1
|
Stefan A, Mucchi A, Hochkoeppler A. The catalytic action of human d-lactate dehydrogenase is severely inhibited by oxalate and is impaired by mutations triggering d-lactate acidosis. Arch Biochem Biophys 2024; 754:109932. [PMID: 38373542 DOI: 10.1016/j.abb.2024.109932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/29/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
d-lactate dehydrogenases are known to be expressed by prokaryotes and by eukaryotic invertebrates, and over the years the functional and structural features of some bacterial representatives of this enzyme ensemble have been investigated quite in detail. Remarkably, a human gene coding for a putative d-lactate dehydrogenase (DLDH) was identified and characterized, disclosing the occurrence of alternative splicing of its primary transcript. This translates into the expression of two human DLDH (hDLDH) isoforms, the molecular mass of which is expected to differ by 2.7 kDa. However, no information on these two hDLDH isoforms is available at the protein level. Here we report on the catalytic action of these enzymes, along with a first analysis of their structural features. In particular, we show that hDLDH is strictly stereospecific, with the larger isoform (hDLDH-1) featuring higher activity at the expense of d-lactate when compared to its smaller counterpart (hDLDH-2). Furthermore, we found that hDLDH is strongly inhibited by oxalate, as indicated by a Ki equal to 1.2 μM for this dicarboxylic acid. Structurally speaking, hDLDH-1 and hDLDH-2 were determined, by means of gel filtration and dynamic light scattering experiments, to be a hexamer and a tetramer, respectively. Moreover, in agreement with previous studies performed with human mitochondria, we identified FAD as the cofactor of hDLDH, and we report here a model of FAD binding by the human d-lactate dehydrogenase. Interestingly, the mutations W323C and T412 M negatively affect the activity of hDLDH, most likely by impairing the enzyme electron-acceptor site.
Collapse
Affiliation(s)
- Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Alberto Mucchi
- Department of Industrial Chemistry "Toso Montanari", Viale Risorgimento 4, 40136, Bologna, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.
| |
Collapse
|
2
|
Vyas VK, Shukla T, Sharma M. Medicinal chemistry approaches for the discovery of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. Future Med Chem 2023; 15:1295-1321. [PMID: 37551689 DOI: 10.4155/fmc-2023-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Malaria is a severe human disease and a global health problem because of drug-resistant strains. Drugs reported to prevent the growth of Plasmodium parasites target various phases of the parasites' life cycle. Antimalarial drugs can inhibit key enzymes that are responsible for the cellular growth and development of parasites. Plasmodium falciparum dihydroorotate dehydrogenase is one such enzyme that is necessary for de novo pyrimidine biosynthesis. This review focuses on various medicinal chemistry approaches used for the discovery and identification of selective P. falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. This comprehensive review discusses recent advances in the selective therapeutic activity of distinct chemical classes of compounds as P. falciparum dihydroorotate dehydrogenase inhibitors and antimalarial drugs.
Collapse
Affiliation(s)
- Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Tanvi Shukla
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| |
Collapse
|
3
|
Zhang Y, Xu Q, Sun Q, Kong R, Liu H, Yi X, Liang Z, Letcher RJ, Liu C. Ustiloxin A inhibits proliferation of renal tubular epithelial cells in vitro and induces renal injury in mice by disrupting structure and respiratory function of mitochondria. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130791. [PMID: 36706486 DOI: 10.1016/j.jhazmat.2023.130791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Recently, we found that Ustiloxin A (UA, a mycotoxin) was widely detected in paddy environment and rice samples from several countries, and was also detected in human urine samples from China. However, the current knowledge about the health risks of UA are limited. In this research, the cytotoxicity of UA in mice renal tubular epithelial cells (mRTECs) was evaluated, and the results indicated that UA arrested cell cycle in G2/M phase via altering cellular morphology and microtubule, and inhibited the proliferation and division of mRTECs. Furthermore, UA could inhibit mitochondrial respiration via binding to the CoQ-binding site in dihydro-orotate dehydrogenase (DHODH) protein, and resulted in mitochondrial damage. These adverse effects of UA on mitochondria might be responsible for the cytotoxicity observed in vitro. In vivo, UA at concentrations that were comparable to the realistic concentrations of human exposure induced renal insufficiency in mice, and this might be associated with the renal mitochondrial damage in mice. However, exposure to UA at those realistic concentrations did not promote the progression from renal insufficiency to renal fibrosis and chronic kidney disease was not observed in mice.
Collapse
Affiliation(s)
- Yongkang Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaolin Xu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Sun
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ren Kong
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hao Liu
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun'e Yi
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengqi Liang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert J Letcher
- Departments of Chemistry and Biology, Carleton University, Ottawa K1S 5B6, ON, Canada
| | - Chunsheng Liu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| |
Collapse
|
4
|
New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition. Int J Mol Sci 2022; 23:ijms23052437. [PMID: 35269583 PMCID: PMC8910288 DOI: 10.3390/ijms23052437] [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: 12/21/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/10/2022] Open
Abstract
The fourth enzymatic reaction in the de novo pyrimidine biosynthesis, the oxidation of dihydroorotate to orotate, is catalyzed by dihydroorotate dehydrogenase (DHODH). Enzymes belonging to the DHODH Class II are membrane-bound proteins that use ubiquinones as their electron acceptors. We have designed this study to understand the interaction of an N-terminally truncated human DHODH (HsΔ29DHODH) and the DHODH from Escherichia coli (EcDHODH) with ubiquinone (Q10) in supported lipid membranes using neutron reflectometry (NR). NR has allowed us to determine in situ, under solution conditions, how the enzymes bind to lipid membranes and to unambiguously resolve the location of Q10. Q10 is exclusively located at the center of all of the lipid bilayers investigated, and upon binding, both of the DHODHs penetrate into the hydrophobic region of the outer lipid leaflet towards the Q10. We therefore show that the interaction between the soluble enzymes and the membrane-embedded Q10 is mediated by enzyme penetration. We can also show that EcDHODH binds more efficiently to the surface of simple bilayers consisting of 1-palmitoyl, 2-oleoyl phosphatidylcholine, and tetraoleoyl cardiolipin than HsΔ29DHODH, but does not penetrate into the lipids to the same degree. Our results also highlight the importance of Q10, as well as lipid composition, on enzyme binding.
Collapse
|
5
|
Orozco Rodriguez JM, Wacklin-Knecht H, Knecht W. Protein-lipid interactions of human dihydroorotate dehydrogenase and three mutants associated with Miller syndrome. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1337-1358. [PMID: 35184687 DOI: 10.1080/15257770.2022.2039393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human dihydroorotate dehydrogenase (DHODH) catalyzes the fourth step of the de novo pyrimidine biosynthesis pathway and uses ubiquinone Q10, a lipophilic molecule located in the inner mitochondrial membrane (IMM), as its co-substrate. DHODH is anchored to the IMM by a single transmembrane helix located at its N-terminus. Nevertheless, how DHODH function is determined by its surrounding membrane environment and protein-lipid interactions, as well as the mechanism by which ubiquinone Q10 accesses the active site of DHODH from within the membrane are still largely unknown. Here, we describe the interaction between wild-type DHODH and three DHODH mutants associated with Miller syndrome and lipids using enzymatic assays, thermal stability assays and Quartz Crystal Microbalance with Dissipation monitoring (QCM-D). Our results provide evidence indicating that the N-terminal part of human DHODH is not only a structural element for mitochondrial import and location of DHODH, but also influences enzymatic activity and utilization of ubiquinone Q10 and ubiquinone analogues in in vitro assays. They also support the role of tetraoleoyl cardiolipin as a lipid interacting with DHODH. Additionally, the results from QCM-D show that the Miller syndrome mutants studied differ in their interactions with supported lipid bilayers compared to wild-type DHODH. These altered interactions add another dimension to the effects of mutations found in Miller syndrome. To the best of our knowledge, this is the first investigation of the protein-lipid interactions of DHODH variants associated with Miller syndrome.
Collapse
Affiliation(s)
| | - Hanna Wacklin-Knecht
- Department of Chemistry, Division of Physical Chemistry, Lund University, Lund, Sweden.,European Spallation Source ERIC, Lund, Sweden
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University, Lund, Sweden
| |
Collapse
|
6
|
Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase. Cell Chem Biol 2018; 25:309-317.e4. [PMID: 29358052 PMCID: PMC5856493 DOI: 10.1016/j.chembiol.2017.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/21/2017] [Accepted: 12/20/2017] [Indexed: 11/23/2022]
Abstract
The interactions between proteins and biological membranes are important for drug development, but remain notoriously refractory to structural investigation. We combine non-denaturing mass spectrometry (MS) with molecular dynamics (MD) simulations to unravel the connections among co-factor, lipid, and inhibitor binding in the peripheral membrane protein dihydroorotate dehydrogenase (DHODH), a key anticancer target. Interrogation of intact DHODH complexes by MS reveals that phospholipids bind via their charged head groups at a limited number of sites, while binding of the inhibitor brequinar involves simultaneous association with detergent molecules. MD simulations show that lipids support flexible segments in the membrane-binding domain and position the inhibitor and electron acceptor-binding site away from the membrane surface, similar to the electron acceptor-binding site in respiratory chain complex I. By complementing MS with MD simulations, we demonstrate how a peripheral membrane protein uses lipids to modulate its structure in a similar manner as integral membrane proteins. Mass spectrometry captures intact complexes of the peripheral membrane protein DHODH Detergent removal in the gas phase reveals lipid and co-factor binding DHODH attaches to the membrane by binding charged phospholipids Lipids stabilize the flexible substrate- and drug-binding site
Collapse
|
7
|
Thillainayagam M, Malathi K, Ramaiah S. In-Silico molecular docking and simulation studies on novel chalcone and flavone hybrid derivatives with 1, 2, 3-triazole linkage as vital inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biomol Struct Dyn 2017; 36:3993-4009. [DOI: 10.1080/07391102.2017.1404935] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, TamilNadu, India
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, TamilNadu, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, TamilNadu, India
| |
Collapse
|
8
|
Singh A, Maqbool M, Mobashir M, Hoda N. Dihydroorotate dehydrogenase: A drug target for the development of antimalarials. Eur J Med Chem 2017; 125:640-651. [DOI: 10.1016/j.ejmech.2016.09.085] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/07/2016] [Accepted: 09/25/2016] [Indexed: 02/03/2023]
|
9
|
Caballero I, Lafuente MJ, Gamo FJ, Cid C. A high-throughput fluorescence-based assay for Plasmodium dihydroorotate dehydrogenase inhibitor screening. Anal Biochem 2016; 506:13-21. [DOI: 10.1016/j.ab.2016.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
|
10
|
Zhu J, Han L, Diao Y, Ren X, Xu M, Xu L, Li S, Li Q, Dong D, Huang J, Liu X, Zhao Z, Wang R, Zhu L, Xu Y, Qian X, Li H. Design, Synthesis, X-ray Crystallographic Analysis, and Biological Evaluation of Thiazole Derivatives as Potent and Selective Inhibitors of Human Dihydroorotate Dehydrogenase. J Med Chem 2015; 58:1123-39. [DOI: 10.1021/jm501127s] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Junsheng Zhu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Le Han
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yanyan Diao
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoli Ren
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Minghao Xu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liuxin Xu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Shiliang Li
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Qiang Li
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Dong Dong
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jin Huang
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaofeng Liu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenjiang Zhao
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rui Wang
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lili Zhu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yufang Xu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuhong Qian
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
11
|
Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
Collapse
Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | | | | | |
Collapse
|
12
|
Moxley MA, Becker DF. Rapid reaction kinetics of proline dehydrogenase in the multifunctional proline utilization A protein. Biochemistry 2011; 51:511-20. [PMID: 22148640 DOI: 10.1021/bi201603f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The multifunctional proline utilization A (PutA) flavoenzyme from Escherichia coli catalyzes the oxidation of proline to glutamate in two reaction steps using separate proline dehydrogenase (PRODH) and Δ(1)-pyrroline-5-carboxylate (P5C) dehydrogenase domains. Here, the kinetic mechanism of PRODH in PutA is studied by stopped-flow kinetics to determine microscopic rate constants for the proline:ubiquinone oxidoreductase mechanism. Stopped-flow data for proline reduction of the flavin cofactor (reductive half-reaction) and oxidation of reduced flavin by CoQ(1) (oxidative half-reaction) were best-fit by a double exponential from which maximum observable rate constants and apparent equilibrium dissociation constants were determined. Flavin semiquinone was not observed in the reductive or oxidative reactions. Microscopic rate constants for steps in the reductive and oxidative half-reactions were obtained by globally fitting the stopped-flow data to a simulated mechanism that includes a chemical step followed by an isomerization event. A microscopic rate constant of 27.5 s(-1) was determined for proline reduction of the flavin cofactor followed by an isomerization step of 2.2 s(-1). The isomerization step is proposed to report on a previously identified flavin-dependent conformational change [Zhang, W. et al. (2007) Biochemistry 46, 483-491] that is important for PutA functional switching but is not kinetically relevant to the in vitro mechanism. Using CoQ(1), a soluble analogue of ubiquinone, a rate constant of 5.4 s(-1) was obtained for the oxidation of flavin, thus indicating that this oxidative step is rate-limiting for k(cat) during catalytic turnover. Steady-state kinetic constants calculated from the microscopic rate constants agree with the experimental k(cat) and k(cat)/K(m) parameters.
Collapse
Affiliation(s)
- Michael A Moxley
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | | |
Collapse
|
13
|
Moxley MA, Tanner JJ, Becker DF. Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli. Arch Biochem Biophys 2011; 516:113-20. [PMID: 22040654 DOI: 10.1016/j.abb.2011.10.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/14/2011] [Accepted: 10/15/2011] [Indexed: 11/16/2022]
Abstract
The multifunctional proline utilization A (PutA) flavoenzyme from Escherichia coli performs the oxidation of proline to glutamate in two catalytic steps using separate proline dehydrogenase (PRODH) and Δ(1)-pyrroline-5-carboxylate (P5C) dehydrogenase domains. In the first reaction, the oxidation of proline is coupled to the reduction of ubiquinone (CoQ) by the PRODH domain, which has a β(8)α(8)-barrel structure that is conserved in bacterial and eukaryotic PRODH enzymes. The structural requirements of the benzoquinone moiety were examined by steady-state kinetics using CoQ analogs. PutA displayed activity with all the analogs tested; the highest k(cat)/K(m) was obtained with CoQ(2). The kinetic mechanism of the PRODH reaction was investigated use a variety of steady-state approaches. Initial velocity patterns measured using proline and CoQ(1), combined with dead-end and product inhibition studies, suggested a two-site ping-pong mechanism for PutA. The kinetic parameters for PutA were not strongly influenced by solvent viscosity suggesting that diffusive steps do not significantly limit the overall reaction rate. In summary, the kinetic data reported here, along with analysis of the crystal structure data for the PRODH domain, suggest that the proline:ubiquinone oxidoreductase reaction of PutA occurs via a rapid equilibrium ping-pong mechanism with proline and ubiquinone binding at two distinct sites.
Collapse
Affiliation(s)
- Michael A Moxley
- Department of Biochemistry, University of Nebraska-Lincoln, United States
| | | | | |
Collapse
|
14
|
Couto SG, Cristina Nonato M, Costa-Filho AJ. Site directed spin labeling studies of Escherichia coli dihydroorotate dehydrogenase N-terminal extension. Biochem Biophys Res Commun 2011; 414:487-92. [PMID: 21986535 DOI: 10.1016/j.bbrc.2011.09.092] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 09/19/2011] [Indexed: 11/29/2022]
Abstract
Dihydroorotate dehydrogenases (DHODHs) are enzymes that catalyze the fourth step of the de novo synthesis of pyrimidine nucleotides. In this reaction, DHODH converts dihydroorotate to orotate, using a flavine mononucleotide as a cofactor. Since the synthesis of nucleotides has different pathways in mammals as compared to parasites, DHODH has gained much attention as a promising target for drug design. Escherichia coli DHODH (EcDHODH) is a family 2 DHODH that interacts with cell membranes in order to promote catalysis. The membrane association is supposedly made via an extension found in the enzyme's N-terminal. In the present work, we used site directed spin labeling (SDSL) to specifically place a magnetic probe at positions 2, 5, 19, and 21 within the N-terminal and thus monitor, by using Electron Spin Resonance (ESR), dynamics and structural changes in this region in the presence of a membrane model system. Overall, our ESR spectra show that the N-terminal indeed binds to membranes and that it experiences a somewhat high flexibility that could be related to the role of this region as a molecular lid controlling the entrance of the enzyme's active site and thus allowing the enzyme to give access to quinones that are dispersed in the membrane and that are necessary for the catalysis.
Collapse
Affiliation(s)
- Sheila G Couto
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, C.P. 369, 13560-970, São Carlos, SP, Brazil
| | | | | |
Collapse
|
15
|
Cowen D, Bedingfield P, McConkey GA, Fishwick CW, Johnson AP. A study of the effects of substituents on the selectivity of the binding of N-arylaminomethylene malonate inhibitors to DHODH. Bioorg Med Chem Lett 2010; 20:1284-7. [DOI: 10.1016/j.bmcl.2009.11.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 11/16/2009] [Accepted: 11/17/2009] [Indexed: 10/20/2022]
|
16
|
Gujjar R, Marwaha A, El Mazouni F, White J, White KL, Creason S, Shackleford DM, Baldwin J, Charman WN, Buckner FS, Charman S, Rathod PK, Phillips MA. Identification of a metabolically stable triazolopyrimidine-based dihydroorotate dehydrogenase inhibitor with antimalarial activity in mice. J Med Chem 2009; 52:1864-72. [PMID: 19296651 DOI: 10.1021/jm801343r] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum causes 1-2 million deaths annually. Yet current drug therapies are compromised by resistance. We previously described potent and selective triazolopyrimidine-based inhibitors of P. falciparum dihydroorotate dehydrogenase (PfDHODH) that inhibited parasite growth in vitro; however, they showed no activity in vivo. Here we show that lack of efficacy against P. berghei in mice resulted from a combination of poor plasma exposure and reduced potency against P. berghei DHODH. For compounds containing naphthyl (DSM1) or anthracenyl (DSM2), plasma exposure was reduced upon repeated dosing. Phenyl-substituted triazolopyrimidines were synthesized leading to identification of analogs with low predicted metabolism in human liver microsomes and which showed prolonged exposure in mice. Compound 21 (DSM74), containing p-trifluoromethylphenyl, suppressed growth of P. berghei in mice after oral administration. This study provides the first proof of concept that DHODH inhibitors can suppress Plasmodium growth in vivo, validating DHODH as a new target for antimalarial chemotherapy.
Collapse
Affiliation(s)
- Ramesh Gujjar
- Department of Chemistry and Global Health and Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Bjelić S, Jelesarov I. A survey of the year 2007 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:289-312. [PMID: 18729242 DOI: 10.1002/jmr.909] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elucidation of the energetic principles of binding affinity and specificity is a central task in many branches of current sciences: biology, medicine, pharmacology, chemistry, material sciences, etc. In biomedical research, integral approaches combining structural information with in-solution biophysical data have proved to be a powerful way toward understanding the physical basis of vital cellular phenomena. Isothermal titration calorimetry (ITC) is a valuable experimental tool facilitating quantification of the thermodynamic parameters that characterize recognition processes involving biomacromolecules. The method provides access to all relevant thermodynamic information by performing a few experiments. In particular, ITC experiments allow to by-pass tedious and (rarely precise) procedures aimed at determining the changes in enthalpy and entropy upon binding by van't Hoff analysis. Notwithstanding limitations, ITC has now the reputation of being the "gold standard" and ITC data are widely used to validate theoretical predictions of thermodynamic parameters, as well as to benchmark the results of novel binding assays. In this paper, we discuss several publications from 2007 reporting ITC results. The focus is on applications in biologically oriented fields. We do not intend a comprehensive coverage of all newly accumulated information. Rather, we emphasize work which has captured our attention with originality and far-reaching analysis, or else has provided ideas for expanding the potential of the method.
Collapse
Affiliation(s)
- Sasa Bjelić
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | | |
Collapse
|
18
|
Phillips MA, Gujjar R, Malmquist NA, White J, El Mazouni F, Baldwin J, Rathod PK. Triazolopyrimidine-based dihydroorotate dehydrogenase inhibitors with potent and selective activity against the malaria parasite Plasmodium falciparum. J Med Chem 2008; 51:3649-53. [PMID: 18522386 PMCID: PMC2624570 DOI: 10.1021/jm8001026] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A Plasmodium falciparum dihydroorotate dehydrogenase ( PfDHODH) inhibitor that is potent ( KI = 15 nM) and species-selective (>5000-fold over the human enzyme) was identified by high-throughput screening. The substituted triazolopyrimidine and its structural analogues were produced by an inexpensive three-step synthesis, and the series showed good association between PfDHODH inhibition and parasite toxicity. This study has identified the first nanomolar PfDHODH inhibitor with potent antimalarial activity in whole cells (EC50 = 79 nM).
Collapse
Affiliation(s)
- Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA.
| | | | | | | | | | | | | |
Collapse
|
19
|
Malmquist NA, Gujjar R, Rathod PK, Phillips MA. Analysis of flavin oxidation and electron-transfer inhibition in Plasmodium falciparum dihydroorotate dehydrogenase. Biochemistry 2008; 47:2466-75. [PMID: 18225919 DOI: 10.1021/bi702218c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (pfDHODH) is a flavin-dependent mitochondrial enzyme that provides the only route to pyrimidine biosynthesis in the parasite. Clinically significant inhibitors of human DHODH (e.g., A77 1726) bind to a pocket on the opposite face of the flavin cofactor from dihydroorotate (DHO). This pocket demonstrates considerable sequence variability, which has allowed species-specific inhibitors of the malarial enzyme to be identified. Ubiquinone (CoQ), the physiological oxidant in the reaction, has been postulated to bind this site despite a lack of structural evidence. To more clearly define the residues involved in CoQ binding and catalysis, we undertook site-directed mutagenesis of seven residues in the structurally defined A77 1726 binding site, which we term the species-selective inhibitor site. Mutation of several of these residues (H185, F188, and F227) to Ala substantially decreased the affinity of pfDHODH-specific inhibitors (40-240-fold). In contrast, only a modest increase in the Kmapp for CoQ was observed, although mutation of Y528 in particular caused a substantial reduction in kcat (40-100-fold decrease). Pre-steady-state kinetic analysis by single wavelength stopped-flow spectroscopy showed that the mutations had no effect on the rate of the DHO-dependent reductive half-reaction, but most reduced the rate of the CoQ-dependent flavin oxidation step (3-20-fold decrease), while not significantly altering the Kdox for CoQ. As with the mutants, inhibitors that bind this site block the CoQ-dependent oxidative half-reaction without affecting the DHO-dependent step. These results identify residues involved in inhibitor binding and electron transfer to CoQ. Importantly, the data provide compelling evidence that the binding sites for CoQ and species-selective site inhibitors do not overlap, and they suggest instead that inhibitors act either by blocking the electron path between flavin and CoQ or by stabilizing a conformation that excludes CoQ binding.
Collapse
Affiliation(s)
- Nicholas A Malmquist
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, USA
| | | | | | | |
Collapse
|