Explainable deep drug-target representations for binding affinity prediction

COLOR: A Compositional Linear Operation-Based Representation of Protein Sequences for Identification of Monomer Contributions to Properties

The properties of biological materials like proteins and nucleic acids are largely determined by their primary sequence. Certain segments in the sequence strongly influence specific functions, but identifying these segments, or so-called motifs, is challenging due to the complexity of sequential data. While deep learning (DL) models can accurately capture sequence-property relationships, the degree of nonlinearity in these models limits the assessment of monomer contributions to a property─a critical step in identifying key motifs. Recent advances in explainable AI (XAI) offer attention and gradient-based methods for estimating monomeric contributions. However, these methods are primarily applied to classification tasks, such as binding site identification, where they achieve limited accuracy (40-45%) and rely on qualitative evaluations. To address these limitations, we introduce a DL model with interpretable steps, enabling direct tracing of monomeric contributions. Inspired by the masking technique commonly used in vision and natural language processing domains, we propose a new metric ( I ) for quantitative analysis on datasets mainly containing distinct properties of anticancer peptides (ACP), antimicrobial peptides (AMP), and collagen. Our model exhibits 22% higher explainability than the gradient and attention-based state-of-the-art models, recognizes critical motifs (RRR, RRI, and RSS) that significantly destabilize ACPs, and identifies motifs in AMPs that are 50% more effective in converting non-AMPs to AMPs. These findings highlight the potential of our model in guiding mutation strategies for designing protein-based biomaterials.

Recent advances in computational and experimental protein-ligand affinity determination techniques

INTRODUCTION

Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved.

AREAS COVERED

In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design.

EXPERT OPINION

The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.

Machine Learning for Sequence and Structure-Based Protein-Ligand Interaction Prediction

Developing new drugs is too expensive and time -consuming. Accurately predicting the interaction between drugs and targets will likely change how the drug is discovered. Machine learning-based protein-ligand interaction prediction has demonstrated significant potential. In this paper, computational methods, focusing on sequence and structure to study protein-ligand interactions, are examined. Therefore, this paper starts by presenting an overview of the data sets applied in this area, as well as the various approaches applied for representing proteins and ligands. Then, sequence-based and structure-based classification criteria are subsequently utilized to categorize and summarize both the classical machine learning models and deep learning models employed in protein-ligand interaction studies. Moreover, the evaluation methods and interpretability of these models are proposed. Furthermore, delving into the diverse applications of protein-ligand interaction models in drug research is presented. Lastly, the current challenges and future directions in this field are addressed.

AI for targeted polypharmacology: The next frontier in drug discovery

In drug discovery, targeted polypharmacology, i.e., targeting multiple molecular targets with a single drug, is redefining therapeutic design to address complex diseases. Pre-selected pharmacological profiles, as exemplified in kinase drugs, promise enhanced efficacy and reduced toxicity. Historically, many of such drugs were discovered serendipitously, limiting predictability and efficacy, but currently artificial intelligence (AI) offers a transformative solution. Machine learning and deep learning techniques enable modeling protein structures, generating novel compounds, and decoding their polypharmacological effects, opening an avenue for more systematic and predictive multi-target drug design. This review explores the use of AI in identifying synergistic co-targets and delineating them from anti-targets that lead to adverse effects, and then discusses advances in AI-enabled docking, generative chemistry, and proteochemometric modeling of proteome-wide compound interactions, in the context of polypharmacology. We also provide insights into challenges ahead.

Using Artificial Intelligence for Drug Discovery: A Bibliometric Study and Future Research Agenda

Drug discovery is usually a rule-based process that is carefully carried out by pharmacists. However, a new trend is emerging in research and practice where artificial intelligence is being used for drug discovery to increase efficiency or to develop new drugs for previously untreatable diseases. Nevertheless, so far, no study takes a holistic view of AI-based drug discovery research. Given the importance and potential of AI for drug discovery, this lack of research is surprising. This study aimed to close this research gap by conducting a bibliometric analysis to identify all relevant studies and to analyze interrelationships among algorithms, institutions, countries, and funding sponsors. For this purpose, a sample of 3884 articles was examined bibliometrically, including studies from 1991 to 2022. We utilized various qualitative and quantitative methods, such as performance analysis, science mapping, and thematic analysis. Based on these findings, we furthermore developed a research agenda that aims to serve as a foundation for future researchers.