Chotpatiwetchkul Warot, Boonyarattanakalin Kanokthip, Gleeson Duangkamol, Gleeson M Paul
Faculty of Pharmacy, Siam University, 38 Petkasem Rd., Phasicharoen, Bangkok, 10160, Thailand.
Org Biomol Chem. 2017 Jul 5;15(26):5593-5601. doi: 10.1039/c7ob01272a.
Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made. In this study the mechanistic proposals for DHPS have been systematically investigated using a hybrid QM/MM method. We aimed to compare the energetics associated with S1 and S2 processes, whether the S1 process involves a carbocation or neutral DHP intermediate, uncover the identity of the general base in the catalytic mechanism, and understand the differences in substrate vs. inhibitor reactivity. Our results suggest a reaction that follows an S1 process with the rate determining step being C-O bond breaking to give a carbocation intermediate. Comparative studies on the inhibitor STZ confirm the experimental observations that it is also a DHPS substrate.
二氢蝶酸合酶（DHPS）催化6-羟甲基-7,8-二氢蝶呤焦磷酸（DHPPP）与对氨基苯甲酸（pABA）缩合，是抗疟疾和抗菌药物的一个经过充分验证的靶点。然而，近年来由于多种突变，其作为治疗靶点的效用已大幅降低。因此，人们在结构生物学和药物化学方面付出了巨大努力来理解和克服这一问题。尽管已经有了详细的晶体结构和多种机理推测，但迄今为止尚未对该蛋白质的机制进行详细的计算分析。在本研究中，使用混合QM/MM方法对DHPS的机理推测进行了系统研究。我们旨在比较与S1和S2过程相关的能量学，S1过程是否涉及碳正离子或中性二氢蝶啶中间体，揭示催化机制中通用碱的身份，并理解底物与抑制剂反应性的差异。我们的结果表明该反应遵循S1过程，速率决定步骤是C-O键断裂生成碳正离子中间体。对抑制剂STZ的比较研究证实了实验观察结果，即它也是DHPS的底物。
