Saravanan Kandasamy, Sivanandam Magudeeswaran, Hunday Govindasamy, Pavan Mysore S, Kumaradhas Poomani
Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India.
Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India.
J Mol Graph Model. 2019 Nov;92:280-295. doi: 10.1016/j.jmgm.2019.07.019. Epub 2019 Aug 3.
Piperine is a pungent alkaloid, largely present in the skin of pepper. It is the most active component of pepper and being used as a medicine in many Asian countries. The effect of piperine on memory impairment and neurodegeneration in Alzheimer's disease model has been investigated. In the present study, we aim to investigate the effect of piperine molecule in different environments (crystal and active site of proteins) from crystallography, molecular docking, QM/MM based charge density analysis and molecular dynamic simulation. The crystal structure of piperine has been used to determine the topological electron density of intermolecular interactions. The O-atoms of piperine is forming C-H⋅⋅⋅O interactions with the neighboring molecules in the crystal, these interactions also confirmed from the Hirshfeld surface. Further, to understand the nature of interactions and the conformational flexibility of piperine in the active site of recombinant human acetylcholinesterase (rhAChE), molecular docking analysis has been performed. The selected docked complex suggests favorable hydrogen bonding and hydrophobic interactions with rhAChE enzyme; notably, the O3 atom of piperine molecule forms strong hydrogen bonding interaction with Glu202 at 1.8 Å. To determine the charge density distribution and the electrostatic properties of piperine molecule in the active site of rhAChE, the piperine-rhAChE complex was minimized at QM/MM energy level; in which, the binding pocket with piperine was considered as QM region. The charge density analysis of piperine and the interacting amino acid groups have been carried out. The topological analysis of O3⋯H-O/Glu202 hydrogen bonding interaction exhibits strong interactions and the electron density ρ(r): 0.242 eÅ and the Laplacian ∇ρ(r): 3.176 eÅ respectively. These results were compared with the corresponding molecule present in the crystal and gas phase environments of piperine. The comparison of active site structure with the corresponding crystal phase and gas phase structures reveal that piperine exhibits large conformational modification in the active site. The molecular dynamics simulation and binding free energy calculations were performed, this gives the stability, binding affinity of the molecule in the active site of rhAChE. The O3⋯H-O/Glu202 interaction shows the high stability (89.2%), this was confirmed from the stability of hydrogen bond analysis. The binding free energy was used to measure the rate of inhibition of enzyme in the presence of ligand molecule. The comparative study allows to understand the nature of piperine molecule in the gas and crystal phases, and amino acids environment.
胡椒碱是一种辛辣生物碱，主要存在于胡椒表皮。它是胡椒中最具活性的成分，在许多亚洲国家被用作药物。人们已经研究了胡椒碱对阿尔茨海默病模型中记忆损伤和神经退行性变的影响。在本研究中，我们旨在通过晶体学、分子对接、基于量子力学/分子力学的电荷密度分析和分子动力学模拟，研究胡椒碱分子在不同环境（蛋白质的晶体和活性位点）中的作用。胡椒碱的晶体结构已被用于确定分子间相互作用的拓扑电子密度。胡椒碱的O原子在晶体中与相邻分子形成C-H⋅⋅⋅O相互作用，这些相互作用也通过 Hirshfeld 表面得到证实。此外，为了了解胡椒碱在重组人乙酰胆碱酯酶（rhAChE）活性位点的相互作用性质和构象灵活性，进行了分子对接分析。所选的对接复合物表明与rhAChE酶存在良好的氢键和疏水相互作用；值得注意的是，胡椒碱分子的O3原子与Glu202形成了1.8 Å的强氢键相互作用。为了确定胡椒碱分子在rhAChE活性位点的电荷密度分布和静电性质，在量子力学/分子力学能量水平上对胡椒碱-rhAChE复合物进行了优化；其中，与胡椒碱结合的口袋被视为量子力学区域。对胡椒碱和相互作用的氨基酸基团进行了电荷密度分析。对O3⋯H-O/Glu202氢键相互作用的拓扑分析显示出强相互作用，电子密度ρ(r)：0.242 eÅ，拉普拉斯算子∇ρ(r)：3.176 eÅ。这些结果与胡椒碱在晶体和气相环境中的相应分子进行了比较。活性位点结构与相应晶体相和气相结构的比较表明，胡椒碱在活性位点表现出较大的构象修饰。进行了分子动力学模拟和结合自由能计算，这给出了分子在rhAChE活性位点上的稳定性和结合亲和力。O3⋯H-O/Glu202相互作用显示出高稳定性（89.2%），这通过氢键分析的稳定性得到了证实。结合自由能用于测量在配体分子存在下酶的抑制率。比较研究有助于了解胡椒碱分子在气相和晶体相以及氨基酸环境中的性质。
