The remarkable cyclization mechanism of the formation of the 6-6-6-5 tetracyclic lanosterol (a key triterpenoid intermediate in the biosynthesis of cholesterol) from the acyclic 2,3-oxidosqualene catalyzed by oxidosqualene cyclase (OSC) has stimulated the interest of chemists and biologists for over a half century. Herein, the elaborate, state-of-the-art two-dimensional (2D) QM/MM MD simulations have clearly shown that the cyclization of the A-C rings involves a nearly concerted, but highly asynchronous cyclization, to yield a stable intermediate with "6-6-5" rings followed by the ring expansion of the C-ring concomitant with the formation of the D-ring to yield the "6-6-6-5" protosterol cation. The calculated reaction barrier of the rate-limiting step (≈22 kcal mol(-1)) is comparable to the experimental kinetic results. Furthermore all previous experimental mutagenic evidence is highly consistent with the identified reaction mechanism.

The cleavage of the magnesium-assisted diphosphate group (the PPi group) is one significant and prevalent rate-limiting step triggering the enzyme catalysis synthesis of terpenoid natural products. However, the PPi cleavage procedure has been rarely studied in most theoretical research of the terpenoid biosynthetic mechanism. In this work, QM­(DFT)/MM MD simulations were employed to illuminate the detailed PPi cleavage mechanism in three different enzyme systems (ATAS, TEAS, and FPPS). We found that the most rational protonation state of the PPi group is highly dependent on the Mg2+ coordination modes and the enzyme classes. The deprotonation of PPi is favorable for triggering the catalysis reaction in ATAS, while monoprotonation in FPPS and biprotonation in TEAS are advantageous. As a result, similar PPi cleavage occurs by means of nucleophilic substitution reactions in TEAS/FPPS/ATAS but presents an SN1, SN2, and borderline mechanism, respectively. Finally, the alternative functions of PPi protonation and Mg2+ coordination modes are discussed.

Development of isoform-selective histone deacetylase (HDAC) inhibitors is of great biological and medical interest. Among 11 zinc-dependent HDAC isoforms, it is particularly challenging to achieve isoform inhibition selectivity between HDAC1 and HDAC2 due to their very high structural similarities. In this work, by developing and applying a novel de novo reaction-mechanism-based inhibitor design strategy to exploit the reactivity difference, we have discovered the first HDAC2-selective inhibitor, β-hydroxymethyl chalcone. Our bioassay experiments show that this new compound has a unique time-dependent selective inhibition on HDAC2, leading to about 20-fold isoform-selectivity against HDAC1. Furthermore, our ab initio QM/MM molecular dynamics simulations, a state-of-the-art approach to study reactions in biological systems, have elucidated how the β-hydroxymethyl chalcone can achieve the distinct time-dependent inhibition toward HDAC2.

Bufospirostenin A (1) and bufogargarizin C (2), two novel steroids with rearranged A/B rings, were isolated from the toad Bufo bufo gargarizans. Compound 1 represents the first spirostanol found in animals. Compound 2 is an unusual bufadienolide with a cycloheptatriene B ring. Their structures were elucidated by spectroscopic analysis, single crystal X-ray diffraction analysis, and computational calculations.