Naz Farha, Shahbaaz Mohd, Khan Shama, Bisetty Krishna, Islam Asimul, Ahmad Faizan, Hassan Md Imtaiyaz
Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
Department of Chemistry, Durban University of Technology, Durban 4000, South Africa.
J Mol Graph Model. 2015 Nov;62:245-252. doi: 10.1016/j.jmgm.2015.10.009. Epub 2015 Oct 21.
MAP/microtubule affinity-regulating kinase 4 (MARK4) plays a central role in the cellular physiology, and it is inseparably linked with many human diseases including cancer, diet induced obesity, type2 diabetes and neurodegenerative disorders. Here, we studied the interaction of PKR-inhibitor with two variants of human MARK4. One variant is named as MARK4-F1 which has 59 N-terminal residues along with kinase domain while another variant is MARK4-F2 which has kinase domain only. Molecular-docking, molecular dynamics (MD) simulation and fluorescence-binding studies were undertaken to understand the role of N-terminal 59-residues in the binding of substrate/inhibitors. Molecular docking studies revealed that the PKR-inhibitor binds in the large hydrophobic cavity of the kinase domain of MARK4 through several hydrophobic and hydrogen-bonded interactions. Furthermore, MD simulation showed a stable parameters for the complexes of both MARK4-F1 and MARK4-F2 to PKR-inhibitor with marginal difference in their binding affinities. A significant decrease in the fluorescence intensity of MARK4 was observed on successive addition of the PKR-inhibitor. Using fluorescence data we have calculated the binding-affinity and the number of binding site of PKR-inhibitor to the MARK4. A significantly high binding affinity was observed for the PKR-inhibitor to the MARK4 variants. However, there is no any significant difference in the binding affinity of PKR-inhibitor to the MARK4 variants was observed, indicating that 59 N-terminal residues of MARK4-F1 are not playing a crucial role in the ligand binding. The present study will provide an insights into designing of new PKR-inhibitor derivative as potent and selective therapeutic agent against many life threatening diseases which are associated with MARK4.
丝裂原活化蛋白激酶/微管亲和力调节激酶4（MARK4）在细胞生理学中发挥着核心作用，并且与包括癌症、饮食诱导的肥胖症、2型糖尿病和神经退行性疾病在内的许多人类疾病密切相关。在此，我们研究了PKR抑制剂与人类MARK4的两种变体之间的相互作用。一种变体名为MARK4-F1，它具有59个N端残基以及激酶结构域，而另一种变体是MARK4-F2，它仅具有激酶结构域。我们进行了分子对接、分子动力学（MD）模拟和荧光结合研究，以了解N端59个残基在底物/抑制剂结合中的作用。分子对接研究表明，PKR抑制剂通过几种疏水和氢键相互作用结合在MARK4激酶结构域的大疏水腔中。此外，MD模拟显示MARK4-F1和MARK4-F2与PKR抑制剂形成的复合物具有稳定的参数，它们的结合亲和力略有差异。连续添加PKR抑制剂后，观察到MARK4的荧光强度显著降低。利用荧光数据，我们计算了PKR抑制剂与MARK4的结合亲和力和结合位点数量。观察到PKR抑制剂对MARK4变体具有显著高的结合亲和力。然而，未观察到PKR抑制剂对MARK4变体的结合亲和力有任何显著差异，这表明MARK4-F1的59个N端残基在配体结合中不发挥关键作用。本研究将为设计新型PKR抑制剂衍生物提供见解，该衍生物可作为针对许多与MARK4相关的危及生命疾病的有效且选择性治疗剂。
