1
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Moyer DC, Reimertz J, Segrè D, Fuxman Bass JI. Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600481. [PMID: 38979177 PMCID: PMC11230171 DOI: 10.1101/2024.06.24.600481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Genome-Scale Metabolic Models (GSMMs) are used for numerous tasks requiring computational estimates of metabolic fluxes, from predicting novel drug targets to engineering microbes to produce valuable compounds. A key limiting step in most applications of GSMMs is ensuring their representation of the target organism's metabolism is complete and accurate. Identifying and visualizing errors in GSMMs is complicated by the fact that they contain thousands of densely interconnected reactions. Furthermore, many errors in GSMMs only become apparent when considering pathways of connected reactions collectively, as opposed to examining reactions individually. Results We present Metabolic Accuracy Check and Analysis Workflow (MACAW), a collection of algorithms for detecting errors in GSMMs. The relative frequencies of errors we detect in manually curated GSMMs appear to reflect the different approaches used to curate them. Changing the method used to automatically create a GSMM from a particular organism's genome can have a larger impact on the kinds of errors in the resulting GSMM than using the same method with a different organism's genome. Our algorithms are particularly capable of identifying errors that are only apparent at the pathway level, including loops, and nontrivial cases of dead ends. Conclusions MACAW is capable of identifying inaccuracies of varying severity in a wide range of GSMMs. Correcting these errors can measurably improve the predictive capacity of a GSMM. The relative prevalence of each type of error we identify in a large collection of GSMMs could help shape future efforts for further automation of error correction and GSMM creation.
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2
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Tang P, Harding CJ, Dickson AL, da Silva RG, Harrison DJ, Czekster CM. Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase. ACS Catal 2024; 14:3090-3102. [PMID: 38449528 PMCID: PMC10913048 DOI: 10.1021/acscatal.3c06260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 03/08/2024]
Abstract
Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.
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Affiliation(s)
- Peijun Tang
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Christopher J. Harding
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Alison L. Dickson
- School
of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Rafael G. da Silva
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - David J. Harrison
- School
of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Clarissa Melo Czekster
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
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3
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Ono J, Matsumura Y, Mori T, Saito S. Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events. J Phys Chem B 2024; 128:20-32. [PMID: 38133567 DOI: 10.1021/acs.jpcb.3c05307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Proteins exhibit conformational fluctuations and changes over various time scales, ranging from rapid picosecond-scale local atomic motions to slower microsecond-scale global conformational transformations. In the presence of these intricate fluctuations, chemical reactions occur and functions emerge. These conformational fluctuations of proteins are not merely stochastic random motions but possess distinct spatiotemporal characteristics. Moreover, chemical reactions do not always proceed along a single reaction coordinate in a quasi-equilibrium manner. Therefore, it is essential to understand spatiotemporal conformational fluctuations of proteins and the conformational change processes associated with reactions. In this Perspective, we shed light on the complex dynamics of proteins and their role in enzyme catalysis by presenting recent results regarding dynamic couplings and disorder in the conformational dynamics of proteins and rare but rapid enzymatic reaction events obtained from molecular dynamics simulations.
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Affiliation(s)
- Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Yoshihiro Matsumura
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
| | - Toshifumi Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Shinji Saito
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
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4
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Bearne SL. Design and evaluation of substrate-product analog inhibitors for racemases and epimerases utilizing a 1,1-proton transfer mechanism. Methods Enzymol 2023; 690:397-444. [PMID: 37858537 DOI: 10.1016/bs.mie.2023.06.014] [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] [Indexed: 10/21/2023]
Abstract
Racemases and epimerases catalyze the inversion of stereochemistry at asymmetric carbon atoms to generate stereoisomers that often play important roles in normal and pathological physiology. Consequently, there is interest in developing inhibitors of these enzymes for drug discovery. A strategy for the rational design of substrate-product analog (SPA) inhibitors of racemases and epimerases utilizing a direct 1,1-proton transfer mechanism is elaborated. This strategy assumes that two groups on the asymmetric carbon atom remain fixed at active-site binding determinants, while the hydrogen and third, motile group move during catalysis, with the latter potentially traveling between an R- and S-pocket at the active site. SPAs incorporate structural features of the substrate and product, often with geminal disubstitution on the asymmetric carbon atom to simultaneously present the motile group to both the R- and S-pockets. For racemases operating on substrates bearing three polar groups (glutamate, aspartate, and serine racemases) or with compact, hydrophobic binding pockets (proline racemase), substituent motion is limited and the design strategy furnishes inhibitors with poor or modest binding affinities. The approach is most successful when substrates have a large, motile hydrophobic group that binds at a plastic and/or capacious hydrophobic site. Potent inhibitors were developed for mandelate racemase, isoleucine epimerase, and α-methylacyl-CoA racemase using the SPA inhibitor design strategy, exhibiting binding affinities ranging from substrate-like to exceeding that of the substrate by 100-fold. This rational approach for designing inhibitors of racemases and epimerases having the appropriate active-site architectures is a useful strategy for furnishing compounds for drug development.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
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5
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Zhu Y, Wang Y, Zhang S, Li J, Li X, Ying Y, Yuan J, Chen K, Deng S, Wang Q. Association of polymicrobial interactions with dental caries development and prevention. Front Microbiol 2023; 14:1162380. [PMID: 37275173 PMCID: PMC10232826 DOI: 10.3389/fmicb.2023.1162380] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Dental caries is a common oral disease. In many cases, disruption of the ecological balance of the oral cavity can result in the occurrence of dental caries. There are many cariogenic microbiota and factors, and their identification allows us to take corresponding prevention and control measures. With the development of microbiology, the caries-causing bacteria have evolved from the traditional single Streptococcus mutans to the discovery of oral symbiotic bacteria. Thus it is necessary to systematically organized the association of polymicrobial interactions with dental caries development. In terms of ecology, caries occurs due to an ecological imbalance of the microbiota, caused by the growth and reproduction of cariogenic microbiota due to external factors or the disruption of homeostasis by one's own factors. To reduce the occurrence of dental caries effectively, and considering the latest scientific viewpoints, caries may be viewed from the perspective of ecology, and preventive measures can be taken; hence, this article systematically summarizes the prevention and treatment of dental caries from the aspects of ecological perspectives, in particular the ecological biofilm formation, bacterial quorum sensing, the main cariogenic microbiota, and preventive measures.
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Affiliation(s)
- Yimei Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Ying Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Shuyang Zhang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Xin Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Yuanyuan Ying
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Jinna Yuan
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Shuli Deng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Qingjing Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
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Eletskaya BZ, Berzina MY, Fateev IV, Kayushin AL, Dorofeeva EV, Lutonina OI, Zorina EA, Antonov KV, Paramonov AS, Muzyka IS, Zhukova OS, Kiselevskiy MV, Miroshnikov AI, Esipov RS, Konstantinova ID. Enzymatic Synthesis of 2-Chloropurine Arabinonucleosides with Chiral Amino Acid Amides at the C6 Position and an Evaluation of Antiproliferative Activity In Vitro. Int J Mol Sci 2023; 24:ijms24076223. [PMID: 37047197 PMCID: PMC10094600 DOI: 10.3390/ijms24076223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
A number of purine arabinosides containing chiral amino acid amides at the C6 position of the purine were synthesized using a transglycosylation reaction with recombinant E. coli nucleoside phosphorylases. Arsenolysis of 2-chloropurine ribosides with chiral amino acid amides at C6 was used for the enzymatic synthesis, and the reaction equilibrium shifted towards the synthesis of arabinonucleosides. The synthesized nucleosides were shown to be resistant to the action of E. coli adenosine deaminase. The antiproliferative activity of the synthesized nucleosides was studied on human acute myeloid leukemia cell line U937. Among all the compounds, the serine derivative exhibited an activity level (IC50 = 16 μM) close to that of Nelarabine (IC50 = 3 μM) and was evaluated as active.
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Affiliation(s)
- Barbara Z. Eletskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
- Correspondence: (B.Z.E.); (I.D.K.)
| | - Maria Ya. Berzina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Ilya V. Fateev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Alexei L. Kayushin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Elena V. Dorofeeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Olga I. Lutonina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Ekaterina A. Zorina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Konstantin V. Antonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Alexander S. Paramonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Inessa S. Muzyka
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Olga S. Zhukova
- State N.N. Blokhin Russian Cancer Research Center, Kashirsky Highway, 24, 115478 Moscow, Russia
| | - Mikhail V. Kiselevskiy
- State N.N. Blokhin Russian Cancer Research Center, Kashirsky Highway, 24, 115478 Moscow, Russia
| | - Anatoly I. Miroshnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Roman S. Esipov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
| | - Irina D. Konstantinova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia
- Correspondence: (B.Z.E.); (I.D.K.)
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7
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Bearne SL. Capturing the free energy of transition state stabilization: insights from the inhibition of mandelate racemase. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220041. [PMID: 36633273 PMCID: PMC9835602 DOI: 10.1098/rstb.2022.0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mandelate racemase (MR) catalyses the Mg2+-dependent interconversion of (R)- and (S)-mandelate. To effect catalysis, MR stabilizes the altered substrate in the transition state (TS) by approximately 26 kcal mol-1 (-ΔGtx), such that the upper limit of the virtual dissociation constant of the enzyme-TS complex is 2 × 10-19 M. Designing TS analogue inhibitors that capture a significant amount of ΔGtx for binding presents a challenge since there are a limited number of protein binding determinants that interact with the substrate and the structural simplicity of mandelate constrains the number of possible isostructural variations. Indeed, current intermediate/TS analogue inhibitors of MR capture less than or equal to 30% of ΔGtx because they fail to fully capitalize on electrostatic interactions with the metal ion, and the strength and number of all available electrostatic and H-bond interactions with binding determinants present at the TS. Surprisingly, phenylboronic acid (PBA), 2-formyl-PBA, and para-chloro-PBA capture 31-38% of ΔGtx. The boronic acid group interacts with the Mg2+ ion and multiple binding determinants that effect TS stabilization. Inhibitors capable of forming multiple interactions can exploit the cooperative interactions that contribute to optimum binding of the TS. Hence, maximizing interactions with multiple binding determinants is integral to effective TS analogue inhibitor design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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8
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Sharma H, Raju B, Narendra G, Motiwale M, Sharma B, Verma H, Silakari O. QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update. ChemistrySelect 2023. [DOI: 10.1002/slct.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Himani Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Gera Narendra
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Mohit Motiwale
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Bhavna Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Himanshu Verma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Om Silakari
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
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9
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Wang Y, Bian Z, Wang Y. Biofilm formation and inhibition mediated by bacterial quorum sensing. Appl Microbiol Biotechnol 2022; 106:6365-6381. [DOI: 10.1007/s00253-022-12150-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022]
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10
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Li J, Wang S, Liu C, Li Y, Wei Y, Fu G, Liu P, Ma H, Huang D, Lin J, Zhang D. Going Beyond the Local Catalytic Activity Space of Chitinase Using a Simulation-Based Iterative Saturation Mutagenesis Strategy. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinlong Li
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Sijia Wang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Cui Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yixin Li
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yu Wei
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, P. R. China
| | - Gang Fu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Hongwu Ma
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Huang
- College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Jianping Lin
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, P. R. China
| | - Dawei Zhang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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11
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Gao S, Zhang W, Barrow SL, Iavarone AT, Klinman JP. Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks. J Biol Chem 2022; 298:102350. [PMID: 35933011 PMCID: PMC9483566 DOI: 10.1016/j.jbc.2022.102350] [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: 04/04/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation (TDHDX-MS) has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend TDHDX from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine or DAA) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different HDX-MS properties for the two ligands, as expected from their 106-fold differences in strength of binding. By contrast, analogous patterns for TDHDX-MS emerge in the presence of both DAA and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended TDHDX to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility vs. site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.
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Affiliation(s)
- Shuaihua Gao
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Samuel L Barrow
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720, United States; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, 94720, United States; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, United States.
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12
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Lawal MM, Vaissier Welborn V. Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase. Chembiochem 2022; 23:e202200097. [PMID: 35303385 DOI: 10.1002/cbic.202200097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Indexed: 11/12/2022]
Abstract
Electrostatic preorganization as well as structural and dynamic heterogeneity are often used to rationalize the remarkable catalytic efficiency of enzymes. However, they are often presented as incompatible because the generation of permanent electrostatic effects implies that the protein structure remains rigid. Here, we use a metric, electric fields, that can treat electrostatic contributions and dynamics effects on equal footing, for a unique perspective on enzymatic catalysis. We find that the residues that contribute the most to electrostatic interactions with the substrate in the active site of Adenylate Kinase (our working example) are also the most flexible residues. Further, entropy-tuning mutations raise flexibility at the picosecond timescale where more conformations can be visited on short time periods, thereby softening the sharp heterogeneity normally visible at the microsecond timescale.
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Affiliation(s)
| | - Valerie Vaissier Welborn
- Virginia Polytechnic Institute and State University, Chemistry, Davidson 421A, 1040 Drillfield Drive, 24073, Blacksburg, UNITED STATES
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13
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Vanadate as a new substrate for nucleoside phosphorylases. J Biol Inorg Chem 2022; 27:221-227. [DOI: 10.1007/s00775-021-01923-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
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14
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Zalloum WA, Zalloum N. Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl-l-lysine Substrate with Histone Deacetylase 8. J Phys Chem B 2021; 125:5321-5337. [PMID: 33998791 DOI: 10.1021/acs.jpcb.1c01696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Targeting the genetic material without destruction is a priority to develop safe anticancer drugs. Histone deacetylase 8 (HDAC8), which is proved to be involved in carcinogenesis, is an enzyme associated with the chromatin for post-translational deacetylation of acetylated lysine. In this study, HDAC8 co-crystallized with the intermediate state tetrapeptide Trapoxin A (TA) inhibitor and the holoenzyme are utilized to find their conformational ensembles. Furthermore, the co-crystallized intermediate gem-diolate TA was used to find optimum interactions with the active site residues by conventional molecular dynamics (MD) simulation and QM/MM umbrella sampling. Finally, the intermediate state of the acetyl-l-lysine substrate was explored by QM/MM steered MD and compared to the binding of the intermediate state of the inhibitor. This research showed that HDAC8 is flexible and exists in conformational ensembles in its holoenzyme state. Binding of the intermediate state TA stabilizes its conformation. The optimum binding to the active site of HDAC8 for structures of gem-diolate TA (intermediate state) and acetyl-l-lysine (intermediate state) was determined according to the corresponding energy profiles. The use of these models will aid in the design of potentially reversible, potent, and selective inhibitors of HDAC8 for cancer treatment.
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Affiliation(s)
- Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O. Box 2882, Amman 11821, Jordan
| | - Needa Zalloum
- Department of Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
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15
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Lockbaum GJ, Henes M, Talledge N, Rusere LN, Kosovrasti K, Nalivaika EA, Somasundaran M, Ali A, Mansky LM, Yilmaz NK, Schiffer CA. Inhibiting HTLV-1 Protease: A Viable Antiviral Target. ACS Chem Biol 2021; 16:529-538. [PMID: 33619959 PMCID: PMC8126997 DOI: 10.1021/acschembio.0c00975] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus that can cause severe paralytic neurologic disease and immune disorders as well as cancer. An estimated 20 million people worldwide are infected with HTLV-1, with prevalence reaching 30% in some parts of the world. In stark contrast to HIV-1, no direct acting antivirals (DAAs) exist against HTLV-1. The aspartyl protease of HTLV-1 is a dimer similar to that of HIV-1 and processes the viral polyprotein to permit viral maturation. We report that the FDA-approved HIV-1 protease inhibitor darunavir (DRV) inhibits the enzyme with 0.8 μM potency and provides a scaffold for drug design against HTLV-1. Analogs of DRV that we designed and synthesized achieved submicromolar inhibition against HTLV-1 protease and inhibited Gag processing in viral maturation assays and in a chronically HTLV-1 infected cell line. Cocrystal structures of these inhibitors with HTLV-1 protease highlight opportunities for future inhibitor design. Our results show promise toward developing highly potent HTLV-1 protease inhibitors as therapeutic agents against HTLV-1 infections.
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Affiliation(s)
- Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nathaniel Talledge
- Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Louis M. Mansky
- Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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16
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Niazy AA. LuxS quorum sensing system and biofilm formation of oral microflora: A short review article. Saudi Dent J 2021; 33:116-123. [PMID: 33679103 PMCID: PMC7910685 DOI: 10.1016/j.sdentj.2020.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
The LuxS quorum sensing system is considered as the main system that most of the oral bacteria use to communicate in order to create biofilms. Here we identified 11 of the most important biofilm formers that utilize the LuxS system and presented current and recent information regarding this system. Though different bacterial species are able to communicate thorough the LuxS system, it was also found that cross kingdom communication can occur between bacteria and fungi and bacteria and epithelial cells. Immune response also plays and important role in mitigating the effects of biofilms. Here we identified 6 of the most important molecules that are involved in the immune response to biofilms. These immune molecules maintain the stability in the oral cavity by preventing bacteria from overwhelming the space and simultaneously minimizing the immune response in order not to cause tissue damage. Here we also discuss current research being done in order to maintain the balance in the oral cavity via inhibiting biofilm formation without eradicating oral bacteria in order to prevent the overgrowth of other organisms such as Candida albicans. One approach being used is inhibiting AI-2 intermediates which leads to lack of quorum sensing communication between bacteria through the use of intermediate analogues. Another approach that found success is the utilization of D forms of sugars where D-ribose and D-galactose have been proven to inhibit the LuxS system and subsequently preventing the process of quorum sensing leading to the reduction in biofilm formation.
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Affiliation(s)
- Abdurahman A. Niazy
- Address: Molecular and Cell Biology Laboratory, Prince Naif bin AbdulAziz Health Research Center, College of Dentistry, King Saud University Medical City, King Saud University, Riyadh 11545, Saudi Arabia.
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17
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Kupski O, Funk LM, Sautner V, Seifert F, Worbs B, Ramsbeck D, Meyer F, Diederichsen U, Buchholz M, Schilling S, Demuth HU, Tittmann K. Hydrazides Are Potent Transition-State Analogues for Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer's Disease. Biochemistry 2020; 59:2585-2591. [PMID: 32551535 DOI: 10.1021/acs.biochem.0c00337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyloidogenic plaques are hallmarks of Alzheimer's disease (AD) and typically consist of high percentages of modified Aβ peptides bearing N-terminally cyclized glutamate residues. The human zinc(II) enzyme glutaminyl cyclase (QC) was shown in vivo to catalyze the cyclization of N-terminal glutamates of Aβ peptides in a pathophysiological side reaction establishing QC as a druggable target for therapeutic treatment of AD. Here, we report crystallographic snapshots of human QC catalysis acting on the neurohormone neurotensin that delineate the stereochemical course of catalysis and suggest that hydrazides could mimic the transition state of peptide cyclization and deamidation. This hypothesis is validated by a sparse-matrix inhibitor screening campaign that identifies hydrazides as the most potent metal-binding group compared to classic Zn binders. The structural basis of hydrazide inhibition is illuminated by X-ray structure analysis of human QC in complex with a hydrazide-bearing peptide inhibitor and reveals a pentacoordinated Zn complex. Our findings inform novel strategies in the design of potent and highly selective QC inhibitors by employing hydrazides as the metal-binding warhead.
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Affiliation(s)
- Oliver Kupski
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lisa-Marie Funk
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Viktor Sautner
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Franziska Seifert
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
| | - Brigitte Worbs
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstraß 2, 37077 Göttingen, Germany
| | - Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Franc Meyer
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstraß 2, 37077 Göttingen, Germany
| | - Mirko Buchholz
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Stephan Schilling
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Hans-Ulrich Demuth
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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18
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Mori T, Saito S. Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase. J Chem Theory Comput 2020; 16:3396-3407. [PMID: 32268066 DOI: 10.1021/acs.jctc.9b01279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle ζ and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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19
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Droplet-based optofluidic systems for measuring enzyme kinetics. Anal Bioanal Chem 2019; 412:3265-3283. [PMID: 31853606 DOI: 10.1007/s00216-019-02294-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 01/05/2023]
Abstract
The study of enzyme kinetics is of high significance in understanding metabolic networks in living cells and using enzymes in industrial applications. To gain insight into the catalytic mechanisms of enzymes, it is necessary to screen an enormous number of reaction conditions, a process that is typically laborious, time-consuming, and costly when using conventional measurement techniques. In recent times, droplet-based microfluidic systems have proved themselves to be of great utility in large-scale biological experimentation, since they consume a minimal sample, operate at high analytical throughput, are characterized by efficient mass and heat transfer, and offer high levels of integration and automation. The primary goal of this review is the introduction of novel microfluidic tools and detection methods for use in high-throughput and sensitive analysis of enzyme kinetics. The first part of this review focuses on introducing basic concepts of enzyme kinetics and describing most common microfluidic approaches, with a particular focus on segmented flow. Herein, the key advantages include accurate control over the flow behavior, efficient mass and heat transfer, multiplexing, and high-level integration with detection modalities. The second part describes the current state-of-the-art platforms for high-throughput and sensitive analysis of enzyme kinetics. In addition to our categorization of recent advances in measuring enzyme kinetics, we have endeavored to critically assess the limitations of each of these detection approaches and propose strategies to improve measurements in droplet-based microfluidics. Graphical abstract.
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20
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Chen S, Kapilashrami K, Senevirathne C, Wang Z, Wang J, Linscott JA, Luo M. Substrate-Differentiated Transition States of SET7/9-Catalyzed Lysine Methylation. J Am Chem Soc 2019; 141:8064-8067. [PMID: 31034218 DOI: 10.1021/jacs.9b02553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transition state stabilization is essential for rate acceleration of enzymatic reactions. Despite extensive studies on various transition state structures of enzymes, an intriguing puzzle is whether an enzyme can accommodate multiple transition states (TSs) to catalyze a chemical reaction. It is experimentally challenging to study this proposition in terms of the choices of suitable enzymes and the feasibility to distinguish multiple TSs. As a paradigm with the protein lysine methyltransferase (PKMT) SET7/9 paired with its physiological substrates H3 and p53, their TSs were solved with experimental kinetic isotope effects as computational constraints. Remarkably, SET7/9 adopts two structurally distinct TSs, a nearly symmetric SN2 and an extremely early SN2, for H3K4 and p53K372 methylation, respectively. The two TSs are also different from those previously revealed for other PKMTs. The setting of multiple TSs is expected to be essential for SET7/9 and likely other PKMTs to act on broad substrates with high efficiency.
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Affiliation(s)
| | | | | | - Zhen Wang
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | | | - Joshua A Linscott
- Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
| | - Minkui Luo
- Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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21
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Cheviet T, Lefebvre-Tournier I, Wein S, Peyrottes S. Plasmodium Purine Metabolism and Its Inhibition by Nucleoside and Nucleotide Analogues. J Med Chem 2019; 62:8365-8391. [PMID: 30964283 DOI: 10.1021/acs.jmedchem.9b00182] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Malaria still affects around 200 million people and is responsible for more than 400,000 deaths per year, mostly children in subequatorial areas. This disease is caused by parasites of the Plasmodium genus. Only a few WHO-recommended treatments are available to prevent or cure plasmodial infections, but genetic mutations in the causal parasites have led to onset of resistance against all commercial antimalarial drugs. New drugs and targets are being investigated to cope with this emerging problem, including enzymes belonging to the main metabolic pathways, while nucleoside and nucleotide analogues are also a promising class of potential drugs. This review highlights the main metabolic pathways targeted for the development of potential antiplasmodial therapies based on nucleos(t)ide analogues, as well as the different series of purine-containing nucleoside and nucleotide derivatives designed to inhibit Plasmodium falciparum purine metabolism.
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Affiliation(s)
- Thomas Cheviet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM , Université Montpellier, Equipe Nucléosides & Effecteurs Phosphorylés , Place E. Bataillon, cc 1704 , 34095 Montpellier , France
| | - Isabelle Lefebvre-Tournier
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM , Université Montpellier, Equipe Nucléosides & Effecteurs Phosphorylés , Place E. Bataillon, cc 1704 , 34095 Montpellier , France
| | - Sharon Wein
- Dynamique des Interactions Membranaires Normales et Pathologiques (DIMNP), UMR 5235 UM-CNRS , Université Montpellier , Place E. Bataillon , 34095 Montpellier , France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 UM-CNRS-ENSCM , Université Montpellier, Equipe Nucléosides & Effecteurs Phosphorylés , Place E. Bataillon, cc 1704 , 34095 Montpellier , France
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22
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Shiba T, Inaoka DK, Takahashi G, Tsuge C, Kido Y, Young L, Ueda S, Balogun EO, Nara T, Honma T, Tanaka A, Inoue M, Saimoto H, Harada S, Moore AL, Kita K. Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:375-382. [PMID: 30910528 DOI: 10.1016/j.bbabio.2019.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
The alternative oxidase (AOX) is a monotopic diiron carboxylate protein which catalyzes the four-electron reduction of dioxygen to water by ubiquinol. Although we have recently determined the crystal structure of Trypanosoma brucei AOX (TAO) in the presence and absence of ascofuranone (AF) derivatives (which are potent mixed type inhibitors) the mechanism by which ubiquinol and dioxygen binds to TAO remain inconclusive. In this article, ferulenol was identified as the first competitive inhibitor of AOX which has been used to probe the binding of ubiquinol. Surface plasmon resonance reveals that AF is a quasi-irreversible inhibitor of TAO whilst ferulenol binding is completely reversible. The structure of the TAO-ferulenol complex, determined at 2.7 Å, provided insights into ubiquinol binding and has also identified a potential dioxygen molecule bound in a side-on conformation to the diiron center for the first time.
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Affiliation(s)
- Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan.
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan.
| | - Gen Takahashi
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Chiaki Tsuge
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan
| | - Yasutoshi Kido
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Parasitology, Graduate School of Medicine, Osaka City University, Abeno-ku, Asahimachi 1-4-3, Osaka 545-8585, Japan
| | - Luke Young
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Satoshi Ueda
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria 2222, Nigeria
| | - Takeshi Nara
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Bunkyo-ku, Hongo 2-1-1, Tokyo, 113-8421, Japan
| | - Teruki Honma
- Systems and Structural Biology Center, RIKEN, Tsurumi, Suehiro 1-7-22, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Systems and Structural Biology Center, RIKEN, Tsurumi, Suehiro 1-7-22, Yokohama, Kanagawa 230-0045, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyamacho-Minami 4, Tottori 680-8552, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Anthony L Moore
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan; Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
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23
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Gair JJ, Qiu Y, Khade RL, Chan NH, Filatov AS, Zhang Y, Lewis JC. Synthesis, Characterization, and Theoretical Investigation of a Transition State Analogue for Proton Transfer during C–H Activation by a Rhodium-Pincer Complex. Organometallics 2019. [DOI: 10.1021/acs.organomet.8b00887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Joseph J. Gair
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Yehao Qiu
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Rahul L. Khade
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander S. Filatov
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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24
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Mori T, Saito S. Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase. J Phys Chem Lett 2019; 10:474-480. [PMID: 30607953 DOI: 10.1021/acs.jpclett.8b03607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Conformational flexibility of protein is essential for enzyme catalysis. Yet, how protein's conformational rearrangements and dynamics contribute to catalysis remains highly controversial. To unravel protein's role in catalysis, it is inevitable to understand the static and dynamic mechanisms simultaneously. To this end, here the Pin1-catalyzed isomerization reaction is studied from the two perspectives. The static view indicates that the hydrogen bonds involving Pin1 rearrange in a tightly coupled manner with isomerization. In sharp contrast, the isomerization dynamics are found to be very rapid; protein's slow conformational rearrangements thus cannot occur simultaneously with isomerization, and the reaction proceeds in a nonequilibrium manner. The distinctive protein conformations necessary to stabilize the transition state are prepared a priori, i.e., as conformational excited states. The present result suggests that enzymatic reaction is not a simple thermal activation from equilibrium directly to the transition state, thus adding a novel perspective to Pauling's view.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji , Okazaki , Aichi 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki , Aichi 444-8585 , Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji , Okazaki , Aichi 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki , Aichi 444-8585 , Japan
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25
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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26
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Roca M, Moliner V, Tuñón I. Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b04199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Roca
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - V. Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - I. Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
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27
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Moggré GJ, Poulin MB, Tyler PC, Schramm VL, Parker EJ. Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase. ACS Chem Biol 2017; 12:2662-2670. [PMID: 28872824 DOI: 10.1021/acschembio.7b00484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first step in histidine biosynthesis, a pathway essential to microorganisms and a validated target for antimicrobial drug design. The ATP-PRT enzyme catalyzes the reversible substitution reaction between phosphoribosyl pyrophosphate and ATP. The enzyme exists in two structurally distinct forms, a short- and a long-form enzyme. These forms share a catalytic core dimer but bear completely different allosteric domains and thus distinct quaternary assemblies. Understanding enzymatic transition states can provide essential information on the reaction mechanisms and insight into how differences in domain structure influence the reaction chemistry, as well as providing a template for inhibitor design. In this study, the transition state structures for ATP-PRT enzymes from Campylobacter jejuni and Mycobacterium tuberculosis (long-form enzymes) and from Lactococcus lactis (short-form) were determined and compared. Intrinsic kinetic isotope effects (KIEs) were obtained at reaction sensitive positions for the reverse reaction using phosphonoacetic acid, an alternative substrate to the natural substrate pyrophosphate. The experimental KIEs demonstrated mechanistic similarities between the three enzymes and provided experimental boundaries for quantum chemical calculations to characterize the transition states. Predicted transition state structures support a dissociative reaction mechanism with a DN*AN‡ transition state. Weak interactions from the incoming nucleophile and a fully dissociated ATP adenine are predicted regardless of the difference in overall structure and quaternary assembly. These studies establish that despite significant differences in the quaternary assembly and regulatory machinery between ATP-PRT enzymes from different sources, the reaction chemistry and catalytic mechanism are conserved.
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Affiliation(s)
- Gert-Jan Moggré
- Maurice
Wilkins Centre, Biomolecular Interaction Centre and Department of
Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Myles B. Poulin
- Department
of Chemistry and Biochemistry, University of Maryland College Park, College
Park, Maryland 20742, United States
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Peter C. Tyler
- Ferrier
Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Emily J. Parker
- Maurice
Wilkins Centre, Biomolecular Interaction Centre and Department of
Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
- Ferrier
Research Institute, Victoria University of Wellington, P.O. Box 33436, Petone 5046, New Zealand
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28
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Firestone RS, Schramm VL. The Transition-State Structure for Human MAT2A from Isotope Effects. J Am Chem Soc 2017; 139:13754-13760. [PMID: 28880543 DOI: 10.1021/jacs.7b05803] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human methionine S-adenosyltransferase (MAT2A) catalyzes the formation of S-adenosylmethionine (SAM) from ATP and methionine. Synthetic lethal genetic analysis has identified MAT2A as an anticancer target in tumor cells lacking expression of 5'-methylthioadenosine phosphorylase (MTAP). Approximately 15% of human cancers are MTAP-/-. The remainder can be rendered MTAP- through MTAP inhibitors. We used kinetic isotope effect (KIE), commitment factor (Cf), and binding isotope effect (BIE) measurements combined with quantum mechanical (QM) calculations to solve the transition state structure of human MAT2A. The reaction is characterized by an advanced SN2 transition state. The bond forming from the nucleophilic methionine sulfur to the 5'-C of ATP is 2.03 Å at the transition state (bond order of 0.67). Departure of the leaving group triphosphate of ATP is well advanced and forms a 2.32 Å bond between the 5'-C of ATP and the oxygen of the triphosphate (bond order of 0.23). Interaction of MAT2A with its MAT2B regulatory subunit causes no change in the intrinsic KIEs, indicating the same transition state structure. The transition state for MAT2A is more advanced along the reaction coordinate (more product-like) than that from the near-symmetrical transition state of methionine adenosyltransferase from E. coli.
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Affiliation(s)
- Ross S Firestone
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York, New York 10461, United States
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29
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Namanja-Magliano HA, Evans GB, Harijan RK, Tyler PC, Schramm VL. Transition State Analogue Inhibitors of 5'-Deoxyadenosine/5'-Methylthioadenosine Nucleosidase from Mycobacterium tuberculosis. Biochemistry 2017; 56:5090-5098. [PMID: 28836767 DOI: 10.1021/acs.biochem.7b00576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mycobacterium tuberculosis 5'-deoxyadenosine/5'-methylthioadenosine nucleosidase (Rv0091) catalyzes the N-riboside hydrolysis of its substrates 5'-methylthioadenosine (MTA) and 5'-deoxyadenosine (5'-dAdo). 5'-dAdo is the preferred substrate, a product of radical S-adenosylmethionine-dependent enzyme reactions. Rv0091 is characterized by a ribocation-like transition state, with low N-ribosidic bond order, an N7-protonated adenine leaving group, and an activated but weakly bonded water nucleophile. DADMe-Immucillins incorporating 5'-substituents of the substrates 5'-dAdo and MTA were synthesized and characterized as inhibitors of Rv0091. 5'-Deoxy-DADMe-Immucillin-A was the most potent among the 5'-dAdo transition state analogues with a dissociation constant of 640 pM. Among the 5'-thio substituents, hexylthio-DADMe-Immucillin-A was the best inhibitor at 87 pM. The specificity of Rv0091 for the Immucillin transition state analogues differs from those of other bacterial homologues because of an altered hydrophobic tunnel accepting the 5'-substituents. Inhibitors of Rv0091 had weak cell growth effects on M. tuberculosis or Mycobacterium smegmatis but were lethal toward Helicobacter pylori, where the 5'-methylthioadenosine nucleosidase is essential in menaquinone biosynthesis. We propose that Rv0091 plays a role in 5'-deoxyadenosine recycling but is not essential for growth in these Mycobacteria.
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Affiliation(s)
- Hilda A Namanja-Magliano
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Gary B Evans
- The Ferrier Research Institute, Victoria University of Wellington , Lower Hutt, Wellington 5040, New Zealand.,The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , Auckland, New Zealand
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington , Lower Hutt, Wellington 5040, New Zealand
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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30
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Koohi M, Shariati M, Haerizade B. Introducing boranorcaradienes with more stability than their corresponding borepins: Reversal of tautomerization via
substituents at theoretical levels. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- M. Koohi
- Young Researchers and Elites Club; North Tehran Branch Islamic Azad University Tehran; Tehran Iran
| | - M. Shariati
- Department of Chemical Engineering; Tafresh University; Tafresh 3951879611 Iran
| | - B.N. Haerizade
- Young Research and Elite Club; Qom Branch Islamic Azad University; Qom Iran
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31
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Selleck C, Clayton D, Gahan LR, Mitić N, McGeary RP, Pedroso MM, Guddat LW, Schenk G. Visualization of the Reaction Trajectory and Transition State in a Hydrolytic Reaction Catalyzed by a Metalloenzyme. Chemistry 2017; 23:4778-4781. [DOI: 10.1002/chem.201700866] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Daniel Clayton
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Nataša Mitić
- Department of Chemistry Maynooth University, Maynooth, Co. Kildare Ireland
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences The University of Queensland, St. Lucia Queensland 4072 Australia
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32
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Firestone RS, Cameron SA, Karp JM, Arcus VL, Schramm VL. Heat Capacity Changes for Transition-State Analogue Binding and Catalysis with Human 5'-Methylthioadenosine Phosphorylase. ACS Chem Biol 2017; 12:464-473. [PMID: 28026167 PMCID: PMC5462123 DOI: 10.1021/acschembio.6b00885] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human 5'-methylthioadenosine phosphorylase (MTAP) catalyzes the phosphorolysis of 5'-methylthioadenosine (MTA). Its action regulates cellular MTA and links polyamine synthesis to S-adenosylmethionine (AdoMet) salvage. Transition state analogues with picomolar dissociation constants bind to MTAP in an entropically driven process at physiological temperatures, suggesting increased hydrophobic character or dynamic structure for the complexes. Inhibitor binding exhibits a negative heat capacity change (-ΔCp), and thus the changes in enthalpy and entropy upon binding are strongly temperature-dependent. The ΔCp of inhibitor binding by isothermal titration calorimetry does not follow conventional trends and is contrary to that expected from the hydrophobic effect. Thus, ligands of increasing hydrophobicity bind with increasing values of ΔCp. Crystal structures of MTAP complexed to transition-state analogues MT-DADMe-ImmA, BT-DADMe-ImmA, PrT-ImmA, and a substrate analogue, MT-tubercidin, reveal similar active site contacts and overall protein structural parameters, despite large differences in ΔCp for binding. In addition, ΔCp values are not correlated with Kd values. Temperature dependence of presteady state kinetics revealed the chemical step for the MTAP reaction to have a negative heat capacity for transition state formation (-ΔCp‡). A comparison of the ΔCp‡ for MTAP presteady state chemistry and ΔCp for inhibitor binding revealed those transition-state analogues most structurally and thermodynamically similar to the transition state. Molecular dynamics simulations of MTAP apoenzyme and complexes with MT-DADMe-ImmA and MT-tubercidin show small, but increased dynamic motion in the inhibited complexes. Variable temperature CD spectroscopy studies for MTAP-inhibitor complexes indicate remarkable protein thermal stability (to Tm = 99 °C) in complexes with transition-state analogues.
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Affiliation(s)
- Ross S. Firestone
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Scott A. Cameron
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jerome M. Karp
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vickery L. Arcus
- Faculty of Science and Engineering, Department of Biological Science, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States,Corresponding Author: Phone: 718-430-2813.
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33
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Adamson C, Pengelly RJ, Shamsi Kazem Abadi S, Chakladar S, Draper J, Britton R, Gloster TM, Bennet AJ. Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars. Angew Chem Int Ed Engl 2016; 55:14978-14982. [PMID: 27783466 PMCID: PMC5132143 DOI: 10.1002/anie.201607431] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Indexed: 11/25/2022]
Abstract
Glycoside hydrolases (GHs) have attracted considerable attention as targets for therapeutic agents, and thus mechanism-based inhibitors are of great interest. We report the first structural analysis of a carbocyclic mechanism-based GH inactivator, the results of which show that the two Michaelis complexes are in 2 H3 conformations. We also report the synthesis and reactivity of a fluorinated analogue and the structure of its covalently linked intermediate (flattened 2 H3 half-chair). We conclude that these inactivator reactions mainly involve motion of the pseudo-anomeric carbon atom, knowledge that should stimulate the design of new transition-state analogues for use as chemical biology tools.
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Affiliation(s)
| | - Robert J. Pengelly
- Biomedical Sciences Research ComplexUniversity of St AndrewsNorth HaughSt Andrews, FifeUK
| | | | - Saswati Chakladar
- Department of ChemistrySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Jason Draper
- Department of ChemistrySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Robert Britton
- Department of ChemistrySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Tracey M. Gloster
- Biomedical Sciences Research ComplexUniversity of St AndrewsNorth HaughSt Andrews, FifeUK
| | - Andrew J. Bennet
- Department of ChemistrySimon Fraser UniversityBurnabyBritish ColumbiaCanada
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34
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Adamson C, Pengelly RJ, Shamsi Kazem Abadi S, Chakladar S, Draper J, Britton R, Gloster TM, Bennet AJ. Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Christopher Adamson
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia Canada
| | - Robert J. Pengelly
- Biomedical Sciences Research Complex; University of St Andrews; North Haugh St Andrews, Fife UK
| | - Saeideh Shamsi Kazem Abadi
- Department of Molecular Biology and Biochemistry; Simon Fraser University; Burnaby British Columbia Canada
| | - Saswati Chakladar
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia Canada
| | - Jason Draper
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia Canada
| | - Robert Britton
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia Canada
| | - Tracey M. Gloster
- Biomedical Sciences Research Complex; University of St Andrews; North Haugh St Andrews, Fife UK
| | - Andrew J. Bennet
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia Canada
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35
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Crous W, Naidoo KJ. Conformational and electrostatic analysis of S N1 donor analogue glycomimetic inhibitors of ST3Gal-I mammalian sialyltransferase. Bioorg Med Chem 2016; 24:4998-5005. [PMID: 27614914 DOI: 10.1016/j.bmc.2016.08.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023]
Abstract
Mammalian sialyltransferases play a role in the metastasis of various cancers in humans. Inhibitors of these enzymes will in principle be able to directly inhibit aberrant sialylation in cancer. Inhibitors of ST3Gal-I resembling the donor component of SN1 Transition State structures were previously evaluated as part of a kinetics study. Here, using classical dynamics simulations and free energy perturbation calculations, we rationalize the performance of three of these donor analogue ST3Gal-I enzyme inhibitors. We find to inhibit the mammalian ST3Gal-I enzyme a donor analogue requires configurationally limited functionality. This is mediated by the binding of the inhibitor to the enzyme. The inhibitor's ability to interact with Y194 and T272 through a charged group such as a carboxylate is especially important. Furthermore, a conformational rigid form approximating the donor substrate is central. Here this is achieved by an intramolecular hydrogen bond formed between the carboxylate group and one of the ribose hydroxyl groups of the cytidine monophosphate (CMP) leaving group. This intramolecular interaction results in the donor substrate conformer complimenting the form of the catalytic binding site. Finally the carboxylate charge is essential for electrostatic pairing with the binding site. Substituting this group for an alcohol or amide results in severe weakening of the ligand binding. The carboxylate thus proves an to be an irreplaceable functional group and an essential pharmacophore.
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Affiliation(s)
- Werner Crous
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
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36
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Konstantinova ID, Fateev IV, Miroshnikov AI. The arsenolysis reaction in the biotechnological method of synthesis of modified purine β-D-arabinonucleosides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016040105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Namanja-Magliano HA, Stratton CF, Schramm VL. Transition State Structure and Inhibition of Rv0091, a 5'-Deoxyadenosine/5'-methylthioadenosine Nucleosidase from Mycobacterium tuberculosis. ACS Chem Biol 2016; 11:1669-76. [PMID: 27019223 DOI: 10.1021/acschembio.6b00144] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a bacterial enzyme that catalyzes the hydrolysis of the N-ribosidic bond in 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH). MTAN activity has been linked to quorum sensing pathways, polyamine biosynthesis, and adenine salvage. Previously, the coding sequence of Rv0091 was annotated as a putative MTAN in Mycobacterium tuberculosis. Rv0091 was expressed in Escherichia coli, purified to homogeneity, and shown to be a homodimer, consistent with MTANs from other microorganisms. Substrate specificity for Rv0091 gave a preference for 5'-deoxyadenosine relative to MTA or SAH. Intrinsic kinetic isotope effects (KIEs) for the hydrolysis of [1'-(3)H], [1'-(14)C], [5'-(3)H2], [9-(15)N], and [7-(15)N]MTA were determined to be 1.207, 1.038, 0.998, 1.021, and 0.998, respectively. A model for the transition state structure of Rv0091 was determined by matching KIE values predicted via quantum chemical calculations to the intrinsic KIEs. The transition state shows a substantial loss of C1'-N9 bond order, well-developed oxocarbenium character of the ribosyl ring, and weak participation of the water nucleophile. Electrostatic potential surface maps for the Rv0091 transition state structure show similarity to DADMe-immucillin transition state analogues. DADMe-immucillin transition state analogues showed strong inhibition of Rv0091, with the most potent inhibitor (5'-hexylthio-DADMe-immucillinA) displaying a Ki value of 87 pM.
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Affiliation(s)
- Hilda A. Namanja-Magliano
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Christopher F. Stratton
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
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38
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Poulin MB, Schneck JL, Matico RE, McDevitt PJ, Huddleston MJ, Hou W, Johnson NW, Thrall SH, Meek TD, Schramm VL. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36. Proc Natl Acad Sci U S A 2016; 113:1197-201. [PMID: 26787850 PMCID: PMC4747696 DOI: 10.1073/pnas.1521036113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. Here, a combination of kinetic isotope effect measurements and quantum chemical modeling was used to provide subangstrom details of the transition state structure for NSD2 enzymatic activity. Kinetic isotope effects were measured for the methylation of isolated HeLa cell nucleosomes by NSD2. NSD2 preferentially catalyzes the dimethylation of H3K36 along with a reduced preference for H3K36 monomethylation. Primary Me-(14)C and (36)S and secondary Me-(3)H3, Me-(2)H3, 5'-(14)C, and 5'-(3)H2 kinetic isotope effects were measured for the methylation of H3K36 using specifically labeled S-adenosyl-l-methionine. The intrinsic kinetic isotope effects were used as boundary constraints for quantum mechanical calculations for the NSD2 transition state. The experimental and calculated kinetic isotope effects are consistent with an SN2 chemical mechanism with methyl transfer as the first irreversible chemical step in the reaction mechanism. The transition state is a late, asymmetric nucleophilic displacement with bond separation from the leaving group at (2.53 Å) and bond making to the attacking nucleophile (2.10 Å) advanced at the transition state. The transition state structure can be represented in a molecular electrostatic potential map to guide the design of inhibitors that mimic the transition state geometry and charge.
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Affiliation(s)
- Myles B Poulin
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Jessica L Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Rosalie E Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Patrick J McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Michael J Huddleston
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Neil W Johnson
- Cancer Epigenetics Discovery Performance Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Sara H Thrall
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Thomas D Meek
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461;
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39
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Evans GB, Cameron SA, Luxenburger A, Guan R, Suarez J, Thomas K, Schramm VL, Tyler PC. Tight binding enantiomers of pre-clinical drug candidates. Bioorg Med Chem 2015; 23:5326-33. [PMID: 26260335 PMCID: PMC4567382 DOI: 10.1016/j.bmc.2015.07.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
MTDIA is a picomolar transition state analogue inhibitor of human methylthioadenosine phosphorylase and a femtomolar inhibitor of Escherichia coli methylthioadenosine nucleosidase. MTDIA has proven to be a non-toxic, orally available pre-clinical drug candidate with remarkable anti-tumour activity against a variety of human cancers in mouse xenografts. The structurally similar compound MTDIH is a potent inhibitor of human and malarial purine nucleoside phosphorylase (PNP) as well as the newly discovered enzyme, methylthioinosine phosphorylase, isolated from Pseudomonas aeruginosa. Since the enantiomers of some pharmaceuticals have revealed surprising biological activities, the enantiomers of MTDIH and MTDIA, compounds 1 and 2, respectively, were prepared and their enzyme binding properties studied. Despite binding less tightly to their target enzymes than their enantiomers compounds 1 and 2 are nanomolar inhibitors.
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Affiliation(s)
- Gary B Evans
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - Scott A Cameron
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand; Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Andreas Luxenburger
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - Rong Guan
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Javier Suarez
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
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40
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Poulin MB, Du Q, Schramm VL. Chemoenzymatic Synthesis of (36)S Isotopologues of Methionine and S-Adenosyl-L-methionine. J Org Chem 2015; 80:5344-7. [PMID: 25884979 DOI: 10.1021/acs.joc.5b00608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Substrates containing isotope labels at specific atoms are required for transition-state analysis based on the measurement of multiple kinetic isotope effects.(36)S-labeled l-methionine and S-adenosyl-l-methionine were synthesized from elemental sulfur using a chemoenzymatic approach with >98% (36)S enrichment. This method provides access to previously inaccessible sulfur isotope-labeled substrates for sulfur kinetic isotope effect studies.
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Affiliation(s)
- Myles B Poulin
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Quan Du
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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41
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Sadeghi Googheri MS, Housaindokht MR, Sabzyan H. Theoretical studies on the deacylation step of acylated Candida Antarctica lipase B: Structural and reaction pathway analysis. J Mol Graph Model 2015; 57:9-19. [DOI: 10.1016/j.jmgm.2015.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/03/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
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42
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Targeting metallo-carbapenemases via modulation of electronic properties of cephalosporins. Biochem J 2015; 464:271-9. [PMID: 25220027 DOI: 10.1042/bj20140364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The global proliferation of metallo-carbapenemase-producing Enterobacteriaceae has created an unmet need for inhibitors of these enzymes. The rational design of metallo-carbapenemase inhibitors requires detailed knowledge of their catalytic mechanisms. Nine cephalosporins, structurally identical except for the systematic substitution of electron-donating and withdrawing groups in the para position of the styrylbenzene ring, were synthesized and utilized to probe the catalytic mechanism of New Delhi metallo-β-lactamase (NDM-1). Under steady-state conditions, K(m) values were all in the micromolar range (1.5-8.1 μM), whereas k(cat) values varied widely (17-220 s(-1)). There were large solvent deuterium isotope effects for all substrates under saturating conditions, suggesting a proton transfer is involved in the rate-limiting step. Pre-steady-state UV-visible scans demonstrated the formation of short-lived intermediates for all compounds. Hammett plots yielded reaction constants (ρ) of -0.34 ± 0.02 and -1.15 ± 0.08 for intermediate formation and breakdown, respectively. Temperature-dependence experiments yielded ΔG(‡) values that were consistent with the Hammett results. These results establish the commonality of the formation of an azanide intermediate in the NDM-1-catalysed hydrolysis of a range cephalosporins with differing electronic properties. This intermediate is a promising target for judiciously designed β-lactam antibiotics that are poor NDM-1 substrates and inhibitors with enhanced active-site residence times.
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43
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Yang Y, Liu Y, Yang D, Li H, Jiang K, Sun J. Theoretical study on the dehydrogenation reaction of dihydrogen bonded phenol–borane-trimethylamine in the excited state. Phys Chem Chem Phys 2015; 17:32132-9. [DOI: 10.1039/c5cp02530c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
No dehydrogenation reaction occurs in the ground state of dihydrogen bonded phenol–BTMA. TS-S10 points to the formation of a hydrogen molecule, while TS-S11 points to the B atom. The dehydrogenation reaction along TS-S10 is energy favorable, unlike that along TS-S11.
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Affiliation(s)
- Yonggang Yang
- College of Physics and Information Engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Yufang Liu
- College of Physics and Information Engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Dapeng Yang
- Physics Laboratory
- North China University of Water Resources and Electric Power
- Zhengzhou 450045
- China
| | - Hui Li
- College of Physics and Information Engineering
- Henan Normal University
- Xinxiang 453007
- China
| | - Kai Jiang
- College of Chemistry and Environmental Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Jinfeng Sun
- College of Physics and Information Engineering
- Henan Normal University
- Xinxiang 453007
- China
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44
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Martínez-González JÁ, Rodríguez A, Puyuelo MP, González M, Martínez R. Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Rogers IL, Naidoo KJ. Profiling Transition-State Configurations on the Trypanosoma cruzi trans-Sialidase Free-Energy Reaction Surfaces. J Phys Chem B 2014; 119:1192-201. [DOI: 10.1021/jp506824r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ian L. Rogers
- Scientific
Computing Research Unit and ‡Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Scientific
Computing Research Unit and ‡Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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46
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Chan J, Sannikova N, Tang A, Bennet AJ. Transition-State Structure for the Quintessential SN2 Reaction of a Carbohydrate: Reaction of α-Glucopyranosyl Fluoride with Azide Ion in Water. J Am Chem Soc 2014; 136:12225-8. [DOI: 10.1021/ja506092h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jefferson Chan
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalia Sannikova
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Ariel Tang
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Bennet
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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47
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Rehr JJ, Vila FD. Dynamic structural disorder in supported nanoscale catalysts. J Chem Phys 2014; 140:134701. [DOI: 10.1063/1.4869178] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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48
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Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. How quickly can a β-hairpin fold from its transition state? J Phys Chem B 2014; 118:3317-25. [PMID: 24611730 PMCID: PMC3969101 DOI: 10.1021/jp500774q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Understanding the structural nature
of the free energy bottleneck(s)
encountered in protein folding is essential to elucidating the underlying
dynamics and mechanism. For this reason, several techniques, including
Φ-value analysis, have previously been developed to infer the
structural characteristics of such high free-energy or transition
states. Herein we propose that one (or few) appropriately placed backbone
and/or side chain cross-linkers, such as disulfides, could be used
to populate a thermodynamically accessible conformational state that
mimics the folding transition state. Specifically, we test this hypothesis
on a model β-hairpin, Trpzip4, as its folding mechanism has
been extensively studied and is well understood. Our results show
that cross-linking the two β-strands near the turn region increases
the folding rate by an order of magnitude, to about (500 ns)−1, whereas cross-linking the termini results in a hyperstable β-hairpin
that has essentially the same folding rate as the uncross-linked peptide.
Taken together, these findings suggest that cross-linking is not only
a useful strategy to manipulate folding free energy barriers, as shown
in other studies, but also, in some cases, it can be used to stabilize
a folding transition state analogue and allow for direct assessment
of the folding process on the downhill side of the free energy barrier.
The calculated free energy landscape of the cross-linked Trpzip4 also
supports this picture. An empirical analysis further suggests, when
folding of β-hairpins does not involve a significant free energy
barrier, the folding time (τ) follows a power law dependence
on the number of hydrogen bonds to be formed (nH), namely, τ = τ0nHα, with
τ0 = 20 ns and α = 2.3.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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49
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Transition-state inhibitors of purine salvage and other prospective enzyme targets in malaria. Future Med Chem 2014; 5:1341-60. [PMID: 23859211 DOI: 10.4155/fmc.13.51] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Malaria is a leading cause of human death within the tropics. The gradual generation of drug resistance imposes an urgent need for the development of new and selective antimalarial agents. Kinetic isotope effects coupled to computational chemistry have provided the relevant details on geometry and charge of enzymatic transition states to facilitate the design of transition-state analogs. These features have been reproduced into chemically stable mimics through synthetic chemistry, generating inhibitors with dissociation constants in the pico- to femto-molar range. Transition-state analogs are expected to contribute to the control of malaria.
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50
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Zhang Y, Evans GB, Clinch K, Crump DR, Harris LD, Fröhlich RFG, Tyler PC, Hazleton KZ, Cassera MB, Schramm VL. Transition state analogues of Plasmodium falciparum and human orotate phosphoribosyltransferases. J Biol Chem 2013; 288:34746-54. [PMID: 24158442 DOI: 10.1074/jbc.m113.521955] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The survival and proliferation of Plasmodium falciparum parasites and human cancer cells require de novo pyrimidine synthesis to supply RNA and DNA precursors. Orotate phosphoribosyltransferase (OPRT) is an indispensible component in this metabolic pathway and is a target for antimalarials and antitumor drugs. P. falciparum (Pf) and Homo sapiens (Hs) OPRTs are characterized by highly dissociative transition states with ribocation character. On the basis of the geometrical and electrostatic features of the PfOPRT and HsOPRT transition states, analogues were designed, synthesized, and tested as inhibitors. Iminoribitol mimics of the ribocation transition state in linkage to pyrimidine mimics using methylene or ethylene linkers gave dissociation constants (Kd) as low as 80 nM. Inhibitors with pyrrolidine groups as ribocation mimics displayed slightly weaker binding affinities for OPRTs. Interestingly, p-nitrophenyl riboside 5'-phosphate bound to OPRTs with Kd values near 40 nM. Analogues designed with a C5-pyrimidine carbon-carbon bond to ribocation mimics gave Kd values in the range of 80-500 nM. Acyclic inhibitors with achiral serinol groups as the ribocation mimics also displayed nanomolar inhibition against OPRTs. In comparison with the nucleoside derivatives, inhibition constants of their corresponding 5'-phosphorylated transition state analogues are largely unchanged, an unusual property for a nucleotide-binding site. In silico docking of the best inhibitor into the HsOPRT active site supported an extensive hydrogen bond network associated with the tight binding affinity. These OPRT transition state analogues identify crucial components of potent inhibitors targeting OPRT enzymes. Despite their tight binding to the targets, the inhibitors did not kill cultured P. falciparum.
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Affiliation(s)
- Yong Zhang
- From the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461 and
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