How Do Modulators Affect the Orthosteric and Allosteric Binding Pockets?

Structural insight into CD20/CD3-bispecific antibodies by molecular modeling

Non-Hodgkin's Lymphoma (NHL) remains a significant challenge in hematology, with chemotherapy and radiation therapy as conventional treatment options, albeit with limitations such as adverse effects. Immunotherapy, particularly bispecific antibodies (BsAbs) T cell engagers (TCEs), has emerged as a promising approach. Despite their potential, TCEs pose challenges, including adverse events like cytokine release syndrome. Understanding the structural details of TCEs and their interactions with target proteins is crucial for optimizing their therapeutic efficacy and toxicity. In this study, we further developed our protocol MCCS-Docker for protein-protein interactions and applied it to investigate the structural intricacies of CD3 interactions with therapeutic antibodies such as OKT3, UCHT1, Mosunetuzumab, Odronextumab, Glofitamab, and Epcoritamab using computational modeling techniques. Our analysis not only approved the effectiveness of our updated MCCS-Docker protocol but also revealed detailed binding interactions between the BsAbs and CD3, elucidating key residues of Tyrosine and Asparagine in the antibodies involved in the binding interface. Molecular dynamics simulations validated the stability of these interactions over time, confirming the reliability of the binding poses generated from docking studies. Overall, our study offered a novel method to predict critical residues in protein-protein interactions and enhanced the understanding of the structural determinants governing BsAb interactions with target proteins, offering valuable insights for designing and optimizing immunotherapeutic agents for NHL and related hematologic malignancies.

CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design

Central nervous system (CNS) drugs have had a significant impact on treating a wide range of neurodegenerative and psychiatric disorders. In recent years, deep learning-based generative models have shown great potential for accelerating drug discovery and improving efficacy. However, specific applications of these techniques in CNS drug discovery have not been widely reported. In this study, we developed the CNSMolGen model, which uses a framework of bidirectional recurrent neural networks (Bi-RNNs) for de novo molecular design of CNS drugs. Results showed that the pretrained model was able to generate more than 90% of completely new molecular structures, which possessed the properties of CNS drug molecules and were synthesizable. In addition, transfer learning was performed on small data sets with specific biological activities to evaluate the potential application of the model for CNS drug optimization. Here, we used drugs against the classical CNS disease target serotonin transporter (SERT) as a fine-tuned data set and generated a focused database against the target protein. The potential biological activities of the generated molecules were verified by using the physics-based induced-fit docking study. The success of this model demonstrates its potential in CNS drug design and optimization, which provides a new impetus for future CNS drug development.

The NERP-4-SNAT2 axis regulates pancreatic β-cell maintenance and function

Insulin secretion from pancreatic β cells is regulated by multiple stimuli, including nutrients, hormones, neuronal inputs, and local signalling. Amino acids modulate insulin secretion via amino acid transporters expressed on β cells. The granin protein VGF has dual roles in β cells: regulating secretory granule formation and functioning as a multiple peptide precursor. A VGF-derived peptide, neuroendocrine regulatory peptide-4 (NERP-4), increases Ca2+ influx in the pancreata of transgenic mice expressing apoaequorin, a Ca2+-induced bioluminescent protein complex. NERP-4 enhances glucose-stimulated insulin secretion from isolated human and mouse islets and β-cell-derived MIN6-K8 cells. NERP-4 administration reverses the impairment of β-cell maintenance and function in db/db mice by enhancing mitochondrial function and reducing metabolic stress. NERP-4 acts on sodium-coupled neutral amino acid transporter 2 (SNAT2), thereby increasing glutamine, alanine, and proline uptake into β cells and stimulating insulin secretion. SNAT2 deletion and inhibition abolish the protective effects of NERP-4 on β-cell maintenance. These findings demonstrate a novel autocrine mechanism of β-cell maintenance and function that is mediated by the peptide-amino acid transporter axis.

Molecular Modeling Study of a Receptor-Orthosteric Ligand-Allosteric Modulator Signaling Complex

Allosteric modulators (AMs) are considered as a perpetual hotspot in research for their higher selectivity and various effects on orthosteric ligands (OL). They are classified in terms of their functionalities as positive, negative, or silent allosteric modulators (PAM, NAM, or SAM, respectively). In the present work, 11 pairs of three-dimensional (3D) structures of receptor-orthosteric ligand and receptor-orthosteric ligand-allosteric modulator complexes have been collected for the studies, including three different systems: GPCR, enzyme, and ion channel. Molecular dynamics (MD) simulations are applied to quantify the dynamic interactions in both the orthosteric and allosteric binding pockets and the structural fluctuation of the involved proteins. Our results showed that MD simulations of moderately large molecules or peptides undergo insignificant changes compared to crystal structure results. Furthermore, we also studied the conformational changes of receptors that bound with PAM and NAM, as well as the different allosteric binding sites in a receptor. There should be no preference for the position of the allosteric binding pocket after comparing the allosteric binding pockets of these three systems. Finally, we aligned four distinct β2 adrenoceptor structures and three N-methyl-d-aspartate receptor (NMDAR) structures to investigate conformational changes. In the β2 adrenoceptor systems, the aligned results revealed that transmembrane (TM) helices 1, 5, and 6 gradually increased outward movement from an enhanced inactive state to an improved active state. TM6 endured the most significant conformational changes (around 11 Å). For NMDAR, the bottom section of NMDAR's ligand-binding domain (LBD) experienced an upward and outward shift during the gradually activating process. In conclusion, our research provides insight into receptor-orthosteric ligand-allosteric modulator studies and the design and development of allosteric modulator drugs using MD simulation.