1
|
Herrscher V, Witjaksono C, Buchotte M, Ferret C, Massicot F, Vasse J, Borel F, Behr J, Seemann M. Irreversible Inhibition of IspG, a Target for the Development of New Antimicrobials, by a 2‐Vinyl Analogue of its MEcPP Substrate. Chemistry 2022; 28:e202200241. [DOI: 10.1002/chem.202200241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Vivien Herrscher
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Clea Witjaksono
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| | - Marie Buchotte
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Claire Ferret
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| | - Fabien Massicot
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Jean‐Luc Vasse
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Franck Borel
- Univ. Grenoble Alpes, CEA, CNRS, IBS 38000 Grenoble France
| | - Jean‐Bernard Behr
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques Institut de Chimie de Strasbourg UMR 7177 Université de Strasbourg/CNRS 4, rue Blaise Pascal 67070 Strasbourg France
| |
Collapse
|
2
|
Munier M, Tritsch D, Krebs F, Esque J, Hemmerlin A, Rohmer M, Stote RH, Grosdemange-Billiard C. Synthesis and biological evaluation of phosphate isosters of fosmidomycin and analogs as inhibitors of Escherichia coli and Mycobacterium smegmatis 1-deoxyxylulose 5-phosphate reductoisomerases. Bioorg Med Chem 2017; 25:684-689. [DOI: 10.1016/j.bmc.2016.11.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 11/26/2022]
|
3
|
Battistini MR, Shoji C, Handa S, Breydo L, Merkler DJ. Mechanistic binding insights for 1-deoxy-D-Xylulose-5-Phosphate synthase, the enzyme catalyzing the first reaction of isoprenoid biosynthesis in the malaria-causing protists, Plasmodium falciparum and Plasmodium vivax. Protein Expr Purif 2015; 120:16-27. [PMID: 26699947 DOI: 10.1016/j.pep.2015.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/04/2015] [Accepted: 12/09/2015] [Indexed: 11/30/2022]
Abstract
We have successfully truncated and recombinantly-expressed 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from both Plasmodium vivax and Plasmodium falciparum. We elucidated the order of substrate binding for both of these ThDP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and D-glyceraldehyde-3-phosphate. These findings are in contrast to other ThDP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful in treatment of malaria.
Collapse
Affiliation(s)
- Matthew R Battistini
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Christopher Shoji
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA
| | - Sumit Handa
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Leonid Breydo
- College of Medicine and Molecular Medicine, University of South Florida Health, 12901 Bruce B. Downs Blvd., MDC 3529, Tampa, FL 33612, USA
| | - David J Merkler
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA.
| |
Collapse
|
4
|
Zhou J, Wu R, Wang B, Cao Z, Yan H, Mo Y. Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Zexing Cao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Honggao Yan
- Center
for Biological Modeling and Departments of Biochemistry and Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yirong Mo
- Department
of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
| |
Collapse
|
5
|
Mechanism and inhibition of 1-deoxy-d-xylulose-5-phosphate reductoisomerase. Bioorg Chem 2014; 57:171-185. [DOI: 10.1016/j.bioorg.2014.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 12/23/2022]
|
6
|
Kholodar SA, Tombline G, Liu J, Tan Z, Allen CL, Gulick AM, Murkin AS. Alteration of the flexible loop in 1-deoxy-D-xylulose-5-phosphate reductoisomerase boosts enthalpy-driven inhibition by fosmidomycin. Biochemistry 2014; 53:3423-31. [PMID: 24825256 PMCID: PMC4045324 DOI: 10.1021/bi5004074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR),
which catalyzes the first committed step in the 2-C-methyl-d-erythritol 4-phosphate pathway of isoprenoid biosynthesis
used by Mycobacterium tuberculosis and other infectious
microorganisms, is absent in humans and therefore an attractive drug
target. Fosmidomycin is a nanomolar inhibitor of DXR, but despite
great efforts, few analogues with comparable potency have been developed.
DXR contains a strictly conserved residue, Trp203, within a flexible
loop that closes over and interacts with the bound inhibitor. We report
that while mutation to Ala or Gly abolishes activity, mutation to
Phe and Tyr only modestly impacts kcat and Km. Moreover, pre-steady-state kinetics
and primary deuterium kinetic isotope effects indicate that while
turnover is largely limited by product release for the wild-type enzyme,
chemistry is significantly more rate-limiting for W203F and W203Y.
Surprisingly, these mutants are more sensitive to inhibition by fosmidomycin,
resulting in Km/Ki ratios up to 19-fold higher than that of wild-type DXR. In
agreement, isothermal titration calorimetry revealed that fosmidomycin
binds up to 11-fold more tightly to these mutants. Most strikingly,
mutation strongly tips the entropy–enthalpy balance of total
binding energy from 50% to 75% and 91% enthalpy in W203F and W203Y,
respectively. X-ray crystal structures suggest that these enthalpy
differences may be linked to differences in hydrogen bond interactions
involving a water network connecting fosmidomycin’s phosphonate
group to the protein. These results confirm the importance of the
flexible loop, in particular Trp203, in ligand binding and suggest
that improved inhibitor affinity may be obtained against the wild-type
protein by introducing interactions with this loop and/or the surrounding
structured water network.
Collapse
Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
| | | | | | | | | | | | | |
Collapse
|
7
|
Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
Collapse
Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
| | | | | | | | | |
Collapse
|
8
|
Li H, Tian J, Sun W, Qin W, Gao WY. Mechanistic insights into 1-deoxy-d-xylulose 5-phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway. FEBS J 2013; 280:5896-905. [DOI: 10.1111/febs.12516] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 09/02/2013] [Accepted: 09/02/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Heng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education); College of Life Sciences; Northwest University; Xi'an China
| | - Jie Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education); College of Life Sciences; Northwest University; Xi'an China
| | - Wei Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry (Ministry of Education); School of Chemistry and Materials Science; Northwest University; Xi'an China
| | - Wei Qin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education); College of Life Sciences; Northwest University; Xi'an China
| | - Wen-Yun Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education); College of Life Sciences; Northwest University; Xi'an China
| |
Collapse
|
9
|
Xue J, Diao J, Cai G, Deng L, Zheng B, Yao Y, Song Y. Antimalarial and Structural Studies of Pyridine-containing Inhibitors of 1-Deoxyxylulose-5-phosphate Reductoisomerase. ACS Med Chem Lett 2013; 4:278-282. [PMID: 23795240 PMCID: PMC3685428 DOI: 10.1021/ml300419r] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 12/11/2012] [Indexed: 11/29/2022] Open
Abstract
1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate isoprene biosynthesis pathway is a target for developing antimalarial drugs. Fosmidomycin, a potent DXR inhibitor, showed safety as well as efficacy against P. falciparum malaria in clinical trials. Based on our previous quantitative structure activity relationship (QSAR) and crystallographic studies, several novel pyridine-containing fosmidomycin derivatives were designed, synthesized and found to be highly potent inhibitors of P. falciparum DXR (PfDXR) having Ki values of 1.9 - 13 nM, with the best one being ~11× more active than fosmidomycin. These compounds also potently block the proliferation of multi-drug resistant P. falciparum with EC50 values as low as 170 nM. A 2.3 Å crystal structure of PfDXR in complex with one of the inhibitors is reported, showing the flexible loop of the protein undergoes conformational changes upon ligand binding and a hydrogen bond and favorable hydrophobic interactions between the pyridine group and PfDXR account for the enhanced activity.
Collapse
Affiliation(s)
| | | | | | - Lisheng Deng
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Baisong Zheng
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Yuan Yao
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Yongcheng Song
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| |
Collapse
|
10
|
de Ruyck J, Wouters J, Poulter CD. Inhibition Studies on Enzymes Involved in Isoprenoid Biosynthesis: Focus on Two Potential Drug Targets: DXR and IDI-2 Enzymes. ACTA ACUST UNITED AC 2011; 7. [PMID: 24339799 DOI: 10.2174/157340811796575317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was first identified and characterised over 40 years ago (IDI-1) and a second convergently evolved isoform (IDI-2) was discovered in 2001. IDI-1 is a metalloprotein found in Eukarya and many species of Bacteria. Its mechanism has been extensively studied. In contrast, IDI-2 requires reduced flavin mononucleotide as a cofactor. The mechanism of action for IDI-2 is less well defined. This review will describe how lead inhibitors are being improved by structure-based drug design and enzymatic assays against DXR to lead to new drug families and how mechanistic probes are being used to address questions about the mechanisms of the isomerases.
Collapse
Affiliation(s)
- Jérôme de Ruyck
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112, USA
| | | | | |
Collapse
|
11
|
Williams SL, Andrew McCammon J. Conformational dynamics of the flexible catalytic loop in Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase. Chem Biol Drug Des 2009; 73:26-38. [PMID: 19152632 DOI: 10.1111/j.1747-0285.2008.00749.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In mycobacteria, the biosynthesis of the precursors to the essential isoprenoids, isopentenyl diphosphate and dimethylallyl pyrophosphate is carried out by the methylerythritol phosphate pathway. This route of synthesis is absent in humans, who utilize the alternative mevalonate acid route, thus making the enzymes of the methylerythritol phosphate pathway of chemotherapeutic interest. One such identified target is the second enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate reductoisomerase. Only limited information is currently available concerning the catalytic mechanism and structural dynamics of this enzyme, and only recently has a crystal structure of Mycobacterium tuberculosis species of this enzyme been resolved including all factors required for binding. Here, the dynamics of the enzyme is studied in complex with NADPH, Mn2+, in the presence and absence of the fosmidomycin inhibitor using conventional molecular dynamics and an enhanced sampling technique, reversible digitally filtered molecular dynamics. The simulations reveal significant differences in the conformational dynamics of the vital catalytic loop between the inhibitor-free and inhibitor-bound enzyme complexes and highlight the contributions of conserved residues in this region. The substantial fluctuations observed suggest that 1-deoxy-D-xylulose 5-phosphate reductoisomerase may be a promising target for computer-aided drug discovery through the relaxed complex method.
Collapse
Affiliation(s)
- Sarah L Williams
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0365, USA
| | | |
Collapse
|
12
|
Ershov YV. 2-C-methylerythritol phosphate pathway of isoprenoid biosynthesis as a target in identifying new antibiotics, herbicides, and immunomodulators: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807020019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|