Molecular Docking and Molecular Dynamics Studies on Selective Synthesis of α-Amyrin and β-Amyrin by Oxidosqualene Cyclases from Ilex Asprella

Abstract

Amyrins are the immediate precursors of many pharmaceutically important pentacyclic triterpenoids. Although various amyrin synthases have been identified, little is known about the relationship between protein structures and the constituent and content of the products. IaAS1 and IaAS2 identified from Ilex asprella in our previous work belong to multifunctional oxidosqualene cyclases and can produce α-amyrin and β-amyrin at different ratios. More than 80% of total production of IaAS1 is α-amyrin; while IaAS2 mainly produces β-amyrin with a yield of 95%. Here, we present a molecular modeling approach to explore the underlying mechanism for selective synthesis. The structures of IaAS1 and IaAS2 were constructed by homology modeling, and were evaluated by Ramachandran Plot and Verify 3D program. The enzyme-product conformations generated by molecular docking indicated that ASP484 residue plays an important role in the catalytic process; and TRP611 residue of IaAS2 had interaction with β-amyrin through π–σ interaction. MM/GBSA binding free energy calculations and free energy decomposition after 50 ns molecular dynamics simulations were performed. The binding affinity between the main product and corresponding enzyme was higher than that of the by-product. Conserved amino acid residues such as TRP257; TYR259; PHE47; TRP534; TRP612; and TYR728 for IaAS1 (TRP257; TYR259; PHE473; TRP533; TRP611; and TYR727 for IaAS2) had strong interactions with both products. GLN450 and LYS372 had negative contribution to binding affinity between α-amyrin or β-amyrin and IaAS1. LYS372 and ARG261 had strong repulsive effects for the binding of α-amyrin with IaAS2. The importance of Lys372 and TRP612 of IaAS1, and Lys372 and TRP611 of IaAS2, for synthesizing amyrins were confirmed by site-directed mutagenesis. The different patterns of residue–product interactions is the cause for the difference in the yields of two products.

The effect of tranexamic acid on myocardial injury in cardiac surgical patients: a systematic review and meta-analysis

“…Level of cTnI also showed a similar trend during 6–48 h postoperatively in two included studies, and it was lower in TXA Group (6 h: WMD: −0.73, 95% CI −0.81 to −0.66, P < 0.001, I 2 = 0%; 24 h: WMD: −0.62, 95% CI −1.10 to −0.15, P = 0.01, I 2 = 77%; 48 h: WMD: −0.64, 95% CI: −0.71 to −0.58, P < 0.001, I 2 = 0%) (Fig. 4a–c) [36,38]. Only one trial incorporated LDH level and no trial for LDHI level.…”

“…2b) [26,37]. Of the eight included comparisons, five compared postoperative CK-MB levels in the TXA group and control [26,27,[36][37][38]. The two groups had roughly the same levels at the end of surgery (WMD: À9.92, 95% CI À31.37 to 11.54, P ¼ 0.36, I 2 ¼ 89%) (Fig.…”

Reciprocal mutations of two multifunctional β-amyrin synthases fromBarbarea vulgarisshift α/β-amyrin ratios

“…Interestingly, the residues investigated to be largely at play in determining the product ratio in B. vulgaris LUP5 enzymes, were not reported previously to determine product ratios in multifunctional β-amyrin synthases. However, several different architecture have been described for OSC enzymes found in plants catalyzing similar reactions ( Srisawat et al, 2019 ; Wu et al, 2019 , 2020 ). Taken together, these biosynthetic mechanisms are dictated by the OSC active center environment, determining the stability of cationic intermediates and correct positioning of the intermediate in order to facilitate product formation ( Ito et al, 2013 , 2017 ).…”

“…Deprotonation of the oleanyl cation results in the formation of β-amyrin or continue with further skeletal rearrangements ( Thimmappa et al, 2014 ; Figure 1 ). Substantial efforts have been undertaken to determine the reaction mechanism and unique structural features of multifunctional β-amyrin synthases in order to predict OSC function from sequence information ( Segura et al, 2003 ; Ito et al, 2017 ; Srisawat et al, 2019 ; Wu et al, 2019 , 2020 ).…”

Discovery of New Inhibitors of Transforming Growth Factor-Beta Type 1 Receptor by Utilizing Docking and Structure-Activity Relationship Analysis

“…With the rapid development of computer software and hardware technology, molecular docking research has been widely used in innovative drug design [10,11]. There is a previous study of ours related to the present work [12] in which two new skeleton structures were found by searching databases, and, subsequently, three compounds (YXY01–03) with certain activity and high safety were designed.…”