is meaningful to investigate the process of Delta variant's receptor-binding domain (RBD) binding to angiotensin-converting enzyme 2 (ACE2). Here, we performed three repeated molecular dynamics simulations for each system to avoid accidents, and the alanine scanning combined with the interaction entropy (ASIE) method was utilized to evaluate the binding free energy. Through the detailed energy and conformational analysis, the binding mechanism of the Delta variant was illustrated. The results showed that the existence of L452R and T478K mutations can trigger the effective hijacking of ACE2 by the Delta variant through the following three ways: (i) these two mutations can significantly enhance the electrostatic energy of the system by the introduction of two positively charged amino acids (Arg and Lys), thereby increasing the binding affinity of RBD and ACE2, (ii) the Loops 1, 3, and 4 in the receptor-binding motif (RBM) of RBD form a tighter conformation under the dominance of the T478K mutation, allowing ACE2 to be captured more effectively than the wild-type system, and (iii) these conformational changes lead to a more stable hydrogen bond in the Delta variant, which further ensures the stability of the binding. In addition, to explore the effect of mutations on the antibody, the key residues contributing to the changes in the binding ability of RBD in the Delta variant with the existing 42 neutralizing monoclonal antibodies (mAbs) have been preliminarily evaluated. The present study reveals the molecular mechanism for the increased infectivity of SARS-CoV-2 caused by mutations, and the key sites that cause antigenic changes were screened. It provides important theoretical insights for the development of novel targeted RBD drugs and antibodies. [ABSTRACT FROM AUTHOR]

The continuous spread of the newly emerged SARS-CoV-2 Omicron variant (B.1.1.529) has become an important reason for the surge in COVID-19 infections. Its numerous mutated residues containing key sites on the receptor-binding domain (RBD) undoubtedly pose new challenges for epidemic control. Although the preventive measures are becoming more sophisticated, the effects of mutations on the binding of the virus to the receptor protein remain to be elucidated. Here, we used molecular dynamics (MD) simulations to investigate the differences in the binding mode between the Omicron variant and the angiotensin-converting enzyme 2 (ACE2) compared to the wild-type strain (WT). Multi-point mutations in the Omicron variant RBD could cause the conformation shift in the large Loop (where T478K and E484A are located), which makes it easier to wrap the N-terminal helix of ACE2 and form tighter contacts. The stronger electrostatic interaction was the main reason for its enhanced binding affinity as compared to WT. This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites. The appearance of these highly polar hydrophilic amino acids may cause local perturbations and affect the electrostatic complementarity of RBD with the ACE2, and further mediate conformational changes. Thus, a more extensive interaction network was found in the mutation system and the complex interaction cluster was formed near E37@ACE2, which was essential for the stable binding of the two. In addition, we speculated that these mutations may affect the electrostatic complementarity with the four potential antibodies to reduce the sensitivity of the virus to antibodies. This study reveals the key details of the Omicron variant binding to ACE2 and provides important theoretical views for the enhanced infectivity of this variant. We hope that these observations can provide timely molecular insights for responding to the Omicron variant pandemic. [ABSTRACT FROM AUTHOR]