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蛋白质共价修饰建模工具全景:计算共价药物发现综述。

Landscape of Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery.

机构信息

Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States.

Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States.

出版信息

J Phys Chem B. 2023 Nov 16;127(45):9663-9684. doi: 10.1021/acs.jpcb.3c04710. Epub 2023 Nov 3.

Abstract

Covalent drug discovery has been a challenging research area given the struggle of finding a sweet balance between selectivity and reactivity for these drugs, the lack of which often leads to off-target activities and hence undesirable side effects. However, there has been a resurgence in covalent drug design following the success of several covalent drugs such as boceprevir (2011), ibrutinib (2013), neratinib (2017), dacomitinib (2018), zanubrutinib (2019), and many others. Design of covalent drugs includes many crucial factors, where "evaluation of the binding affinity" and "a detailed mechanistic understanding on covalent inhibition" are at the top of the list. Well-defined experimental techniques are available to elucidate these factors; however, often they are expensive and/or time-consuming and hence not suitable for high throughput screens. Recent developments in methods provide promise in this direction. In this report, we review a set of recent publications that focused on developing and/or implementing novel techniques in "Computational Covalent Drug Discovery (CCDD)". We also discuss the advantages and disadvantages of these approaches along with what improvements are required to make it a great tool in medicinal chemistry in the near future.

摘要

共价药物发现一直是一个具有挑战性的研究领域,因为在这些药物的选择性和反应性之间找到一个理想的平衡非常困难,而缺乏这种平衡往往会导致非靶标活性,从而产生不理想的副作用。然而,随着几种共价药物的成功,如博赛替尼(2011 年)、依鲁替尼(2013 年)、奈拉替尼(2017 年)、达可替尼(2018 年)、泽布替尼(2019 年)和许多其他药物的成功,共价药物设计又重新兴起。共价药物的设计包括许多关键因素,其中“结合亲和力的评估”和“对共价抑制的详细机制理解”是最重要的因素。有许多明确的实验技术可以阐明这些因素;然而,它们通常昂贵且/或耗时,因此不适合高通量筛选。方法的最新发展在这方面提供了希望。在本报告中,我们回顾了一组最近的出版物,这些出版物集中在开发和/或实施“计算共价药物发现(CCDD)”中的新方法。我们还讨论了这些方法的优缺点,以及在不久的将来使其成为药物化学中一个很好的工具需要进行哪些改进。

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