Envisioning an enzymatic Diels–Alder reaction by in situ acid–base catalyzed diene generation

Abstract

We present and evaluate a new and potentially efficient route for enzyme-mediated Diels-Alder reactions, utilizing general acid-base catalysis. The viability of employing the active site of ketosteroid isomerase is demonstrated.

Computational Enzyme Design: Advances, Hurdles and Possible Ways Forward

“…We recently presented an acid/base-mediated mechanism that utilized the catalytic machinery of ketosteroid isomerase. [85] This preliminary study indicated a dramatic rate enhancement of a reaction that is very slow in solution, provided that the substrates could bind to the active site and form pre-arranged conformations.…”

Computational strategies for the design of new enzymatic functions

“…100,101,102 The computational protocol employs molecular docking, MD and quantum chemical calculations at DFT level to find reasonable candidate protein and substrate combinations for which protein-substrate interactions were optimized. The estimation of the free energy of activation is based on two steps; the free energy difference going from the bound state to conformations named as the “near attack-conformation” (NAC), 103 and the energy required to go from NAC to the TS.…”

“…In particular, efforts were focused in finding and optimizing a protein structure for a suitable oxyanion hole that would stabilize the LUMO of the dienophile, 101 or in developing a route based on in situ acid-base catalysed diene generation. 102 …”

Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase

“…Pseudomonas testosteroni KSI (PDB code 1QJG) 16 in the previous theoretical study 11 , and the five small models (Models 1-5), which consist of the substrate, the general base (Asp38), and zero-three surrounding residues (Tyr14, Asp99, and Tyr55), were built using the structure of the large model (Model6). In these models, only the side chains of the residues were considered and ends of the side chains were capped by an H atom or a CH 3 group mimicking the backbone.…”

“…In a recent theoretical study 11 with the aim to design a catalyst for the Diels-Alder reactions, it was found that a native enzyme, ketosteroid isomerase (KSI), has the potential to catalyze an acid-base induced Diels-Alder reaction, and it was indicated that its catalytic efficiency can be improved further by rational design. This is an attractive finding, since Diels-Alder is an important reaction for synthesis of cyclic compounds, and cyclic structures are common motifs in drug candidates.…”