Hemavathy Nagarajan, Ranganathan Sampathkumar, Umashankar Vetrivel, Jeyakanthan Jeyaraman
Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
Centre for Bioinformatics, KBIRVO, Vision Research Foundation, Chennai, India.
Cell Biochem Biophys. 2025 Mar 18. doi: 10.1007/s12013-025-01718-1.
LIM Kinases (LIMKs) have emerged as critical therapeutic targets in cancer research due to their central role in regulating cytoskeletal dynamics and cell motility via cofilin phosphorylation. Allosteric inhibitors, which bind outside the ATP-binding pocket, offer distinct advantages over ATP-competitive inhibitors, such as increased specificity, reduced off-target effects, and the ability to overcome resistance. This study investigates a series of novel tetrapeptides mimicking the binding mode of TH470, an allosteric LIMK inhibitor, using in silico docking and molecular dynamics simulations to identify potential lead compounds with high specificity, binding affinity, and favorable pharmacokinetic properties. Structural analyses revealed critical interactions between TH470 and LIMKs, particularly with conserved residues such as Thr405 (gatekeeper residue), Ile408 (hinge region), and Asp469 (XDFG motif), which are essential for stabilizing inhibitor binding. Molecular dynamics simulations confirmed the stability of TH470-LIMK1 and TH470-LIMK2 complexes, with lower RMS deviations and robust interaction patterns enhancing binding affinity. From the set of tetrapeptides mimicking TH470 binding mode, only YFYW, WPHW, and YWFP for LIMK1, and PYWG, FYWV, and WFVW for LIMK2 demonstrated high binding affinities, non-toxic profiles, and promising anti-cancer, anti-angiogenic, and anti-inflammatory properties. Among the studied peptides, LIMK1-YFYW and LIMK2-WFVW exhibited the most substantial binding affinities, supported by high hydrogen bond occupancy with key residues such as Ile416 and Thr405. The findings highlight the therapeutic potential of allosteric peptide inhibitors targeting LIMK-mediated pathways in cancer progression. The study underscores the importance of specific interactions with conserved LIMK residues, providing a foundation for further developing selective inhibitors to modulate actin dynamics and combat cancer-related processes.
LIM激酶（LIMKs）已成为癌症研究中的关键治疗靶点，因为它们在通过抑制丝切蛋白磷酸化来调节细胞骨架动力学和细胞运动中起着核心作用。与ATP竞争性抑制剂相比，结合在ATP结合口袋之外的变构抑制剂具有明显优势，如特异性增强、脱靶效应降低以及克服耐药性的能力。本研究使用计算机对接和分子动力学模拟，研究了一系列模拟变构LIMK抑制剂TH470结合模式的新型四肽，以鉴定具有高特异性、结合亲和力和良好药代动力学特性的潜在先导化合物。结构分析揭示了TH470与LIMKs之间的关键相互作用，特别是与保守残基如Thr405（守门残基）、Ile408（铰链区）和Asp469（XDFG基序）之间的相互作用，这些对于稳定抑制剂结合至关重要。分子动力学模拟证实了TH470-LIMK1和TH470-LIMK2复合物的稳定性，较低的均方根偏差和强大的相互作用模式增强了结合亲和力。在模拟TH470结合模式的四肽组中，只有针对LIMK1的YFYW、WPHW和YWFP，以及针对LIMK2的PYWG、FYWV和WFVW表现出高结合亲和力、无毒特性以及有前景的抗癌、抗血管生成和抗炎特性。在所研究的肽中，LIMK1-YFYW和LIMK2-WFVW表现出最强的结合亲和力，与Ile416和Thr405等关键残基的高氢键占有率支持了这一点。这些发现突出了靶向LIMK介导的癌症进展途径的变构肽抑制剂的治疗潜力。该研究强调了与保守的LIMK残基进行特异性相互作用的重要性，为进一步开发调节肌动蛋白动力学和对抗癌症相关过程的选择性抑制剂奠定了基础。
