GPCRSPACE: A New GPCR Real Expanded Library Based on Large Language Models Architecture and Positive Sample Machine Learning Strategies.

The quest for novel therapeutics targeting G protein-coupled receptors (GPCRs), essential in numerous physiological processes, is crucial in drug discovery. Despite the abundance of GPCR-targeting drugs, many receptors lack selective modulators, indicating a significant untapped therapeutic potential. To bridge this gap, we introduce GPCRSPACE, a novel GPCR-focused purchasable real chemical library developed using the G protein-coupled receptors large language models (GPCR LLM) architecture.

Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining.

Accurate prediction of molecular properties is fundamental in drug discovery and development, providing crucial guidance for effective drug design. A critical factor in achieving accurate molecular property prediction lies in the appropriate representation of molecular structures. Presently, prevalent deep learning-based molecular representations rely on 2D structure information as the primary molecular representation, often overlooking essential three-dimensional (3D) conformational information due to the inherent limitations of 2D structures in conveying atomic spatial relationships.

MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules.

Artificial intelligence (AI)-based molecular design methods, especially deep generative models for generating novel molecule structures, have gratified our imagination to explore unknown chemical space without relying on brute-force exploration. However, whether designed by AI or human experts, the molecules need to be accessibly synthesized and biologically evaluated, and the trial-and-error process remains a resources-intensive endeavor. Therefore, AI-based drug design methods face a major challenge of how to prioritize the molecular structures with potential for subsequent drug development.

Graph neural network approaches for drug-target interactions.

Developing new drugs remains prohibitively expensive, time-consuming, and often involves safety issues. Accurate prediction of drug-target interactions (DTIs) can guide the drug discovery process and thus facilitate drug development. Non-Euclidian data such as drug-like molecule structures, key pocket residue structures, and protein interaction networks can be represented effectively using graphs.

Drug target inference by mining transcriptional data using a novel graph convolutional network framework.

A fundamental challenge that arises in biomedicine is the need to characterize compounds in a relevant cellular context in order to reveal potential on-target or off-target effects. Recently, the fast accumulation of gene transcriptional profiling data provides us an unprecedented opportunity to explore the protein targets of chemical compounds from the perspective of cell transcriptomics and RNA biology. Here, we propose a novel Siamese spectral-based graph convolutional network (SSGCN) model for inferring the protein targets of chemical compounds from gene transcriptional profiles.

Multi-instance learning of graph neural networks for aqueous pKa prediction.

Motivation: The acid dissociation constant (pKa) is a critical parameter to reflect the ionization ability of chemical compounds and is widely applied in a variety of industries. However, the experimental determination of pKa is intricate and time-consuming, especially for the exact determination of micro-pKa information at the atomic level. Hence, a fast and accurate prediction of pKa values of chemical compounds is of broad interest.

Regulating Glucose Metabolism with Prodrug Nanoparticles for Promoting Photoimmunotherapy of Pancreatic Cancer.

The low immunogenicity, insufficient infiltration of T lymphocytes, and dismal response to immune checkpoint blockade therapy pose major difficulties in immunotherapy of pancreatic cancer. Photoimmunotherapy by photodynamic therapy (PDT) can induce an antitumor immune response by triggering immunogenic cell death in the tumor cells. Notwithstanding, PDT-driven oxygen consumption and microvascular damage can further aggravate hypoxia to exaggerates glycolysis, leading to lactate accumulation and immunosuppressive tumor microenvironment.

TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments.

Motivation: Identifying compound-protein interaction (CPI) is a crucial task in drug discovery and chemogenomics studies, and proteins without three-dimensional structure account for a large part of potential biological targets, which requires developing methods using only protein sequence information to predict CPI. However, sequence-based CPI models may face some specific pitfalls, including using inappropriate datasets, hidden ligand bias and splitting datasets inappropriately, resulting in overestimation of their prediction performance.

Results: To address these issues, we here constructed new datasets specific for CPI prediction, proposed a novel transformer neural network named TransformerCPI, and introduced a more rigorous label reversal experiment to test whether a model learns true interaction features.

Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism.

Hunting for chemicals with favorable pharmacological, toxicological, and pharmacokinetic properties remains a formidable challenge for drug discovery. Deep learning provides us with powerful tools to build predictive models that are appropriate for the rising amounts of data, but the gap between what these neural networks learn and what human beings can comprehend is growing. Moreover, this gap may induce distrust and restrict deep learning applications in practice.

Deep Learning Enhancing Kinome-Wide Polypharmacology Profiling: Model Construction and Experiment Validation.

The kinome-wide virtual profiling of small molecules with high-dimensional structure-activity data is a challenging task in drug discovery. Here, we present a virtual profiling model against a panel of 391 kinases based on large-scale bioactivity data and the multitask deep neural network algorithm. The obtained model yields excellent internal prediction capability with an auROC of 0.

KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules.

Motivation: The large-scale kinome-wide virtual profiling for small molecules is a daunting task by experimental and traditional in silico drug design approaches. Recent advances in deep learning algorithms have brought about new opportunities in promoting this process.

Results: KinomeX is an online platform to predict kinome-wide polypharmacology effect of small molecules based solely on their chemical structures.

Artificial intelligence in drug design.

Thanks to the fast improvement of the computing power and the rapid development of the computational chemistry and biology, the computer-aided drug design techniques have been successfully applied in almost every stage of the drug discovery and development pipeline to speed up the process of research and reduce the cost and risk related to preclinical and clinical trials. Owing to the development of machine learning theory and the accumulation of pharmacological data, the artificial intelligence (AI) technology, as a powerful data mining tool, has cut a figure in various fields of the drug design, such as virtual screening, activity scoring, quantitative structure-activity relationship (QSAR) analysis, de novo drug design, and in silico evaluation of absorption, distribution, metabolism, excretion and toxicity (ADME/T) properties. Although it is still challenging to provide a physical explanation of the AI-based models, it indeed has been acting as a great power to help manipulating the drug discovery through the versatile frameworks.