Purohit Apoorva, Cheng Xiaolin
Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States.
J Chem Theory Comput. 2025 Feb 25;21(4):2067-2078. doi: 10.1021/acs.jctc.4c01440. Epub 2024 Dec 19.
Polyphosphate nucleotides, such as ATP, ADP, GTP, and GDP, play a crucial role in modulating protein functions through binding and/or catalytically activating proteins (enzymes). However, accurately calculating the binding free energies for these charged and flexible ligands poses challenges due to slow conformational relaxation and the limitations of force fields. In this study, we examine the accuracy and reliability of alchemical free energy simulations with fixed-charge force fields for the binding of four nucleotides to nine proteins of various classes, including kinases, ATPases, and GTPases. Our results indicate that the alchemical simulations effectively reproduce experimental binding free energies for all proteins that do not undergo significant conformational changes between their triphosphate nucleotide-bound and diphosphate nucleotide-bound states, with 87.5% (7 out of 8) of the absolute binding free energy results for 4 proteins within ±2 kcal/mol of experimental values and 88.9% (8 out of 9) of the relative binding free energy results for 9 proteins within ±3 kcal/mol of experimental values. However, our calculations show significant inaccuracies when divalent ions are included, suggesting that nonpolarizable force fields may not accurately capture interactions involving these ions. Additionally, the presence of highly charged and flexible ligands necessitates extensive conformational sampling to account for the long relaxation times associated with long-range electrostatic interactions. The simulation strategy presented here, along with its demonstrated accuracy across multiple protein classes, will be valuable for predicting the binding of nucleotides or their analogs to protein targets.
多磷酸核苷酸，如ATP、ADP、GTP和GDP，通过与蛋白质（酶）结合和/或催化激活蛋白质，在调节蛋白质功能中发挥关键作用。然而，由于构象弛豫缓慢和力场的局限性，准确计算这些带电且灵活的配体的结合自由能具有挑战性。在本研究中，我们研究了使用固定电荷力场的炼金术自由能模拟对于四种核苷酸与九种不同类型蛋白质（包括激酶、ATP酶和GTP酶）结合的准确性和可靠性。我们的结果表明，对于所有在其三磷酸核苷酸结合态和二磷酸核苷酸结合态之间不发生显著构象变化的蛋白质，炼金术模拟有效地重现了实验结合自由能，4种蛋白质的绝对结合自由能结果中有87.5%（8个中的7个）在实验值的±2千卡/摩尔范围内，9种蛋白质的相对结合自由能结果中有88.9%（9个中的8个）在实验值的±3千卡/摩尔范围内。然而，我们的计算表明，当包含二价离子时存在显著误差，这表明非极化力场可能无法准确捕捉涉及这些离子的相互作用。此外，高度带电且灵活的配体的存在需要广泛的构象采样，以考虑与长程静电相互作用相关的长弛豫时间。这里提出的模拟策略，以及其在多种蛋白质类型中展示的准确性，对于预测核苷酸或其类似物与蛋白质靶点的结合将是有价值的。
