Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations

The substitution of methyl (Me or −CH3) by trifluoromethyl (TFM or −CF3) is frequently used in medicinal chemistry. However, the exact effect of −CH3/–CF3 substitution on bioactivity is still controversial. We compiled a data set containing 28 003 pairs of compounds with the only difference that −CH3 is substituted by −CF3, and the statistical results showed that the replacement of −CH3 with −CF3 does not improve bioactivity on average. Yet, 9.19% substitution of −CH3 by −CF3 could increase the biological activity by at least an order. A PDB survey revealed that −CF3 prefers Phe, Met, Leu, and Tyr, while −CH3 prefers Leu, Met, Cys, and Ile. If we substitute the −CH3 by −CF3 near Phe, His, and Arg, the bioactivity is most probably improved. We performed QM/MM calculations for 39 −CH3/–CF3 pairs of protein–ligand complexes and found that the −CH3/–CF3 substitution does achieve a large energy gain in some systems, although the mean energy difference is subtle, which is consistent with the statistical survey. The −CF3 substitution on the benzene ring could be particularly effective at gaining binding energy. The maximum improvements in energy achieved −4.36 kcal/mol by QM/MM calculation. Moreover, energy decompositions from MM/GBSA calculations showed that the large energy gains for the −CH3/–CF3 substitution are largely driven by the electrostatic energy or the solvation free energy. These findings may shed some light on the biological activity profile for −CH3/–CF3 substitution, which should be useful for further drug discovery and drug design.

将甲基（methyl，缩写为Me或−CH3）替换为三氟甲基（trifluoromethyl，缩写为TFM或−CF3）是药物化学（medicinal chemistry）中常用的修饰策略。然而，−CH3与−CF3的替换对生物活性的确切影响仍存在争议。我们构建了一个包含28003对化合物的数据集，该数据集内的化合物仅存在−CH3被−CF3替换这一处差异。统计结果显示，平均而言，将−CH3替换为−CF3并不会提升化合物的生物活性，但其中9.19%的替换案例可使生物活性至少提升一个数量级。通过PDB（Protein Data Bank，蛋白质数据库）调研发现，−CF3更倾向于与苯丙氨酸（Phenylalanine, Phe）、甲硫氨酸（Methionine, Met）、亮氨酸（Leucine, Leu）和酪氨酸（Tyrosine, Tyr）产生相互作用，而−CH3则更偏好亮氨酸、甲硫氨酸、半胱氨酸（Cysteine, Cys）和异亮氨酸（Isoleucine, Ile）。若在苯丙氨酸（Phe）、组氨酸（Histidine, His）和精氨酸（Arginine, Arg）附近将−CH3替换为−CF3，化合物的生物活性大概率会得到显著提升。我们针对39对含−CH3/−CF3替换的蛋白质-配体复合物开展了QM/MM（Quantum Mechanics/Molecular Mechanics，量子力学/分子力学）计算，结果发现，尽管平均能量差异微小，但在部分体系中，−CH3/−CF3替换确实能带来显著的能量增益，这与前述统计调研结果一致。苯环上的−CF3替换在获取结合能方面尤为高效，经QM/MM计算，该类替换可实现的最大能量改善为−4.36 kcal/mol。此外，通过MM/GBSA（Molecular Mechanics/Generalized Born Surface Area，分子力学/广义玻恩表面积）计算得到的能量分解结果显示，−CH3与−CF3替换所带来的显著能量增益，主要由静电能或溶剂化自由能驱动。上述研究结果可为−CH3/−CF3替换的生物活性特征提供理论参考，对后续药物发现与药物设计工作具有重要的指导价值。