Tingjun Hou

Precision Design of Fluorogenic Probes via Orthogonal Tuning of Binding and Photophysics for Isoform-Selective ALDH2 Imaging.

Fluorogenic probes that report enzyme activity are essential for studying biological functions. However, designing them for targets with low catalytic turnover and narrow substrate specificity remains a significant challenge. Here, we present a precision design framework that separates the requirements for sensitivity and selectivity by integrating molecular docking, quantum chemical modeling of fluorogenic mechanisms, and targeted fine-tuning of the probe structures. As a proof of concept, we developed A5, a fluorogenic substrate for aldehyde dehydrogenase 2 (ALDH2) that exhibits high isoform selectivity and a >240-fold signal enhancement over the standard NADH assay. A5 enables quantitative imaging of ALDH2 activity across multiple biological scales─in blood samples, live cells, and intact mouse brains─and supports the identification of small-molecule activators with therapeutic potential in an Alzheimer's disease model. This work establishes a modular strategy for creating activity-based probes tailored to challenging enzymatic targets, with broad applications in precision imaging, drug discovery, and mechanistic biochemistry.

LumiCharge: Spherical Harmonic Convolutional Networks for Atomic Charge Prediction in Drug Discovery.

Atomic charge is crucial in drug design for analyzing reactive sites and interactions between ligands and targets. While quantum mechanical methods offer high accuracy, they are generally computationally costly. Conversely, empirical approaches, while computationally efficient, frequently suffer from lack of precision and generalizability. Recent a number of machine learning-based models have been developed for atomic charge predictions, but they struggle with accurately representing molecular structures and capturing the chemical environments affecting atomic charges, thus limiting their generalization and accuracy. To overcome these limitations, we propose LumiCharge, a novel atomic charge prediction framework that incorporates high-order spherical harmonics convolutions and explicitly models multibody interactions. In constructing this model, we employ a strategy that integrates both high- and low-order information, enhancing its geometric spatial perception capability, which is currently underexplored in the field. Benchmark evaluations demonstrate that LumiCharge outperforms state-of-the-art (SOTA) models by 30%-60% across diverse data sets. Additionally, in cross-scale experiments, LumiCharge demonstrates exceptional extrapolation capability and robustness across molecules of varying sizes, effectively overcoming the limitations imposed by molecular sizes. On an external halogen-containing test set, LumiCharge achieves an RMSE of 0.055e, meeting practical application requirements. Finally, a case study of virtual screening for the androgen receptor (AR) target further validates its outstanding accuracy compared to the OPLS3e force field and other deep learning (DL)-based baseline models, highlighting its exceptional generalization capacity and practical utility in real-world scenarios.

Unraveling the Efficacy of AR Antagonists Bearing N-(4-(Benzyloxy)phenyl)piperidine-1-sulfonamide Scaffold in Prostate Cancer Therapy by Targeting LBP Mutations.

Point mutations in the androgen receptor (AR) are significant drivers of resistance in prostate cancer (PCa), posing a great challenge to the development of effective treatment strategies. Building on our previous discovery of the suboptimal AR antagonist T1-12, we developed LT16, which contains an N-(4-(benzyloxy)phenyl)piperidine-1-sulfonamide scaffold through structural optimization and comprehensive screening against T878A-mutated AR. LT16 outperformed existing antiandrogens by fully antagonizing clinical AR mutations and effectively suppressing castration- and enzalutamide-resistant LNCaP cells proliferation in vitro. Mechanically, LT16 was found to disrupt AR nuclear translocation, hinder AR homodimerization, and suppress transcription of AR-regulated genes by competitive binding to the ligand binding pocket. Further in vivo experiments demonstrated that LT16 significantly reduced both regular- and enzalutamide-resistant LNCaP tumor volume and serum prostate-specific antigen levels in mice. These findings position LT16 as a promising and innovative therapeutic for advanced PCa, particularly in cases where resistance to current therapies is a concern.

PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide-Protein Interaction Prediction

Accurate prediction of the peptide-protein interaction (PepPI) is crucial for developing peptide-based therapeutics and vaccines. However, this computational task has traditionally faced significant challenges, such as the scarcity of structure data along with the corresponding label of the binding affinity for bound complexes. To address these challenges, we introduce PepBAN, a deep learning framework for modeling PepPI predictions. PepBAN incorporates two technical advancements: (1) adopting the protein language model ESM-2 to characterize proteins and ESM-2 or a graph-based foundation model for peptides without structure data and (2) leveraging the conditional domain adversarial learning to enhance generalization across a broad range of protein targets, especially when there are limited binding data. At the core of PepBAN is a bilinear attention network (BAN) that effectively learns the pattern of pairwise local interactions, enables the identification of key residues participating in the peptide-protein interactions, and offers an intuitive approach to interpret the underlying mechanisms of PepPIs via analyzing attention weights. Our numerical experiments demonstrated that PepBAN outperformed the previous state-of-the-art models across several well-established benchmark studies. Furthermore, we evaluated PepBAN's applicability in predicting cyclic peptide-protein interactions, a task that poses significant challenges due to the presence of noncanonical amino acids. These nonstandard residues require specialized handling, which most existing sequence-based PepPI prediction models did not adequately address, and we adopt an atom-resolved molecular graph approach to process cyclic peptides. Despite this complexity, PepBAN demonstrated a clear advantage by achieving a superior prediction performance and offering a distinct edge in tackling the emerging chemical space of cyclic peptides, which has great potential for novel therapeutic development. In summary, PepBAN serves as a valuable tool for advancing peptide-based drug and therapeutic development.

Discovery of N-(thiazol-2-yl) Furanamide Derivatives as Potent Orally Efficacious AR Antagonists with Low BBB Permeability.

Resistance-conferring mutations in the androgen receptor (AR) ligand-binding pocket (LBP) compromise the effectiveness of clinically approved orthosteric AR antagonists. Targeting the dimerization interface pocket (DIP) of AR presents a promising therapeutic approach. In this study, we report the design and optimization of N-(thiazol-2-yl) furanamide derivatives as novel AR DIP antagonists, among which C13 was the most promising candidate. C13 exhibited excellent AR antagonistic activity (IC50 = 0.010 μM), effectively blocked AR dimerization and nuclear translocation, and demonstrated potent efficacy in several castration-resistant prostate cancer (CRPC) cells. Notably, C13 showed superior efficacy against variant drug-resistant AR mutants, along with favorable metabolic stability, excellent pharmacokinetic properties, and low brain distribution. Furthermore, oral administration of C13 achieved 123.4% tumor growth inhibition in an LNCaP xenograft model without apparent toxicity. As a noncompetitive binder, C13 complements current LBP-targeting AR inhibitors and represents a promising therapy for drug-resistant PCa.

SynGFN: learning across chemical space with generative flow-based molecular discovery

Accelerating Covalent Drug Discovery: Recent Advances in Covalent Docking Tools

Covalent inhibitors have garnered renewed attention in recent years, with their rational design becoming increasingly critical in drug discovery. Among the technologies facilitating the discovery of covalent inhibitors, covalent docking has emerged as a pivotal tool in various stages of drug development including virtual screening, lead optimization, and mechanistic studies. Since its inception as an extension of conventional docking methods in the early 2000s, covalent docking tools have undergone substantial advancements. This review provides a comprehensive overview of covalent docking algorithms, systematically categorizing their approaches according to covalent bond formation, which primarily include tethered docking, biased docking, and dynamic covalent docking approaches. A comparative analysis of current covalent docking tools is provided, alongside a critical discussion of remaining challenges. Special emphasis is placed on the growing impact of artificial intelligence (AI) in shaping novel methodologies and expanding the capabilities of covalent docking. Finally, we discuss prospects for advancing covalent docking methodologies and their applications in drug discovery.

Allosteric Cooperativity Mechanism Investigation of Orthosteric and Allosteric Ligands in Modulating AR Activity: A Molecular Dynamics Study

The androgen receptor (AR) represents a pivotal therapeutic target for prostate cancer. However, existing orthosteric ligand-binding pocket (LBP) antagonists [e.g., enzalutamide (ENZ)] encounter significant obstacles due to resistance-conferring mutations in the LBP. Allosteric antagonists targeting the BF3 site exhibit great potential in overcoming such resistance but have low inhibitory efficacy. In our study, we employed an integrated computational modeling strategy, including Gaussian-accelerated molecular dynamics (GaMD), MM/GBSA free-energy calculations, and elastic network model (ENM)-based signaling communication pathway analyses. This approach is used to probe the cooperativity of allosteric BF3 antagonists [e.g., VPC-13808 (VPC)] with diverse orthosteric LBP ligands [e.g., ENZ and testosterone (TES)] in suppressing AR activity. Herein, four types of AR systems were examined: AR bound to LBP agonist (AR·TES), LBP antagonists (e.g., AR·ENZ), and combinations of LBP agonist/antagonist with BF3 antagonist (e.g., AR·TES·VPC and AR·ENZ·VPC). Results indicate that BF3 antagonists can synergize with the LBP antagonist to amplify conformational flexibility in H12 and induce anticorrelated dynamics of H12 with H3 and H4. This induces the downward movement of H12 and its displacement away from H3/H4, triggering the wide opening of the AF2 binding cleft and substantially reducing the coactivator recruitment. Furthermore, the BF3 antagonist can interact with specific residues (e.g., F673, F826, L830, and Y834) and cooperate with the LBP agonist or antagonist to allosterically perturb the AF2 conformation. Multiple short- and/or long-range BF3→AF2 and LBP→AF2 signaling transition pathways are involved, such as F673→Y834→L722→L812→L744→V746→L873→ENZ→L880/V889/V891. These mechanistic insights establish the foundation for developing novel AR BF3 antagonist and LBP-BF3 combination therapies, suggesting a promising avenue for enhancing the efficacy and overcoming the resistance in castration-resistant prostate cancer treatment.

ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction

Atomic charge is a fundamental quantum chemical property essential for advancing drug design and discovery. Although quantum mechanics (QM) methods offer the highest level of accuracy, their computational demands scale quadratically with the number of atoms, limiting their practicality for large-scale applications. In light of this, empirical and semiempirical methods have been introduced to improve computational efficiency, albeit often at the expense of accuracy. The advent of artificial intelligence has witnessed a growing application of machine learning (ML) techniques to accelerate atomic charge predictions. However, existing ML models often suffer from low accuracy and limited generalization capabilities. To address these challenges, we introduce an advanced equivariant graph attention neural network specifically engineered to model long-range atomic electrostatic interactions with high precision. This model introduces a sophisticated global graph attention mechanism, enabling it to capture charge contributions across multiple scales. By utilizing a combination of structural symmetry-preserving transformations and multiscale attention, our approach not only preserves the inherent symmetries of molecular structures but also substantially improves the model's accuracy, generalization, and robustness in complex scenarios. Our empirical analyses demonstrate that, compared to leading baseline models, the proposed model improves charge prediction accuracy by over 40% on average across various charge-calculation schemes. Remarkably, the model achieves superior performance on the external RESP (restrained electrostatic potential) test data sets, with a 54.6% improvement over the baseline. Additionally, we evaluated our charge model under the setting of virtual screening, where it outperforms both the OPLS3 charges and baseline deep learning models across all evaluation metrics, highlighting its extensive potential for scientific discovery.

PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction

Accurate modeling of protein-peptide interactions is essential for understanding fundamental biological processes and designing peptide-based drugs. However, predicting the complex structures of these interactions remains challenging, primarily due to the high conformational flexibility of peptides. To support a fair and systematic evaluation of recent deep learning (DL) approaches, we introduce PepPCBench, a benchmarking framework tailored to assess protein folding neural networks (PFNNs) in protein-peptide complex prediction. As part of this framework, we curated PepPCSet, a data set of 261 experimentally resolved complexes with peptides ranging from 5 to 30 residues. We benchmark five full-atom PFNNs, including AlphaFold3 (AF3), AlphaFold-Multimer (AFM), Chai-1, HelixFold3 (HF3), and RoseTTAFold-All-Atom (RFAA), using comprehensive evaluation metrics. Our benchmarking reveals meaningful performance differences among these methods and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy. While AF3 shows strong performance in structure prediction, further analysis indicates that confidence metrics correlate poorly with experimental binding affinities, underscoring the need for improved scoring strategies and generalizability. By providing a reproducible and extensible framework, PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction.

CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening

The interest in covalent drugs has resurged in recent decades, spurring the development of numerous specialized computational docking tools to facilitate covalent ligand design and screening. Herein, we present CarsiDock-Cov, a new paradigm distinguishing itself as the first deep learning (DL)-guided approach for covalent docking. CarsiDock-Cov retains the core components of its non-covalent predecessor, leveraging a DL model pretrained on millions of docking complexes to predict protein–ligand distance matrices, along with a dedicated-designed geometric optimization procedure to convert these distances into refined binding poses. Additionally, it incorporates several key enhancements specifically tailored to optimize the protocol for covalent docking applications. Our approach has been extensively validated on multiple public datasets regarding the docking and screening of covalent ligands, and the results indicate that our approach not only achieves comparably improved applicability compared to its non-covalent predecessor, but also exhibits competitive performance against various state-of-the-art covalent docking tools. Collectively, our approach represents a significant advance in covalent docking methodology, offering an automated and efficient solution that shows considerable promise for accelerating covalent drug discovery and design.

EpiMII: Integrating Structure and Graph Neural Networks for MHC-II Epitope and Neoantigen Design

MHC-II neoantigens play a critical role in immunotherapy, either as direct effectors or through their influence on CD8+ T cells. However, only a small fraction of tumor DNA mutations qualify as functional neoantigens, and current prediction tools often lack accuracy, leading to the low immunogenicity of predicted neoantigens in vivo. Here, we present EpiMII, a Graph Neural Network model for MHC-II epitope design, which learns from the structural features of epitopes to predict their sequences. To train EpiMII, we constructed a reliable, large dataset containing 142,934 MHC-II epitope structures. This approach achieves a 4.2x improvement over ProteinMPNN, with a sequence recovery rate of 78.0% for known MHC-II epitopes in the Protein Data Bank. As a case study, we designed a neoantigen from hepatocellular carcinoma. All five designed epitopes significantly activated CD4+ T cells in vitro and induced secretion of IFN-γ and TNF-α. Notably, one epitope treatment significantly reduced tumor volume in mice in vivo. EpiMII offers a novel and efficient approach for identifying MHC-II epitopes/neoantigens, potentially contributing to vaccine development.