Molecular Bio-Computation & Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.
Molecules. 2020 Sep 16;25(18):4239. doi: 10.3390/molecules25184239.
Covalent inhibition has recently gained a resurgence of interest in several drug discovery areas. The expansion of this approach is based on evidence elucidating the selectivity and potency of covalent inhibitors when bound to particular amino acids of a biological target. The unexpected covalent inhibition of heat shock protein 72 (HSP72) by covalently targeting Lys-56 instead of Cys-17 was an interesting observation. However, the structural basis and conformational changes associated with this preferential coupling to Lys-56 over Cys-17 remain unclear. To resolve this mystery, we employed structural and dynamic analyses to investigate the structural basis and conformational dynamics associated with the unexpected covalent inhibition. Our analyses reveal that the coupling of the irreversible inhibitor to Lys-56 is intrinsically less dynamic than Cys-17. Conformational dynamics analyses further reveal that the coupling of the inhibitor to Lys-56 induced a closed conformation of the nucleotide-binding subdomain (NBD) α-helices, in contrast, an open conformation was observed in the case of Cys-17. The closed conformation maintained the crucial salt-bridge between Glu-268 and Lys-56 residues, which strengthens the interaction affinity of the inhibitor nearly identical to adenosine triphosphate (ADP/Pi) bound to the HSP72-NBD. The outcome of this report provides a substantial shift in the conventional direction for the design of more potent covalent inhibitors.
共价抑制作用在几个药物发现领域最近重新引起了人们的兴趣。这种方法的扩展是基于这样的证据：当共价抑制剂结合到生物靶标的特定氨基酸时，其选择性和效力。出乎意料的是，热休克蛋白 72（HSP72）通过共价靶向 Lys-56 而不是 Cys-17 而被共价抑制，这是一个有趣的观察结果。然而，与这种优先与 Lys-56 而不是 Cys-17 偶联相关的结构基础和构象变化尚不清楚。为了解决这个谜团，我们采用结构和动态分析来研究与这种出乎意料的共价抑制相关的结构基础和构象动力学。我们的分析表明，不可逆抑制剂与 Lys-56 的偶联本质上比 Cys-17 的偶联不那么动态。构象动力学分析进一步表明，抑制剂与 Lys-56 的偶联诱导核苷酸结合亚基（NBD）α-螺旋的闭合构象，而在 Cys-17 的情况下观察到开放构象。闭合构象保持了 Glu-268 和 Lys-56 残基之间的关键盐桥，这增强了抑制剂的相互作用亲和力，几乎与 HSP72-NBD 结合的三磷酸腺苷（ADP/Pi）相同。本报告的结果为更有效的共价抑制剂的设计提供了一个实质性的转变，偏离了传统的方向。
