Solid-State NMR, Crystallographic, and Computational Investigation of Bisphosphonates and Farnesyl Diphosphate Synthase−Bisphosphonate Complexes

Bisphosphonates are a class of molecules in widespread use in treating bone resorption diseases
and are also of interest as immunomodulators and anti-infectives. They function by inhibiting the enzyme
farnesyl diphosphate synthase (FPPS), but the details of how these molecules bind are not fully understood.
Here, we report the results of a solid-state 13C, 15N, and 31P magic-angle sample spinning (MAS) NMR and
quantum chemical investigation of several bisphosphonates, both as pure compounds and when bound to
FPPS, to provide information about side-chain and phosphonate backbone protonation states when bound
to the enzyme. We then used computational docking methods (with the charges assigned by NMR) to
predict how several bisphosphonates bind to FPPS. Finally, we used X-ray crystallography to determine
the structures of two potent bisphosphonate inhibitors, finding good agreement with the computational
results, opening up the possibility of using the combination of NMR, quantum chemistry and molecular
docking to facilitate the design of other, novel prenytransferase inhibitors.

双膦酸盐（Bisphosphonates）是一类广泛应用于骨吸收疾病治疗的分子，同时作为免疫调节剂与抗感染药物也受到学界关注。此类分子通过抑制法尼基二磷酸合酶（farnesyl diphosphate synthase, FPPS）发挥功能，但其与该酶的结合细节尚未完全明晰。本研究针对多种双膦酸盐，分别以纯化合物及结合FPPS的状态，开展了固态13C、15N及31P魔角样品旋转（magic-angle sample spinning, MAS）核磁共振波谱与量子化学研究，以明确其结合于酶时的侧链与膦酸酯骨架的质子化状态。随后，我们采用经核磁共振赋值电荷的计算对接方法，预测了多种双膦酸盐与FPPS的结合模式。最后，通过X射线晶体学测定了两种强效双膦酸盐抑制剂的晶体结构，其结果与计算模拟结果吻合良好，为结合使用核磁共振、量子化学与分子对接技术辅助设计新型异戊烯基转移酶抑制剂提供了可能。