Singh Kushal, Muttathukattil Aswathy N, Singh Prashant Chandra, Reddy Govardhan
Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru560012, Karnataka, India.
School of Chemical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Jadavpur, Kolkata700032, India.
J Phys Chem B. 2022 Dec 1;126(47):9759-9770. doi: 10.1021/acs.jpcb.2c05117. Epub 2022 Nov 16.
Understanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm) to the active site of hen egg-white lysozyme (HEWL). HEWL serves as a model system for enzymes with two acidic residues in the active site and ligands with Gdm moieties, which can bind to the active sites of such enzymes and are present in several approved drugs treating various disorders. The computed free energy surface (FES) shows that Gdm binds to the HEWL active site using two dominant binding pathways populating multiple intermediates. We show that the residues close to the active site that can anchor the ligand could play a critical role in ligand binding. Using a Markov state model, we quantified the lifetimes and kinetic pathways connecting the different states in the FES. The protonation and deprotonation of the acidic residues in the active site in response to the pH change strongly influence the Gdm binding. There is a sharp jump in the ligand-binding rate constant when the pH approaches the largest p of the acidic residue present in the active site. The simulations reveal that, at most, three Gdm can bind at the active site, with the Gdm bound in the cavity of the active site acting as a scaffold for the other two Gdm ions binding. These results can aid in providing greater insights into designing novel molecules containing Gdm moieties that can have high binding affinities to inhibit the function of enzymes with acidic residues in their active site.
理解配体与其蛋白质靶点的结合机制以及各种因素对结合热力学的影响对于合理药物设计至关重要。溶液pH是影响配体与蛋白质腔结合的关键因素之一，尤其是在功能对pH敏感的酶中。通过计算机模拟，我们研究了pH对胍离子（Gdm）与鸡蛋清溶菌酶（HEWL）活性位点结合的影响。HEWL作为活性位点有两个酸性残基且配体带有Gdm部分的酶的模型系统，这类配体可与此类酶的活性位点结合且存在于几种治疗各种疾病的获批药物中。计算得到的自由能表面（FES）表明，Gdm通过两条主要的结合途径与HEWL活性位点结合，这些途径存在多个中间体。我们表明，靠近活性位点且能锚定配体的残基在配体结合中可能起关键作用。使用马尔可夫状态模型，我们量化了FES中不同状态之间的寿命和动力学途径。活性位点中酸性残基响应pH变化的质子化和去质子化强烈影响Gdm的结合。当pH接近活性位点中存在的酸性残基的最大pKa时，配体结合速率常数会急剧跃升。模拟结果表明，活性位点最多可结合三个Gdm，结合在活性位点腔内的Gdm作为另外两个Gdm离子结合的支架。这些结果有助于更深入地了解设计含有Gdm部分的新型分子，这些分子可具有高结合亲和力以抑制活性位点带有酸性残基的酶的功能。
