Rationalizing the Unprecedented Stereochemistry of an Enzymatic Nitrile Synthesis through a Combined Computational and Experimental Approach

Abstract

In this contribution, the unique and unprecedented stereochemical phenomenon of an aldoxime dehydratase‐catalyzed enantioselective dehydration of racemic E‐ and Z‐aldoximes with selective formation of both enantiomeric forms of a chiral nitrile is rationalized by means of molecular modelling, comprising in silico mutations and docking studies. This theoretical investigation gave detailed insight into why with the same enzyme the use of racemic E‐ and Z‐aldoximes leads to opposite forms of the chiral nitrile. The calculated mutants with a larger or smaller cavity in the active site were then prepared and used in biotransformations, showing the theoretically predicted decrease and increase of the enantioselectivities in these nitrile syntheses. This validated model also enabled the rational design of mutants with a smaller cavity, which gave superior enantioselectivities compared to the known wild‐type enzyme, with excellent E‐values of up to E>200 when the mutant OxdRE‐Leu145Phe was utilized.

Rational Biocatalyst Design for a Cyanide‐Free Synthesis of Long‐Chain Fatty Nitriles from Their Aldoximes

“…As an enzyme for this initial docking study, we chose the aldoxime dehydratase from Rhodococcus erythropolis (OxdRE) since crystal structures are available for this enzyme (PDB 3a15, 3a16, 3a17) [24] , and based on these data we previously could successfully design mutants in a molecular modeling study for the synthesis of chiral nitriles using the software MOE. [25] Due to the availability of this suitable docking model based on MOE, [26] which also has been proven to be a powerful tool in several other works, [27,28] we used this software MOE again for the current study (Figure 2). Interestingly the docking study revealed that the fatty aldoximes do not need to be fully incorporated in the active site.…”

Nitrile biosynthesis in nature: how and why?

“…245 Protein engineering, culture condition optimization, and chemo-enzymatic cascade of characterized aldoxime dehydratases are in fast growing development, and more exciting progresses can be expected. 246,247…”

“…245 Protein engineering, culture condition optimization, and chemo-enzymatic cascade of characterized aldoxime dehydratases are in fast growing development, and more exciting progresses can be expected. 246,247 9 Author contributions Mingyu Liu: investigation, visualization, and writingoriginal dra; Shengying Li: conceptualization, funding acquisition, and writingreview & editing.…”

Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational–Experimental Synergy Study on Emerging Pollutants

“…Moreover, it has been reported that ipso -hydroxylation and subsequent fragmentation are unusual microbial pathways to degrade sulfonamide antibiotics in the environment, but until now there is no research focusing on whether this emerging fragmentation pathway of sulfonamide antibiotics exists in human metabolism. Recent decades have witnessed the increasing connection between computational and experimental chemistry to solve a wide array of enzyme-catalyzed reaction mechanisms. ,− The present work illustrates a highly promising synergistic interplay between experiments and computations working toward metabolic mechanisms of sulfonamide antibiotics, with a focus on sulfamethoxazole (SMX) metabolism catalyzed by human CYP450 enzymes as SMX is one of the most widely applied sulfonamide antibiotics for the treatment of urinary tract infections, bronchitis, and prostatitis for human beings and is becoming a ubiquitous pollutant in the environment . Moreover, some other widely applied sulfonamide antibiotics are studied as well to confirm if the metabolic profiles obtained by SMX is universal or not, including sulphadoxine, sulfadimethoxine, sulfapyridine, sulphamerazine, sulphabromomethazine, sulphameter, sulphachloropyrazine, and sulphadimethoxine.…”