Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
Nature. 2023 Apr;616(7958):673-685. doi: 10.1038/s41586-023-05905-z. Epub 2023 Apr 26.
Computer-aided drug discovery has been around for decades, although the past few years have seen a tectonic shift towards embracing computational technologies in both academia and pharma. This shift is largely defined by the flood of data on ligand properties and binding to therapeutic targets and their 3D structures, abundant computing capacities and the advent of on-demand virtual libraries of drug-like small molecules in their billions. Taking full advantage of these resources requires fast computational methods for effective ligand screening. This includes structure-based virtual screening of gigascale chemical spaces, further facilitated by fast iterative screening approaches. Highly synergistic are developments in deep learning predictions of ligand properties and target activities in lieu of receptor structure. Here we review recent advances in ligand discovery technologies, their potential for reshaping the whole process of drug discovery and development, as well as the challenges they encounter. We also discuss how the rapid identification of highly diverse, potent, target-selective and drug-like ligands to protein targets can democratize the drug discovery process, presenting new opportunities for the cost-effective development of safer and more effective small-molecule treatments.
计算机辅助药物发现已经存在了几十年,尽管在过去的几年里,学术界和制药业都在大力采用计算技术。这种转变主要是由大量关于配体性质及其与治疗靶点及其 3D 结构结合的数据、丰富的计算能力以及数十亿类似药物的小分子按需虚拟库的出现所定义的。要充分利用这些资源,就需要快速的计算方法来进行有效的配体筛选。这包括基于结构的大规模化学空间虚拟筛选,快速迭代筛选方法进一步促进了这一过程。在没有受体结构的情况下,深度学习对配体性质和靶标活性的预测也有很高的协同作用。本文综述了配体发现技术的最新进展,以及它们在重塑药物发现和开发全过程方面的潜力,以及它们所面临的挑战。我们还讨论了如何快速识别对蛋白质靶标具有高度多样性、效力高、选择性和类药性的配体,从而使药物发现过程民主化,为更安全、更有效的小分子治疗的经济有效开发带来新的机遇。