Ali Mohd Sajid, Al-Lohedan Hamad A, Bhati Rittik, Muthukumaran Jayaraman
Department of Chemistry, College of Science, King Saud University, P.O. Box-2455, Riyadh, 11451, Saudi Arabia.
Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, India.
Heliyon. 2024 May 7;10(10):e30818. doi: 10.1016/j.heliyon.2024.e30818. eCollection 2024 May 30.
Warfarin is a cardiovascular drug, used to treat or inhibit the coagulation of the blood. In this paper, we have studied the interaction of lysozyme with warfarin using several experimental (fluorescence, UV-visible and circular dichroism spectroscopies) and computational (molecular docking, molecular dynamics and DFT) approaches. Experimental studies have suggested that there was a strong interaction between lysozyme and warfarin. Inner filter effect played important role in fluorescence experimental data which show that the emission intensity of lysozyme decreased on the addition of warfarin, however, after inner filter effect correction the actual outcome turned out be the fluorescence enhancement. The extent of binding, increased with temperature rise. The interaction was primarily taken place via the dominance of hydrophobic forces. Small amount of warfarin didn't influence the secondary structure of lysozyme; however, the higher concentration of warfarin caused a decrease in the helicity of the protein and a consequent partial unfolding. Molecular docking studies were also performed which revealed that warfarin binds with lysozyme mainly with hydrophobic forces along with a significant contribution of hydrogen bonding. The flexibility of warfarin played important role in fitting the molecule into the binding pocket of lysozyme. Frontier molecular orbitals of warfarin, using DFT, in free as well as complexed form have also been calculated and discussed. Molecular dynamics simulations of unbound and warfarin bound lysozyme reveal a stable complex with slightly higher RMSD values in the presence of warfarin. Despite slightly increased RMSF values, the overall compactness and folding properties remain consistent, emphasizing strong binding towards lysozyme through the results obtained from intermolecular hydrogen bonding analysis. Essential dynamics analysis suggests warfarin induces slight structural changes without significantly altering the conformation, additionally supported by SASA patterns. Aside from the examination of global and essential motion, the MM/PBSA-based analysis of binding free energy elucidates the significant binding of warfarin to lysozyme, indicating a binding free energy of -13.3471 kcal/mol.
华法林是一种心血管药物，用于治疗或抑制血液凝固。在本文中，我们使用了多种实验方法（荧光、紫外可见和圆二色光谱）和计算方法（分子对接、分子动力学和密度泛函理论）研究了溶菌酶与华法林的相互作用。实验研究表明，溶菌酶与华法林之间存在强烈的相互作用。内滤效应在荧光实验数据中起重要作用，该数据表明添加华法林后溶菌酶的发射强度降低，然而，经过内滤效应校正后，实际结果却是荧光增强。结合程度随温度升高而增加。这种相互作用主要是通过疏水作用的主导而发生的。少量的华法林不会影响溶菌酶的二级结构；然而，较高浓度的华法林会导致蛋白质螺旋度降低，从而导致部分展开。还进行了分子对接研究，结果表明华法林与溶菌酶的结合主要是通过疏水作用，同时氢键也有重要贡献。华法林的灵活性在将分子拟合到溶菌酶的结合口袋中起重要作用。还计算并讨论了华法林在游离态和络合态下使用密度泛函理论的前线分子轨道。未结合和结合华法林的溶菌酶的分子动力学模拟显示，在存在华法林的情况下，形成了一个稳定的复合物，其均方根偏差（RMSD）值略高。尽管均方根波动（RMSF）值略有增加，但整体紧凑性和折叠特性保持一致，通过分子间氢键分析得到的结果强调了对华法林与溶菌酶的强结合。主成分动力学分析表明，华法林诱导了轻微的结构变化，但没有显著改变构象，表面可及面积（SASA）模式也支持这一点。除了对全局和主成分运动的研究外，基于MM/PBSA的结合自由能分析阐明了华法林与溶菌酶的显著结合，表明结合自由能为-13.3471千卡/摩尔。
