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.
Shi Li, Hongyan Du, Hui Zhang et al.· WIREs Computational Molecula...· 2 citations
Accurate prediction of metalloprotein-ligand interactions is critical for metalloprotein-targeted drug discovery. Conventional docking tools and existing deep learning (DL) models fail to reliably capture metal-ligand interactions, hampering the discovery of potent metalloprotein inhibitors. Here, we propose MetalloDock, the first DL-based docking framework specially designed for metalloprotein targets. By innovatively integrating an autoregressive spatial decoding engine with a physics-constrained geometric generation paradigm, MetalloDock can precisely reconstruct metal coordination geometries and accurately capture metal-ligand interactions, which enhance both the accuracy of metalloprotein-ligand docking and binding affinity prediction. Extensive evaluations on our custom-built benchmark data set demonstrate that MetalloDock outperforms existing methods, including AlphaFold3, in docking success rate and virtual screening performance for metalloprotein targets. In real-world applications, MetalloDock successfully identified multiple novel hit compounds in a virtual screening campaign targeting the prostate-specific membrane antigen. Additionally, it enabled rational drug design for acidic polymerase endonuclease, leading to the discovery of potent inhibitors. These results highlight the broad applicability of MetalloDock in accelerating metalloprotein-targeted drug discovery and provide a standardized framework for future evaluation of metalloprotein-specific docking algorithms.
Hui Zhang, Xujun Zhang, Qun Su et al.· Journal of the American Chem...· 5 citations
ConspectusThe field of covalent drug discovery has witnessed a remarkable resurgence in recent years, a trend underscored by the approval of more than 125 covalent drugs by the US FDA as of 2025, which demonstrates their immense therapeutic potential. Driven by ever-increasing computational power and vast amounts of data, deep learning (DL) is profoundly transforming numerous fields, from natural language processing to drug discovery. In the development of covalent drugs, in particular, advanced computational methods centered on data-driven approaches and artificial intelligence (AI) exhibit immense potential. The realization of this potential depends on the construction of a synergistic ecosystem. Here, we define this "ecosystem" as an integrated set of components─including (i) curated covalent-relevant databases, (ii) AI/physics-based predictive and scoring models, (iii) interoperable computational workflows spanning site identification, docking/virtual screening, and lead optimization, and (iv) closed-loop feedback that systematically incorporates experimental outcomes to update data resources and refine/validate models. This begins with the systematic collection of past experimental results to build high-quality databases. These databases, in turn, provide the foundation for developing AI-driven computational tools capable of precisely interfacing with and accelerating downstream tasks, such as molecular docking (for generating physically plausible conformations and conducting large-scale virtual screening) and lead optimization. The application of these AI tools not only guides experimental design, but the resulting key data also feed back into and enrich the databases. Furthermore, in the cutting-edge field of covalent drugs, the precise identification of "druggable" covalent sites on target proteins has emerged as another critically important downstream task.In this Account, we describe a computational and AI-driven ecosystem for structure-based covalent drug discovery and highlight our contributions to this field. By explicitly linking databases, models, workflows, and experimental feedback into a single framework, this Account moves beyond a simple inventory of individual tools to instead offer a systematic and panoramic perspective on an integrated ecosystem for covalent drug discovery, driven by data and computational engines including AI. We focus on how this ecosystem systematically addresses the challenges from covalent binding site identification to lead discovery, thereby fundamentally accelerating the development of next-generation covalent therapies. We first articulate the philosophy behind the construction and updating of covalent databases, emphasizing the necessity of high-quality data. Subsequently, we delve into a suite of cutting-edge, AI-driven computational methods, exploring the potential of deep learning in tasks such as molecular docking, covalent binding site prediction, and lead optimization. To bridge the gap between computational theory and experimental validation, we will use the discovery of potent covalent CRM1 inhibitors as a specific case study, detailing how our customized, structure-based virtual screening pipeline was utilized to achieve a seamless workflow from computational prediction to biological validation. This section is intended to offer actionable guidance for experimental researchers seeking to leverage these powerful computational tools. Finally, we highlight the limitations and potential pitfalls of this AI engine─concerns that are equally relevant when developing AI-driven covalent docking algorithms. Building on our group's recent benchmarking of AI docking methods, we objectively evaluate current performance and discuss how transformative advances such as AlphaFold3 may reshape the field.
Shi Li, Hongyan Du, Xujun Zhang et al.· Accounts of Chemical Researc...· 4 citations