1
|
Ganjoo A, Babu V. Recombinant Amidases: Recent Insights and its Applications in the Production of Industrially Important Fine Chemicals. Mol Biotechnol 2025; 67:910-924. [PMID: 38598092 DOI: 10.1007/s12033-024-01123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
The current research for the synthesis of industrially important fine chemicals is more inclined towards developing enzyme-based processes. The biotransformation reactions wherein microbial cells/enzymes are used, have become essential in making the process efficient, green, and economical. Amongst industrially important enzymes, amidase is one of the most versatile tools in biocatalysis and biotransformation reactions. It shows broad substrate specificity and sturdy functional characteristics because of its promiscuous nature. Further, advancement in the area led to the development of amidase recombinant systems, which are developed using biotechnology and enzyme engineering tools. Additionally, recombinant amidases may be instrumental in commercializing the synthesis of fine chemicals such as hydroxamic acids that have a significant pharmaceutical market. Hence, the present review focuses on highlighting and assimilating the tools and techniques used in developing recombinant systems followed by their applications.
Collapse
Affiliation(s)
- Ananta Ganjoo
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vikash Babu
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
2
|
Li ZL, Pei S, Chen Z, Huang TY, Wang XD, Shen L, Chen X, Wang QQ, Wang DX, Ao YF. Machine learning-assisted amidase-catalytic enantioselectivity prediction and rational design of variants for improving enantioselectivity. Nat Commun 2024; 15:8778. [PMID: 39389964 PMCID: PMC11467325 DOI: 10.1038/s41467-024-53048-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 09/30/2024] [Indexed: 10/12/2024] Open
Abstract
Biocatalysis is an attractive approach for the synthesis of chiral pharmaceuticals and fine chemicals, but assessing and/or improving the enantioselectivity of biocatalyst towards target substrates is often time and resource intensive. Although machine learning has been used to reveal the underlying relationship between protein sequences and biocatalytic enantioselectivity, the establishment of substrate fitness space is usually disregarded by chemists and is still a challenge. Using 240 datasets collected in our previous works, we adopt chemistry and geometry descriptors and build random forest classification models for predicting the enantioselectivity of amidase towards new substrates. We further propose a heuristic strategy based on these models, by which the rational protein engineering can be efficiently performed to synthesize chiral compounds with higher ee values, and the optimized variant results in a 53-fold higher E-value comparing to the wild-type amidase. This data-driven methodology is expected to broaden the application of machine learning in biocatalysis research.
Collapse
Affiliation(s)
- Zi-Lin Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuxin Pei
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Ziying Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Teng-Yu Huang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Lin Shen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai, China.
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai, China.
- Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing, Yantai, China.
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
3
|
Lavrov KV, Shemyakina AO, Grechishnikova EG, Gerasimova TV, Kalinina TI, Novikov AD, Leonova TE, Ryabchenko LE, Bayburdov TA, Yanenko AS. A new concept of biocatalytic synthesis of acrylic monomers for obtaining water-soluble acrylic heteropolymers. Metab Eng Commun 2024; 18:e00231. [PMID: 38222043 PMCID: PMC10787234 DOI: 10.1016/j.mec.2023.e00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024] Open
Abstract
Rhodococcus strains were designed as model biocatalysts (BCs) for the production of acrylic acid and mixtures of acrylic monomers consisting of acrylamide, acrylic acid, and N-alkylacrylamide (N-isopropylacrylamide). To obtain BC strains, we used, among other approaches, adaptive laboratory evolution (ALE), based on the use of the metabolic pathway of amide utilization. Whole genome sequencing of the strains obtained after ALE, as well as subsequent targeted gene disruption, identified candidate genes for three new amidases that are promising for the development of BCs for the production of acrylic acid from acrylamide. New BCs had two types of amidase activities, acrylamide-hydrolyzing and acrylamide-transferring, and by varying the ratio of these activities in BCs, it is possible to influence the ratio of monomers in the resulting mixtures. Based on these strains, a prototype of a new technological concept for the biocatalytic synthesis of acrylic monomers was developed for the production of water-soluble acrylic heteropolymers containing valuable N-alkylacrylamide units. In addition to the possibility of obtaining mixtures of different compositions, the advantages of the concept are a single starting reagent (acrylamide), more unification of processes (all processes are based on the same type of biocatalyst), and potentially greater safety for personnel and the environment compared to existing chemical technologies.
Collapse
Affiliation(s)
- Konstantin V. Lavrov
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Anna O. Shemyakina
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Elena G. Grechishnikova
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Tatyana V. Gerasimova
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Tatyana I. Kalinina
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Andrey D. Novikov
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Tatyana E. Leonova
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Ludmila E. Ryabchenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Telman A. Bayburdov
- Saratov Chemical Plant of Acrylic Polymers “AKRYPOL”, 410059, Saratov, Russia
| | - Alexander S. Yanenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| |
Collapse
|
4
|
Mao Z, Song M, Zhao R, Liu Y, Zhu Y, Liu X, Liang H, Zhang H, Wu X, Wang G, Li F, Zhang L. Characterization of two novel hydrolases from Sphingopyxis sp. DBS4 for enantioselective degradation of chiral herbicide diclofop-methyl. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133967. [PMID: 38457978 DOI: 10.1016/j.jhazmat.2024.133967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Diclofop-methyl, an aryloxyphenoxypropionate (AOPP) herbicide, is a chiral compound with two enantiomers. Microbial detoxification and degradation of various enantiomers is garnering immense research attention. However, enantioselective catabolism of diclofop-methyl has been rarely explored, especially at the molecular level. This study cloned two novel hydrolase genes (dcmA and dcmH) in Sphingopyxis sp. DBS4, and characterized them for diclofop-methyl degradation. DcmA, a member of the amidase superfamily, exhibits 26.1-45.9% identity with functional amidases. Conversely, DcmH corresponded to the DUF3089 domain-containing protein family (a family with unknown function), sharing no significant similarity with other biochemically characterized proteins. DcmA exhibited a broad spectrum of substrates, with preferential hydrolyzation of (R)-(+)-diclofop-methyl, (R)-(+)-quizalofop-ethyl, and (R)-(+)-haloxyfop-methyl. DcmH also preferred (R)-(+)-quizalofop-ethyl and (R)-(+)-haloxyfop-methyl degradation while displaying no apparent enantioselective activity towards diclofop-methyl. Using site-directed mutagenesis and molecular docking, it was determined that Ser175 was the fundamental residue influencing DcmA's activity against the two enantiomers of diclofop-methyl. For the degradation of AOPP herbicides, DcmA is an enantioselective amidase that has never been reported in research. This study provided novel hydrolyzing enzyme resources for the remediation of diclofop-methyl in the environment and deepened the understanding of enantioselective degradation of chiral AOPP herbicides mediated by microbes.
Collapse
Affiliation(s)
- Zhenbo Mao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Man Song
- College of Chemistry and Materials Science, Huaibei Normal University, 235000 Huaibei, China
| | - Ruiqi Zhao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Yuan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Yumeng Zhu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Xinyu Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Hailong Liang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Huijun Zhang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Guangli Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Long Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China; Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, 235000 Huaibei, China.
| |
Collapse
|
5
|
Wannenmacher N, Heberle M, Yu X, Demircan A, Wanner DM, Pfeffer C, Peters R. Diastereospecific Enantiodivergent Allylation of Pyrazolones as an Entry to β‐Aminoamides. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Nick Wannenmacher
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| | - Martin Heberle
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| | - Xin Yu
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| | - Aysegül Demircan
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| | - Daniel M. Wanner
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| | - Camilla Pfeffer
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| | - René Peters
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 D-70569 Stuttgart Germany
| |
Collapse
|
6
|
Xu PW, Cui XY, Chen C, Zhou F, Yu JS, Ao YF, Zhou J. Enantioselective Synthesis of C α-Tetrasubstituted N-Hydroxyl-α-amino Nitriles via Cyanation of Ketonitrones Using Me 2(CH 2Cl)SiCN. Org Lett 2021; 23:8471-8476. [PMID: 34644098 DOI: 10.1021/acs.orglett.1c03176] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Here, we report an unprecedented catalytic enantioselective cyanation of ketonitrones enabled by the bifunctional cyanating reagent Me2(CH2Cl)SiCN. This approach allows facile access to optically active N-hydroxyl-α-amino nitriles that are of high synthetic value but difficult to acquire by other methods. The use of bifunctional cyanating reagent Me2(CH2Cl)SiCN not only achieves an enantioselectivity higher than that with TMSCN but also enables various diversification reactions of the resulting silylated adducts. This represents the first enantioselective catalytic nucleophilic addition reaction of unactivated ketone-derived nitrones, exhibiting the potential of such tetrasubstituted C═N bonds for asymmetric synthesis of N-hydroxy α-amino acids and other N-hydroxy tertiary amines.
Collapse
Affiliation(s)
- Peng-Wei Xu
- Shanghai Key Laboratory of Green Chemistry and Chemical Process and Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai 200062, China
| | - Xiao-Yuan Cui
- Shanghai Key Laboratory of Green Chemistry and Chemical Process and Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai 200062, China
| | - Chen Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Process and Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai 200062, China
| | - Feng Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Process and Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai 200062, China
| | - Jin-Sheng Yu
- Shanghai Key Laboratory of Green Chemistry and Chemical Process and Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai 200062, China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jian Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Process and Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai 200062, China.,Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education, Hainan Normal University, Haikou 571158, China
| |
Collapse
|
7
|
Hu H, Wang Q, Wang D, Ao Y. Modification of the Enantioselectivity of Biocatalytic
meso
‐Desymmetrization for Synthesis of Both Enantiomers of
cis
‐1,2‐Disubstituted Cyclohexane by Amidase Engineering. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hui‐Juan Hu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry Chinese Academy of Sciences Beijing 100190 People's Republic of China
- State Key Laboratory of NBC Protection for Civilian Beijing 102205 People's Republic of China
| | - Qi‐Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry Chinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - De‐Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry Chinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Yu‐Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry Chinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| |
Collapse
|
8
|
Hu HJ, Wang QQ, Wang DX, Ao YF. Enantioselective biocatalytic desymmetrization for synthesis of enantiopure cis-3,4-disubstituted pyrrolidines. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
9
|
Ao YF, Hu HJ, Zhao CX, Chen P, Huang T, Chen H, Wang QQ, Wang DX, Wang MX. Reversal and Amplification of the Enantioselectivity of Biocatalytic Desymmetrization toward Meso Heterocyclic Dicarboxamides Enabled by Rational Engineering of Amidase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01220] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui-Juan Hu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Cheng-Xin Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei-Xiang Wang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
10
|
Tan W, Liu J, Li Z, Xu Z, Xin W, Xi L. Cloning, expression and biochemical characterization of a novel amidase from Thauera sinica K11. Protein Expr Purif 2020; 177:105751. [PMID: 32931916 DOI: 10.1016/j.pep.2020.105751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
A novel amidase (TAM) was identified and cloned from the genome of Thauera sinica K11. The recombinant protein was purified to homogeneity by one-step affinity chromatography for up to 26.4-fold with a yield of 38.1%. Gel filtration chromatography and SDS-PAGE revealed that the enzyme was a tetramer with a subunit of approximately 37.5 kDa. The amidase exhibited the maximum acyl transfer activity at 45 °C and pH 7.0, and it was highly stable over a wide pH range of 6.0-11.0. Inhibition of enzyme activity was observed in the presence of metal ions, thiol reagents and organic solvents. TAM showed a broad substrate spectrum toward aliphatic, aromatic and heterocyclic amides. For linear aliphatic monoamides, the acyl transfer activity of TAM was decreased with the extension of the carbon chain length, and thus the highest activity of 228.2 U/mg was obtained when formamide was used as substrate. This distinct selectivity of amidase to linear aliphatic monoamides expanded the findings of signature amidases to substrate specificity.
Collapse
Affiliation(s)
- Wenfei Tan
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianguo Liu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Ziyi Li
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Zhenzhen Xu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wen Xin
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Lijun Xi
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| |
Collapse
|
11
|
Singh RV, Sharma H, Ganjoo A, Kumar A, Babu V. Novel amidase catalysed process for the synthesis of vorinostat drug. J Appl Microbiol 2020; 129:1589-1597. [PMID: 32594558 DOI: 10.1111/jam.14753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/27/2022]
Abstract
AIM Presently, N-hydroxy-N'-phenyloctanediamide (vorinostat) which is an effective histone deacetylase inhibitor, is being synthesized chemically. Hence, present study aims to develop an eco-friendly approach for the synthesis of vorinostat from N'-phenyloctanediamide through biotransformation. METHODS AND RESULTS Using the amidase of Bacillus smithii IIIMB2907 in time course conversion and organic solvent compatibility, maximum bioconversion was observed at 12 h of reaction time and in presence of ethanol, respectively. Potassium phosphate buffer of pH 7·0 supported maximum bioconversion of N'-phenyloctanediamide (10 mmol l-1 ) into N-hydroxy-N'- phenyloctanediamide at 40°C. Bench scale study was successfully carried out with 83% yield of purified vorinostat. CONCLUSION In this study, an eco-friendly approach for the biotransformation of N'-phenyloctanediamide into vorinostat was developed by using cell free extract of thermophilic strain B. smithii IIIMB2907. SIGNIFICANCE AND IMPACT OF THE STUDY Microbial amidase has achieved remarkable attention in the field of biotransformation for the green synthesis of hydroxamic acids. Utilization of amidase from B. smithii IIIMB2907, specifically in the synthesis of vorinostat drug is a foremost attempt in the development a novel process and can also be employed in the synthesis of its derivatives as well.
Collapse
Affiliation(s)
- R V Singh
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - H Sharma
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - A Ganjoo
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - A Kumar
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - V Babu
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
12
|
Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
Collapse
Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| |
Collapse
|
13
|
Mourelle-Insua Á, Méndez-Sánchez D, Galman JL, Slabu I, Turner NJ, Gotor-Fernández V, Lavandera I. Efficient synthesis of α-alkyl-β-amino amides by transaminase-mediated dynamic kinetic resolutions. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01004a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A transaminase-catalyzed dynamic kinetic resolution is described for the stereoselective synthesis of a series of α-alkyl-β-amino amides.
Collapse
Affiliation(s)
- Ángela Mourelle-Insua
- Organic and Inorganic Chemistry Department
- University of Oviedo
- 33006 Oviedo
- Spain
- School of Chemistry
| | | | - James L. Galman
- School of Chemistry
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Iustina Slabu
- School of Chemistry
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Nicholas J. Turner
- School of Chemistry
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | | | - Iván Lavandera
- Organic and Inorganic Chemistry Department
- University of Oviedo
- 33006 Oviedo
- Spain
| |
Collapse
|
14
|
Sharma H, Singh RV, Raina C, Babu V. Amide hydrolyzing potential of amidase from halotolerant bacterium Brevibacterium sp. IIIMB2706. BIOCATAL BIOTRANSFOR 2018. [DOI: 10.1080/10242422.2018.1494733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Hitesh Sharma
- Fermentation Technology Division, CSIR–Indian Institute of Integrative Medicine, Jammu, India
| | - Rahul Vikram Singh
- Fermentation Technology Division, CSIR–Indian Institute of Integrative Medicine, Jammu, India
| | - Chand Raina
- Fermentation Technology Division, CSIR–Indian Institute of Integrative Medicine, Jammu, India
| | - Vikash Babu
- Fermentation Technology Division, CSIR–Indian Institute of Integrative Medicine, Jammu, India
| |
Collapse
|
15
|
Ruan LT, Zheng RC, Zheng YG. A novel amidase from Brevibacterium epidermidis ZJB-07021: gene cloning, refolding and application in butyrylhydroxamic acid synthesis. ACTA ACUST UNITED AC 2016; 43:1071-83. [DOI: 10.1007/s10295-016-1786-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
Abstract
A novel amidase gene (bami) was cloned from Brevibacterium epidermidis ZJB-07021 by combination of degenerate PCR and high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). The deduced amino acid sequence showed low identity (≤55 %) with other reported amidases. The bami gene was overexpressed in Escherichia coli, and the resultant inclusion bodies were refolded and purified to homogeneity with a recovery of 22.6 %. Bami exhibited a broad substrate spectrum towards aliphatic, aromatic and heterocyclic amides, and showed the highest acyl transfer activity towards butyramide with specific activity of 1331.0 ± 24.0 U mg−1. Kinetic analysis demonstrated that purified Bami exhibited high catalytic efficiency (414.9 mM−1 s−1) for acyl transfer of butyramide, with turnover number (K cat) of 3569.0 s−1. Key parameters including pH, substrate/co-substrate concentration, reaction temperature and catalyst loading were investigated and the Bami showed maximum acyl transfer activity at 50 °C, pH 7.5. Enzymatic catalysis of 200 mM butyramide with 15 μg mL−1 purified Bami was completed in 15 min with a BHA yield of 88.1 % under optimized conditions. The results demonstrated the great potential of Bami for the production of a variety of hydroxamic acids.
Collapse
Affiliation(s)
- Li-Tao Ruan
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Ren-Chao Zheng
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Yu-Guo Zheng
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| |
Collapse
|
16
|
Ruan LT, Zheng RC, Zheng YG, Shen YC. Purification and characterization of R -stereospecific amidase from Brevibacterium epidermidis ZJB-07021. Int J Biol Macromol 2016; 86:893-900. [DOI: 10.1016/j.ijbiomac.2016.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 11/25/2022]
|
17
|
Guo FM, Wu JP, Yang LR, Xu G. Soluble and functional expression of a recombinant enantioselective amidase from Klebsiella oxytoca KCTC 1686 in Escherichia coli and its biochemical characterization. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
18
|
Chen F, Xie T, Yue Y, Qian S, Chao Y, Pei J. Molecular dynamic analysis of mutant Y195I α-cyclodextrin glycosyltransferase with switched product specificity from α-cyclodextrin to γ-cyclodextrin. J Mol Model 2015. [PMID: 26216223 DOI: 10.1007/s00894-015-2734-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alpha-cyclodextrin (α-CD) glycosyltransferase (α-CGTase) can convert starch into α-CD blended with various proportions of β-cyclodextrin (β-CD) and/or γ-cyclodextrin (γ-CD). In this study, we verified the catalytic characteristics of purified Y195I α-CGTase and elucidated the mechanism of action with molecular dynamic (MD) simulations. We found that purified Y195I α-CGTase produced less α-CD, slightly more β-CD, and significantly more γ-CD than wild-type α-CGTase. Correspondingly, α-CD-based K m values increased, and β-CD- and γ-CD-based K m values decreased. MD simulation studies revealed that the dynamic trajectories of the substrate oligosaccharide chain in the mutant CGTase binding site were significantly different from those in the wild-type enzyme, with reduced hydrophobic interaction, finally resulting in different product specificity and more γ-CD formation.
Collapse
Affiliation(s)
- Fangjin Chen
- Center for Quantitative Biology, AAIS, Peking University, Beijing, China, 100871
| | | | | | | | | | | |
Collapse
|
19
|
Presence of multiple acyltranferases with diverse substrate specificity in Bacillus smithii strain IITR6b2 and characterization of unique acyltransferase with nicotinamide. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
20
|
Xie T, Hou Y, Li D, Yue Y, Qian S, Chao Y. Structural basis of a mutant Y195I α-cyclodextrin glycosyltransferase with switched product specificity from α-cyclodextrin to β-/γ-cyclodextrin. J Biotechnol 2014; 182-183:92-6. [DOI: 10.1016/j.jbiotec.2014.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/17/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
|
21
|
Yue Y, Song B, Xie T, Sun Y, Chao Y, Qian S. Enhancement of α-cyclodextrin product specificity by enriching histidines of α-cyclodextrin glucanotransferase at remote subsite −6. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Site-saturation mutagenesis of central tyrosine 195 leading to diverse product specificities of an α-cyclodextrin glycosyltransferase from Paenibacillus sp. 602-1. J Biotechnol 2013; 170:10-6. [PMID: 24246271 DOI: 10.1016/j.jbiotec.2013.10.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 11/20/2022]
Abstract
Central tyrosine 195 plays an important role in the active site of cyclodextrin glycosyltransferase (CGTase) that is highly conservative among various CGTases. However, a detailed functional understanding of this subsite is lacking. In this study, we applied site-directed saturation mutagenesis to investigate the effect of tyrosine 195 on the hydrolytic activity and cyclization specificity of an α-CGTase. A total of 17 mutant CGTases were obtained and heterologously expressed in E. coli. The mutant Y195F α-CGTase showed similar characteristics with wild-type α-CGTase. The other mutant α-CGTases showed considerably lower activity for starch-degradation and cyclodextrin (CD) formation. Interestingly, we found that the main product of mutant Y195R α-CGTase was γ-CDs (50%), not α-CDs (35%). The mutant Y195I α-CGTase drastically altered the CD specificity of α-CGTase, which showed a switch toward the synthesis of both β- and γ-CDs with percentages of 34% and 38%, respectively. Other mutant CGTases retained the α-CD as the main product but with lower percentages than wild-type α-CGTase. Mutant Y195F, Y195I, and Y195R CGTases showed an optimal temperature of 50°C and pH 6.5. The mutants Y195I and Y195R also showed better thermostability. These findings suggested that aromatic amino acids Tyr or Phe at the 195 position were important for the amylolytic activity and cyclization specificity of α-CGTase. The mutants Y195I CGTase and Y195R CGTase have potential applications for γ-CD production in the future.
Collapse
|
23
|
Jin LQ, Liu ZQ, Xu JM, Zheng RC, Zheng YG, Shen YC. Efficient biocatalytic hydrolysis of 2-chloronicotinamide for production of 2-chloronicotinic acid by recombinant amidase. CATAL COMMUN 2013. [DOI: 10.1016/j.catcom.2013.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
24
|
Mehta PK, Bhatia SK, Bhatia RK, Bhalla TC. Purification and characterization of a novel thermo-active amidase from Geobacillus subterraneus RL-2a. Extremophiles 2013; 17:637-48. [DOI: 10.1007/s00792-013-0547-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/12/2013] [Indexed: 11/30/2022]
|