Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630003, India.
Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, 600006, India.
J Comput Aided Mol Des. 2022 Jun;36(6):459-482. doi: 10.1007/s10822-022-00459-0. Epub 2022 Jun 2.
LIMK2 inhibitors are one of the potential therapeutic modalities for treating various diseases. In the current scenario, there is a paucity of effective LIMK inhibitors that are highly specific with minimal off-target effects. To date, the conformational transitions of LIMK2 from DFGαC (CIDI) (active) to DFGαC (CODO) (inactive) states are yet to be probed and are essential for capturing the unique, druggable conformations. Therefore, this study was intended to capture the diverse conformational states of LIMK2 for accelerating the rational identification of conformation specific inhibitors through high-end structural bioinformatics protocols. Hence, in this study, molecular modelling followed by an extensive microsecond timescale of molecular dynamics simulation was performed encompassing perturbation response scanning, metapath, and community analysis towards the conformational sampling of LIMK2. Overall this study precisely identifies the conformational ensemble of LIMK2 the intermediate inactive states namely, CIDO, CinterDinter, CIDinter, CinterDI, CinterDO, CODI, CODinter apart from CIDI and CODO. This also facilitated observing that β8 preceding XDFG, αC (F373, L374), and αD (L413) as the major effectors that may facilitate the regulation of varying conformational transitions among the states. Additionally, the conserved β sheets and the loops namely, C.l, b.l, and G/P.loop were observed to be involved in the metapath for allosteric communication among the intermediates with CIDI and CODO state. Moreover, only the CODO state was observed to have closed type A.l, while the CIDI and other intermediate states except for CIDO were observed to have open-DFG out type A.l, thereby enabling the binding of substrate. Apart from these, the druggable site analysis inferred that the CIDI and CODO states harbor prominent druggable sites spanning the conserved N-lobe, while the intermediates were observed to have unraveled allosteric druggable sites distal from the ATP binding site, majorly spanning the C-lobe of LIMK2. Thus, this study provides potential insights into the intermediate conformational druggable states of LIMK2 and also the druggable conformations, especially the inactive states of LIMK2, as a specific therapeutic targeting mode. Thus, providing a widened avenue to ponder the allosteric sites or the isoform selectivity conformations for targeting LIMK2 in various disease conditions.
LIMK2 抑制剂是治疗各种疾病的潜在治疗方法之一。在当前情况下，缺乏高度特异性且脱靶效应最小的有效 LIMK 抑制剂。迄今为止，LIMK2 从 DFGαC（CIDI）（活性）到 DFGαC（CODO）（非活性）状态的构象转变尚未被探测到，对于捕获独特的、可成药构象至关重要。因此，本研究旨在捕获 LIMK2 的多种构象状态，通过高端结构生物信息学协议加速对构象特异性抑制剂的合理识别。因此，在这项研究中，进行了分子建模，然后进行了广泛的微秒时间尺度的分子动力学模拟，包括扰动响应扫描、元路径和社区分析，以对 LIMK2 的构象进行采样。总的来说，这项研究精确地确定了 LIMK2 的构象集合，包括中间非活性状态，即 CIDO、CinterDinter、CIDinter、CinterDI、CinterDO、CODI 和 CODinter，除了 CIDI 和 CODO。这也有助于观察到，β8 先于 XDFG、αC（F373、L374）和 αD（L413）作为主要效应物，可能促进状态之间的不同构象转变的调节。此外，还观察到保守的β 片层和环，即 C.l、b.l 和 G/P.loop，参与了中间状态与 CIDI 和 CODO 状态之间的变构通讯的元路径。此外，仅观察到 CODO 状态具有封闭的 A.l 型，而 CIDI 和其他中间状态（除了 CIDO）具有开放的 DFG 外 A.l 型，从而能够结合底物。除此之外，可成药性分析推断，CIDI 和 CODO 状态具有跨越保守 N 结构域的突出可成药性位点，而中间状态则具有从 ATP 结合位点解开的变构可成药性位点，主要跨越 LIMK2 的 C 结构域。因此，这项研究为 LIMK2 的中间构象可成药性状态以及可成药性构象（特别是 LIMK2 的非活性状态）提供了潜在的见解，作为一种特定的治疗靶向模式。因此，为在各种疾病情况下靶向 LIMK2 的变构位点或同工型选择性构象提供了更广泛的途径。
