Computer-aided molecular design and optimization of potent inhibitors disrupting APC‒Asef interaction

Artificial Intelligence in Molecular Optimization: Current Paradigms and Future Frontiers

Molecular optimization plays a pivotal role in many domains since it holds promise for improving the properties of lead molecules. The advent of artificial intelligence (AI)-driven molecular optimization has revolutionized lead optimization workflows, which have significantly accelerated the development of drug candidates. However, AI models are also confronted with new challenges in practical molecular optimization, such as high-dimensional chemical space and data sparsity issues. This paper initially highlights the inherent benefits of molecular optimization in terms of optimizing the properties and maintaining the structural similarity of lead molecules, thereby highlighting its critical role in drug discovery. The next section systematically categorizes and analyzes existing AI-aided molecular optimization methods, comprising iterative search in discrete chemical space, end-to-end generation in continuous latent space, and iterative search in continuous latent space methods. Finally, we discuss the key challenges in AI-aided molecular optimization methods, including molecular representations, dataset selection, the properties to be optimized, and optimization algorithms, while proposing potential solutions and future research directions. In summary, this review provides a comprehensive analysis of existing representative AI-aided molecular optimization methods, thereby offering guidance for future research directions.

The value of coimmunoprecipitation (Co-IP) assays in drug discovery

INTRODUCTION

Co-IP assays are well-established technologies widely applicated for investigating the mechanisms underlying protein-protein interactions and identifying protein-protein interaction modulators. These assays play an important role in elucidating the complex networks of protein interactions critical for cellular functions.

AREAS COVERED

This review covers a technical protocol of standard Co-IP. The research contents and conclusions of Co-IP in protein-protein interactions and protein-protein interaction modulators are summarized. Finally, three derivations of Co-IP assays are introduced. Literature was surveyed from original publications, standard sources, PubMed and clinical trials through 14 April 2025.

EXPERT OPINION

To perform Co-IP successfully, researchers must consider the selection of specific antibody, remission of nonspecific binding and detection limitations for transient or weak interactions. Co-IP assays offer several advantages over tandem affinity purification and pull-down methods, particularly in their applicability to primary cells. This allows for the study of PPIs in a natural cellular environment. Conventional Co-IP assays often struggle to detect weak or transient interactions and can suffer from nonspecific binding contamination. However, advancements in Co-IP techniques address these challenges, enhancing sensitivity and specificity, and enabling the detection of subtle interactions while distinguishing specific binding events. This makes Co-IP a powerful tool for exploring the dynamics of protein interactions in living systems.

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.