A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights

The spike protein encoded by the SARS-CoV-2 has become one of the most studied macromolecules in recent years due to its central role in COVID-19 pathogenesis. The spike protein's receptor-binding domain (RBD) directly interacts with the host-encoded receptor protein, ACE2. This review critically examines computational insights into RBD's interaction with ACE2 and with therapeutic antibodies designed to interfere with this interaction. We begin by summarizing insights from early computational studies on pre-pandemic SARS-CoV-1 RBD interactions and how these early studies shaped the understanding of SARS-CoV-2. Next, we highlight key theoretical contributions that revealed the molecular mechanisms behind the binding affinity of SARS-CoV-2 RBD against ACE2, and the structural changes that have enhanced the infectivity of emerging variants. Special attention is given to the "RBD charge rule", a predictive framework for determining variant infectivity based on the electrostatic properties of the RBD. Towards applying the computational insights to therapy, we discuss a multiscale computational protocol for optimizing monoclonal antibodies to improve binding affinity across multiple spike protein variants, including representatives from the Omicron family. Finally, we explore how these insights can inform the development of future vaccines and therapeutic interventions for combating future coronavirus diseases.

QM/MM study reveals novel mechanism of KRAS and KRASG12R catalyzed GTP hydrolysis

As a crucial drug target, KRAS can regulate most cellular processes involving guanosine triphosphate (GTP) hydrolysis. However, the mechanism of GTP hydrolysis has remained controversial over the past decades. Here, several different GTP hydrolysis mechanisms catalyzed by wild-type KRAS (WT-KRAS) and KRASG12R mutants were discussed via four QM/MM calculation models. Based on the computational results, a Mg2+-coordinated H2O-mediated GTP hydrolysis mechanism was proposed. In this mechanism, a Mg2+-coordinated H2O first protonates the fully deprotonated GTP, and then the Mg2+ coordinated hydroxyl anion is generated. The Pγ-O bond is formed via the SN2 attack of the second H2O on the Pγ atom of the GTP, leading to the simultaneous cleavage of the Pγ-O bond. Meanwhile, the hydroxyl anion coordinated to Mg2+ and generated in the first step acts as a proton acceptor from water. This Mg2+ coordinated H2O-involved GTP hydrolysis mechanism may also be suitable for Mg2+-catalyzed ATP hydrolysis. Furthermore, the mechanism of GTP hydrolysis catalyzed by the KRASG12R mutant, whose hydrolysis rate was approximately 40-fold slower than WT-KRAS, was also discussed. Our QM/MM calculations reveal that GTP is easily protonated by the residue R12, and the energy barrier of GTP hydrolysis catalyzed by the KRASG12R mutant is lower than the corresponding barrier for WT-KRAS. Nevertheless, molecular dynamics (MD) simulations reveal that R12, a residue characterized by significant steric hindrance, is positioned at the GTP site where the nucleophilic attack by water occurs during Pγ-O bond formation, thereby strongly impeding the approach of water molecules to GTP. As a result, the GTP hydrolysis rate catalyzed by the KRASG12R mutant was severely impaired. Uncovering the GTP hydrolysis mechanism catalyzed by the WT-KRAS and KRASG12R mutant may also give a reasonable explanation for the relationship between the KRASG12R mutation and the occurrence of cancer. We hope this finding will provide useful guidance for drug discovery that targets KRAS.

Binding affinity between coronavirus spike protein and human ACE2 receptor

Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.

Transformation of peptides to small molecules in medicinal chemistry: Challenges and opportunities

Peptides are native binders involved in numerous physiological life procedures, such as cellular signaling, and serve as ready-made regulators of biochemical processes. Meanwhile, small molecules compose many drugs owing to their outstanding advantages of physiochemical properties and synthetic convenience. A novel field of research is converting peptides into small molecules, providing a convenient portable solution for drug design or peptidomic research. Endowing properties of peptides onto small molecules can evolutionarily combine the advantages of both moieties and improve the biological druggability of molecules. Herein, we present eight representative recent cases in this conversion and elaborate on the transformation process of each case. We discuss the innovative technological methods and research approaches involved, and analyze the applicability conditions of the approaches and methods in each case, guiding further modifications of peptides to small molecules. Finally, based on the aforementioned cases, we summarize a general procedure for peptide-to-small molecule modifications, listing the technological methods available for each transformation step and providing our insights on the applicable scenarios for these methods. This review aims to present the progress of peptide-to-small molecule modifications and propose our thoughts and perspectives for future research in this field.