Computer-aided understanding and engineering of enzymatic selectivity

Wu, Lunjie; Qin, Lei; Nie, Yao; Xu, Yan; Zhao, Yi‐Lei

doi:10.1016/j.biotechadv.2021.107793

Cited by 45 publications

(25 citation statements)

References 269 publications

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“…The spatial arrangement of the active pocket and enzyme–substrate interaction directly determines the enzyme selectivity . To identify the key residues regulating enzyme selectivity, we performed mutagenesis to identify the residues constituting the IDO active pocket.…”

Section: Resultsmentioning

confidence: 99%

“…The spatial arrangement of the active pocket and enzyme− substrate interaction directly determines the enzyme selectivity. 55 To identify the key residues regulating enzyme selectivity, we performed mutagenesis to identify the residues constituting the IDO active pocket. First, using a previously described strategy for selecting sites to be mutated, 56 the substrates (L-Ile and L-Nle) were separately docked into IDO, and 11 residues within 4 Å of the substrate were selected (Y92, Q94, N99, Y100, H150, D172, D173, E174, L241, V243, and T244).…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Molecular Insights into the Regioselectivity of the Fe(II)/2-Ketoglutarate-Dependent Dioxygenase-Catalyzed C–H Hydroxylation of Amino Acids

Jing

et al. 2022

ACS Catal.

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l-Isoleucine dioxygenase (IDO) directly catalyzes the C–H bond hydroxylation of several hydrophobic aliphatic amino acids. However, the ambiguous selectivity of IDO prevents its application in chiral hydroxy amino acid production. The hydroxylation of l-norleucine by IDO, which produces 4-hydroxynorleucine and 5-hydroxynorleucine with obvious regioselectivity, was used to investigate the mechanism of IDO regioselectivity. Along with computational structural analysis and high-throughput screening, the IDO structure revealed single-site variants (T244A, T244G, and T244S) with enhanced regioselectivity; for example, the 4-hydroxynorleucine purity in regioisomeric products increased from 78.9% (by wild-type IDO) to 95.1%, 96.6%, and 95.3%, respectively. Molecular dynamics simulations showed that mutating T244 into smaller amino acids fine-tuned the substrate binding pose. For asymmetric catalysis requiring precise positioning, this change expanded the most frequent distances between the substrate C4 or C5 and Fe2+, giving a maximum 4-hydroxynorleucine purity of 96.6%. We improved the understanding of the regioselectivity of Fe(II)/2-ketoglutarate-dependent dioxygenases and provide a route for diversifying C–H hydroxylation-based active compounds.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Molecular Insights into the Regioselectivity of the Fe(II)/2-Ketoglutarate-Dependent Dioxygenase-Catalyzed C–H Hydroxylation of Amino Acids

Jing

et al. 2022

ACS Catal.

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“…Studies aimed at monitoring the variation of stereoselectivity in function of the substrate or the experimental conditions are lacking, and the absolute configuration of the products has been assigned only in rare cases. Computational approaches, such as ab-initio protein folding, molecular docking, and molecular dynamics, could provide useful information for understanding the origin of stereoselectivity (or lack thereof) and supporting the engineering of the active site of the enzyme [ 61 ]. The use of the modern techniques of directed evolution appear even more promising in obtaining engineered biocatalysts with enhanced stereoselectivity and substrate scope [ 62 ].…”

Section: Discussionmentioning

confidence: 99%

Stereoselective Promiscuous Reactions Catalyzed by Lipases

Patti

Sanfilippo

2022

IJMS

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The ability of lipases to display activity beyond their physiological reactions, so-called “catalytic promiscuity”, has gained increasing interest in the last two decades as an important tool for expanding the application of these enzymes in organic synthesis. Some lipases have been shown to be effective in catalyzing a variety of C-C bond formation reactions and most of the investigations have been directed to the optimization of the products yield through a careful tuning of the experimental parameters. Despite the fact that new stereogenic carbons are formed in many of the tested reactions, the target products have been often obtained in racemic form and examples of an efficient asymmetric induction by the used lipases are quite limited. The aim of this review, mainly focused on those lipase-catalyzed promiscuous reactions in which optically active products have been obtained, is to offer a current state of art together with a perspective in this field of asymmetric synthesis.

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“…The birth of protein engineering technology has opened up a new route for researchers to develop excellent biocatalysts by redesigning natural enzymes (Marshall et al, 2021;Watanabe et al, 2021;Xiong et al, 2021). Many enzyme engineering design strategies have emerged, such as directed evolution, rational, semi-rational, de novo, computer-assisted, and artificial intelligence (Bunzel et al, 2021;Narayanan et al, 2021;Tunyasuvunakool et al, 2021;Woolfson, 2021;Wu et al, 2021). These strategies have been used to improve enzyme stability, activity, and selectivity for substrates.…”

Section: Discussion and Prospectsmentioning

confidence: 99%

Mini Review: Advances in 2-Haloacid Dehalogenases

et al. 2021

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The 2-haloacid dehalogenases (EC 3.8.1.X) are industrially important enzymes that catalyze the cleavage of carbon–halogen bonds in 2-haloalkanoic acids, releasing halogen ions and producing corresponding 2-hydroxyl acids. These enzymes are of particular interest in environmental remediation and environmentally friendly synthesis of optically pure chiral compounds due to their ability to degrade a wide range of halogenated compounds with astonishing efficiency for enantiomer resolution. The 2-haloacid dehalogenases have been extensively studied with regard to their biochemical characterization, protein crystal structures, and catalytic mechanisms. This paper comprehensively reviews the source of isolation, classification, protein structures, reaction mechanisms, biochemical properties, and application of 2-haloacid dehalogenases; current trends and avenues for further development have also been included.

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Computer-aided understanding and engineering of enzymatic selectivity

Cited by 45 publications

References 269 publications

Molecular Insights into the Regioselectivity of the Fe(II)/2-Ketoglutarate-Dependent Dioxygenase-Catalyzed C–H Hydroxylation of Amino Acids

Molecular Insights into the Regioselectivity of the Fe(II)/2-Ketoglutarate-Dependent Dioxygenase-Catalyzed C–H Hydroxylation of Amino Acids

Stereoselective Promiscuous Reactions Catalyzed by Lipases

Mini Review: Advances in 2-Haloacid Dehalogenases

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