1
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Yang L, Li X, Zhao L, Hu W, Qian Y. Design, synthesis and bioactivity evaluation of novel monomethyl auristatin F analogues. Mol Divers 2024:10.1007/s11030-024-10873-1. [PMID: 38762686 DOI: 10.1007/s11030-024-10873-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 05/20/2024]
Abstract
Monomethyl auristatin F (MMAF), a synthetic analogue of the natural compound dolastatin 10, has garnered significant attention in cancer research due to its high potency in vitro. While previous studies have focused on modifying the N-terminal extension of the amino group and the C-terminal modification of the carboxyl group, there has been limited exploration into modifying the P1 and P5 side chains. In this study, we substituted the valine residue at the P1 position with various natural or unnatural amino acids and introduced triazole functional groups at the P5 side chain. Compounds 11k and 18d exhibited excellent inhibition on tubulin. Additionally, compound 18d demonstrated enhanced cytotoxicity against HCT116 cells compared to the parent compound MMAF, suggesting its potential as a cytotoxic payload for further antibody-drug conjugates (ADCs) development.
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Affiliation(s)
- Lisheng Yang
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xinglin Li
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lei Zhao
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Wenhao Hu
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Yu Qian
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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Ghatak A, Shanbhag AP, Datta S. Reducing the vicissitudes of heterologous prochiral substrate catalysis by alcohol dehydrogenases through machine learning algorithms. Biochem Biophys Res Commun 2024; 691:149298. [PMID: 38011820 DOI: 10.1016/j.bbrc.2023.149298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/31/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
Alcohol dehydrogenases (ADHs) are popular catalysts for synthesizing chiral synthons a vital step for active pharmaceutical intermediate (API) production. They are grouped into three superfamilies namely, medium-chain (MDRs), short-chain dehydrogenase/reductases (SDRs), and iron-containing alcohol dehydrogenases. The former two are used extensively for producing various chiral synthons. Many studies screen multiple enzymes or engineer a specific enzyme for catalyzing a substrate of interest. These processes are resource-intensive and intricate. The current study attempts to decipher the ability to match different ADHs with their ideal substrates using machine learning algorithms. We explore the catalysis of 284 antibacterial ketone intermediates, against MDRs and SDRs to demonstrate a unique pattern of activity. To facilitate machine learning we curated a dataset comprising 33 features, encompassing 4 descriptors for each compound. Subsequently, an ensemble of machine learning techniques viz. Partial Least Squares (PLS) regression, k-Nearest Neighbors (kNN) regression, and Support Vector Machine (SVM) regression, was harnessed. Moreover, the assimilation of Principal Component Analysis (PCA) augmented precision and accuracy, thereby refining and demarcating diverse compound classes. As such, this classification is useful for discerning substrates amenable to diverse alcohol dehydrogenases, thereby mitigating the reliance on high-throughput screening or engineering in identifying the optimal enzyme for specific substrate.
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Affiliation(s)
- Arindam Ghatak
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India; Biomoneta Research Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India
| | - Anirudh P Shanbhag
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India.
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS), UAS GKVK, Bangalore, 560065, India
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3
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Zhou J, Zhang L, Wang Y, Song W, Huang Y, Mu Y, Schmitz W, Zhang SY, Lin H, Chen HZ, Ye F, Zhang L. The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202313109. [PMID: 37779101 DOI: 10.1002/anie.202313109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily members acyl-ACP reductases FabG and FabI are indispensable core enzymatic modules and catalytic orientation controllers in type-II fatty acid biosynthesis. Herein, we report their distinct substrate allosteric recognition and enantioselective reduction mechanisms. FabG achieves allosteric regulation of ACP and NADPH through ACP binding across two adjacent FabG monomers, while FabI follows an irreversible compulsory order of substrate binding in that NADH binding must precede that of ACP on a discrete FabI monomer. Moreover, FabG and FabI utilize a backdoor residue Phe187 or a "rheostat" α8 helix for acyl chain length selection, and their corresponding triad residues Ser142 or Tyr145 recognize the keto- or enoyl-acyl substrates, respectively, facilitating initiation of nucleophilic attack by NAD(P)H. The other two triad residues (Tyr and Lys) mediate subsequent proton transfer and (R)-3-hydroxyacyl- or saturated acyl-ACP production.
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Affiliation(s)
- Jiashen Zhou
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yiran Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Wenyan Song
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuzhou Huang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, 97074, Germany
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Biomedical Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Fei Ye
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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4
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Li Q, Gao R, Li Y, Fan B, Ma C, He YC. Improved biotransformation of lignin-valorized vanillin into vanillylamine in a sustainable bioreaction medium. BIORESOURCE TECHNOLOGY 2023; 384:129292. [PMID: 37295479 DOI: 10.1016/j.biortech.2023.129292] [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: 05/09/2023] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
Lignin is a critical biopolymer for creating a large number of highly valuable biobased compounds. Vanillin, one of lignin-derived aromatics, can be used to synthesize vanillylamine that is a key fine chemical and pharmaceutical intermediate. To produce vanillylamine, a productive whole-cell-catalyzed biotransformation of vanillin was developed in deep eutectic solvent - surfactant - H2O media. One newly created recombinant E. coli 30CA cells expressing ω-transaminase and L-alanine dehydrogenase was employed to transform 50 mM and 60 mM vanillin into vanillylamine in the yield of 82.2% and 8.5% under 40 °C, respectively. The biotransamination efficiency was enhanced by introducing surfactant PEG-2000 (40 mM) and deep eutectic solvent ChCl:LA (5.0 wt%, pH 8.0), and the highest vanillylamine yield reached 90.0% from 60 mM vanillin. Building an effective bioprocess was utilized for transamination of lignin-derived vanillin to vanillylamine with newly created bacteria in an eco-friendly medium, which had potential application for valorization of lignin to value-added compounds.
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Affiliation(s)
- Qi Li
- School of Pharmacy, National-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Changzhou University, Changzhou 213164, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Lifes, Hubei University, Wuhan 430062, Hubei Province, PR China
| | - Ruiying Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Lifes, Hubei University, Wuhan 430062, Hubei Province, PR China
| | - Yucheng Li
- School of Pharmacy, National-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Changzhou University, Changzhou 213164, PR China
| | - Bo Fan
- School of Pharmacy, National-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Changzhou University, Changzhou 213164, PR China
| | - Cuiluan Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Lifes, Hubei University, Wuhan 430062, Hubei Province, PR China
| | - Yu-Cai He
- School of Pharmacy, National-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Changzhou University, Changzhou 213164, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Lifes, Hubei University, Wuhan 430062, Hubei Province, PR China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
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5
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Ketoreductase-assisted synthesis of chiral selective tert-butyl{5-[(4-cyanophenyl)(hydroxy)methyl]-2-fluorophenyl}carbamate: process minutiae, optimization and characterization. CHEMICAL PAPERS 2023. [DOI: 10.1007/s11696-023-02698-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6
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Preeti R, Reena R, Sindhu R, Awasthi MK, Pandey A, Binod P. Biosynthesis of (S)-1-(1-naphthyl) ethanol by microbial ketoreductase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9036-9047. [PMID: 35819672 DOI: 10.1007/s11356-022-21749-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
(S)-1-(1-naphthyl) ethanol (SNE) is a chiral drug intermediate for the production of mevinic acid analog, a potent cholesterol agent. It acts as an HMG-CoA reductase inhibitor and is hence used in the synthesis of statins. Statins are lipid-lowering drugs used to lower cholesterol in the body. In our present study, we carried out whole-cell bioreduction of 1-Acetonaphthone to enantiopure SNE using selected microorganisms acquired by soil acclimation technique. The microorganism which exhibited higher bioreduction activity was determined using high-performance liquid chromatography (HPLC), and it was identified as Pichia kudriavzevii by ITS primer sequencing. After optimizing the parameters, Pichia sp. produced SNE with good conversion (75%), yield (67%), and excellent enantiomeric excess (100%). The microbial enzyme showed higher activity at 24-h-old supernatant. The crude and partially purified enzyme exhibited a specific activity of 51.13 U/mL and 62.72 U/mL, respectively, with a 1.22 purification fold.
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Affiliation(s)
- Ranjan Preeti
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum, 695 019, Kerala, India
| | - Rooben Reena
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum, 695 019, Kerala, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum, 695 019, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West Agriculture and Forestry University, Yangling, 712 100, Shaanxi, China
| | - Ashok Pandey
- Centre for Innovation and Translational Research, Indian Institute for Toxicology Research, Council of Scientific and Industrial Research, 31 MG Marg, Lucknow, 226 001, India
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248007, Uttarakhand, India
- Centre for Energy and Environmental Sustainability, Uttar Pradesh, Lucknow, 226029, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum, 695 019, Kerala, India.
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
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7
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Dong H, Chang MCY. Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hongjun Dong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720-3200, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
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8
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Solieri L. The revenge of Zygosaccharomyces yeasts in food biotechnology and applied microbiology. World J Microbiol Biotechnol 2021; 37:96. [PMID: 33969449 DOI: 10.1007/s11274-021-03066-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/28/2021] [Indexed: 12/01/2022]
Abstract
Non-conventional yeasts refer to a huge and still poorly explored group of species alternative to the well-known model organism Saccharomyces cerevisiae. Among them, Zygosaccharomyces rouxii and the sister species Zygosaccharomyces bailii are infamous for spoiling food and beverages even in presence of several food preservatives. On the other hand, their capability to cope with a wide range of process conditions makes these yeasts very attractive factories (the so-called "ZygoFactories") for bio-converting substrates poorly permissive for the growth of other species. In balsamic vinegar Z. rouxii is the main yeast responsible for converting highly concentrated sugars into ethanol, with a preference for fructose over glucose (a trait called fructophily). Z. rouxii has also attracted much attention for the ability to release important flavor compounds, such as fusel alcohols and the derivatives of 4-hydroxyfuranone, which markedly contribute to fragrant and smoky aroma in soy sauce. While Z. rouxii was successfully proposed in brewing for producing low ethanol beer, Z. bailii is promising for lactic acid and bioethanol production. Recently, several research efforts exploited omics tools to pinpoint the genetic bases of distinctive traits in "ZygoFactories", like fructophily, tolerance to high concentrations of sugars, lactic acid and salt. Here, I provided an overview of Zygosaccharomyces industrially relevant phenotypes and summarized the most recent findings in disclosing their genetic bases. I suggest that the increasing number of genomes available for Z. rouxii and other Zygosaccharomyces relatives, combined with recently developed genetic engineering toolkits, will boost the applications of these yeasts in biotechnology and applied microbiology.
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Affiliation(s)
- L Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy.
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9
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Shanbhag AP. FabG: from a core to circumstantial catalyst. Biotechnol Lett 2019; 41:675-688. [PMID: 31037463 DOI: 10.1007/s10529-019-02678-2] [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: 03/05/2019] [Accepted: 04/22/2019] [Indexed: 12/30/2022]
Abstract
Core biochemical pathways such as Fatty-acid synthesis II (FAS II) is ascribed to the synthesis of fatty-acids, biotin and lipoic acid in prokaryotes. It has two dehydrogenases namely, FabG and FabI which interact with the fatty-acid chain bound to Acyl-carrier protein (ACP), a well-studied enzyme which binds to substrates of varying lengths. This protein-protein interaction 'broadens' the active site of these dehydrogenases thus, contributing to their flexible nature. This property is exploited for catalysing numerous chiral synthons, alkanes, long-chain alcohols and secondary metabolites in industries especially with FabG. FASI relegates FASII in eukaryotes making it a 'relic gene pool' and an antibacterial drug target with diverse inhibitor and substrate markush. FabG often substitutes other dehydrogenases for producing secondary metabolites in nature. This redundancy is probably due to gene duplication or addition events possibly making FabG, a progenitor to some of the complex short-chain dehydrogenases used in organisms and industries today.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India. .,Bugworks Research India Pvt. Ltd, C-CAMP, NCBS Campus, UAS-GKVK, Bellary Road, Bangalore, 560065, India.
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