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Teixeira O, Martins IBS, Froes TQ, de Araújo AS, Nonato MC. Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition. Biochim Biophys Acta Gen Subj 2023; 1867:130378. [PMID: 37150227 DOI: 10.1016/j.bbagen.2023.130378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Tuberculosis (TB) is a leading cause of death worldwide. TB represents a serious public health threat, and it is characterized by high transmission rates, prevalence in impoverished regions, and high co-infection rates with HIV. Moreover, the serious side effects of long-term treatment that decrease patient adherence, and the emergence of multi-resistant strains of Mycobacterium tuberculosis, the causing agent of TBs, pose several challenges for its eradication. The search for a new TB treatment is necessary and urgent. Dihydroorotate dehydrogenase (DHODH) is responsible for the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. DHODH has been considered an attractive target against infectious diseases. As a first step towards exploiting DHODH as a drug target against TB, we performed a full kinetic characterization of both bacterial MtDHODH and its human ortholog (HsDHDOH) using both substrates coenzyme Q0 (Q0) and vitamin K3 (K3). MtDHODH follows a ping-pong mechanism of catalysis and shares similar catalytic parameters with the human enzyme. Serendipitously, Q0 was found to inhibit MtDHODH (KI (Q0) = 138 ± 31 μM). To the best of our knowledge, Q0 is the first non-orotate like dihydroorotate-competitive inhibitor for class 2 DHODHs ever described. Molecular dynamics simulations along with in silico solvent mapping allowed us to successfully probe protein flexibility and correlate it with the druggability of binding sites. Together, our results provide the starting point for the design of a new generation of potent and selective inhibitors against MtDHODH.
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Affiliation(s)
- Olívia Teixeira
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Ingrid Bernardes Santana Martins
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto de Biociências, Letras e Ciências Exatas, Departamento de Física, UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Thamires Quadros Froes
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Alexandre Suman de Araújo
- Instituto de Biociências, Letras e Ciências Exatas, Departamento de Física, UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil.
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Sousa FM, Pires P, Barreto A, Refojo PN, Silva MS, Fernandes PB, Carapeto AP, Robalo TT, Rodrigues MS, Pinho MG, Cabrita EJ, Pereira MM. Unveiling the membrane bound dihydroorotate: Quinone oxidoreductase from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148948. [PMID: 36481274 DOI: 10.1016/j.bbabio.2022.148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia Pires
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Andreia Barreto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Micael S Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro B Fernandes
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Ana P Carapeto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago T Robalo
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mário S Rodrigues
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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Discovery of potential natural dihydroorotate dehydrogenase inhibitors and their synergism with brequinar via integrated molecular docking, dynamic simulations and in vitro approach. Sci Rep 2022; 12:19037. [PMID: 36351991 PMCID: PMC9646789 DOI: 10.1038/s41598-022-23006-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
The critical function of dihydroorotate dehydrogenase (DHODH) in pyrimidine synthesis attracted a great interest throughout beyond decades. Inhibitors of human DHODH (hDHODH) have validated efficacy for remedy of many immunological diseases. Brequinar and leflunomide are examples of such compounds. However, most of such immunosuppressive medications suffer from a lot of side effects and accompanied by adverse metabolic disturbances and toxicities. So that, immunomodulation utilizing natural products received the attention of many researchers. In this study, computer-aided molecular docking, molecular dynamic (MD) simulations and biochemical testing were utilized to find new pharmacologically active chemical entities from natural sources to combat immunosuppressive diseases. More specifically, Glide docking was used for a structure-based virtual screening of in-house 3D database of compounds retrieved from some traditionally known immunomodulatory plants surveyed from literature. The top five scored plants were found to be Zingiber officinale, Curcuma longa, Glycyrrhiza glabra, Allium sativum and Olea europaea. In vitro hDHODH inhibitory assays illustrated the ability of Allium sativum and silymarin standard hits; specifically, silibinin, to significantly inhibit the hDHODH enzyme. Molecular docking and MD simulations revealed a strong binding of the discovered hits within the active site. Following that, the most promising hits were tested separately with brequinar in a fixed-ratio combination setting to assess their combined effects on hDHODH catalytic inhibition. The binary combination of silibinin and brequinar revealed that in this combination, brequinar could be utilized at a dose 9.33-fold less when compared to its single-use to produce 99% inhibition for hDHODH enzyme. These findings confirmed that this binary mixture is an excellent combination providing better therapeutic effects and lower side effects.
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Identification of novel Plasmodium falciparum dihydroorotate dehydrogenase inhibitors for malaria using in silico studies. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Identification of 3,4-Dihydro-2 H,6 H-pyrimido[1,2- c][1,3]benzothiazin-6-imine Derivatives as Novel Selective Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase. Int J Mol Sci 2021; 22:ijms22137236. [PMID: 34281290 PMCID: PMC8268581 DOI: 10.3390/ijms22137236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022] Open
Abstract
Plasmodium falciparum's resistance to available antimalarial drugs highlights the need for the development of novel drugs. Pyrimidine de novo biosynthesis is a validated drug target for the prevention and treatment of malaria infection. P. falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the oxidation of dihydroorotate to orotate and utilize ubiquinone as an electron acceptor in the fourth step of pyrimidine de novo biosynthesis. PfDHODH is targeted by the inhibitor DSM265, which binds to a hydrophobic pocket located at the N-terminus where ubiquinone binds, which is known to be structurally divergent from the mammalian orthologue. In this study, we screened 40,400 compounds from the Kyoto University chemical library against recombinant PfDHODH. These studies led to the identification of 3,4-dihydro-2H,6H-pyrimido[1,2-c][1,3]benzothiazin-6-imine and its derivatives as a new class of PfDHODH inhibitor. Moreover, the hit compounds identified in this study are selective for PfDHODH without inhibition of the human enzymes. Finally, this new scaffold of PfDHODH inhibitors showed growth inhibition activity against P. falciparum 3D7 with low toxicity to three human cell lines, providing a new starting point for antimalarial drug development.
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Watanabe T. Synthesis and Structure−Activity Relationship Study of Intervenolin, an Antitumor and Anti-Helicobacter pylori Quinolone Natural Product. HETEROCYCLES 2021. [DOI: 10.3987/rev-21-957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Sato D, Hartuti ED, Inaoka DK, Sakura T, Amalia E, Nagahama M, Yoshioka Y, Tsuji N, Nozaki T, Kita K, Harada S, Matsubayashi M, Shiba T. Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target. Genes (Basel) 2020; 11:genes11121468. [PMID: 33297567 PMCID: PMC7762340 DOI: 10.3390/genes11121468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/23/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella, an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway. Therefore, the enzymes of the de novo pathway are considered potential drug target candidates for the design of compounds with activity against this parasite. Although, DHODHs from E. tenella (EtDHODH), Plasmodium falciparum (PfDHODH), and human (HsDHODH) show distinct sensitivities to classical DHODH inhibitors, in this paper, we identify ferulenol as a potent inhibitor of both EtDHODH and HsDHODH. Additionally, we report the crystal structures of EtDHODH and HsDHODH in the absence and presence of ferulenol. Comparison of these enzymes showed that despite similar overall structures, the EtDHODH has a long insertion in the N-terminal helix region that assumes a disordered configuration. In addition, the crystal structures revealed that the ferulenol binding pocket of EtDHODH is larger than that of HsDHODH. These differences can be explored to accelerate structure-based design of inhibitors specifically targeting EtDHODH.
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Affiliation(s)
- Dan Sato
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Endah Dwi Hartuti
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Madoka Nagahama
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Yukina Yoshioka
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Naotoshi Tsuji
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan;
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Makoto Matsubayashi
- Division of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Orai Kita, Izumisano, Osaka 598-8531, Japan;
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
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Dihydroorotate dehydrogenase inhibitors in anti-infective drug research. Eur J Med Chem 2019; 183:111681. [PMID: 31557612 DOI: 10.1016/j.ejmech.2019.111681] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/01/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023]
Abstract
Pyrimidines are essential for the cell survival and proliferation of living parasitic organisms, such as Helicobacter pylori, Plasmodium falciparum and Schistosoma mansoni, that are able to impact upon human health. Pyrimidine building blocks, in human cells, are synthesised via both de novo biosynthesis and salvage pathways, the latter of which is an effective way of recycling pre-existing nucleotides. As many parasitic organisms lack pyrimidine salvage pathways for pyrimidine nucleotides, blocking de novo biosynthesis is seen as an effective therapeutic means to selectively target the parasite without effecting the human host. Dihydroorotate dehydrogenase (DHODH), which is involved in the de novo biosynthesis of pyrimidines, is a validated target for anti-infective drug research. Recent advances in the DHODH microorganism field are discussed herein, as is the potential for the development of DHODH-targeted therapeutics.
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Chibli LA, Rosa AL, Nonato MC, Da Costa FB. Untargeted LC-MS metabolomic studies of Asteraceae species to discover inhibitors of Leishmania major dihydroorotate dehydrogenase. Metabolomics 2019; 15:59. [PMID: 30949823 DOI: 10.1007/s11306-019-1520-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/25/2019] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Interesting data about the family Asteraceae as a new source of Leishmania major dihydroorotate dehydrogenase (LmDHODH) inhibitors are presented. This key macromolecular target for parasites causing neglected diseases catalyzes the fourth reaction of the de novo pyrimidine biosynthetic pathway, which takes part in major cell functions, including DNA and RNA biosynthesis. OBJECTIVES We aimed to (1) determine LmDHODH inhibitor candidates, revealing the type of chemistry underlying such bioactivity, and (2) predict the inhibitory potential of extracts from new untested plant species, classifying them as active or inactive based on their LC-MS based metabolic fingerprints. METHODS Extracts from 150 species were screened for the inhibition of LmDHODH, and untargeted UHPLC-(ESI)-HRMS metabolomic studies were carried out in combination with in silico approaches. RESULTS The IC50 values determined for a subset of 59 species ranged from 148 µg mL-1 to 9.4 mg mL-1. Dereplication of the metabolic fingerprints allowed the identification of 48 metabolites. A reliable OPLS-DA model (R2 > 0.9, Q2 > 0.7, RMSECV < 0.3) indicated the inhibitor candidates; nine of these metabolites were identified using data from isolated chemical standards, one of which-4,5-di-O-E-caffeoylquinic acid (IC50 73 µM)-was capable of inhibiting LmDHODH. The predictive OPLS model was also effective, with 60% correct predictions for the test set. CONCLUSION Our approach was validated for (1) the discovery of LmDHODH inhibitors or interesting starting points for the optimization of new leishmanicides from Asteraceae species and (2) the prediction of extracts from untested species, classifying them as active or inactive.
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Affiliation(s)
- Lucas A Chibli
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Annylory L Rosa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Maria Cristina Nonato
- Laboratory of Protein Crystallography, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Fernando B Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil.
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Nonato MC, de Pádua RA, David JS, Reis RA, Tomaleri GP, D'Muniz Pereira H, Calil FA. Structural basis for the design of selective inhibitors for Schistosoma mansoni dihydroorotate dehydrogenase. Biochimie 2019; 158:180-190. [DOI: 10.1016/j.biochi.2019.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/10/2019] [Indexed: 10/27/2022]
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Miyazaki Y, Inaoka DK, Shiba T, Saimoto H, Sakura T, Amalia E, Kido Y, Sakai C, Nakamura M, Moore AL, Harada S, Kita K. Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol 2018; 9:997. [PMID: 30233375 PMCID: PMC6131557 DOI: 10.3389/fphar.2018.00997] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/13/2018] [Indexed: 12/15/2022] Open
Abstract
Human dihydroorotate dehydrogenase (HsDHODH) is a key enzyme of pyrimidine de novo biosynthesis pathway. It is located on the mitochondrial inner membrane and contributes to the respiratory chain by shuttling electrons to the ubiquinone pool. We have discovered ascofuranone (1), a natural compound produced by Acremonium sclerotigenum, and its derivatives are a potent class of HsDHODH inhibitors. We conducted a structure–activity relationship study and have identified functional groups of 1 that are essential for the inhibition of HsDHODH enzymatic activity. Furthermore, the binding mode of 1 and its derivatives to HsDHODH was demonstrated by co-crystallographic analysis and we show that these inhibitors bind at the ubiquinone binding site. In addition, the cytotoxicities of 1 and its potent derivatives 7, 8, and 9 were studied using human cultured cancer cells. Interestingly, they showed selective and strong cytotoxicity to cancer cells cultured under microenvironment (hypoxia and nutrient-deprived) conditions. The selectivity ratio of 8 under this microenvironment show the most potent inhibition which was over 1000-fold higher compared to that under normal culture condition. Our studies suggest that under microenvironment conditions, cancer cells heavily depend on the pyrimidine de novo biosynthesis pathway. We also provide the first evidence that 1 and its derivatives are potential lead candidates for drug development which target the HsDHODH of cancer cells living under a tumor microenvironment.
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Affiliation(s)
- Yukiko Miyazaki
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daniel K Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Takaya Sakura
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasutoshi Kido
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Chika Sakai
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mari Nakamura
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Anthony L Moore
- Biochemistry and Medicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
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Ohishi T, Masuda T, Abe H, Hayashi C, Adachi H, Ohba SI, Igarashi M, Watanabe T, Mimuro H, Amalia E, Inaoka DK, Mochizuki K, Kita K, Shibasaki M, Kawada M. Monotherapy with a novel intervenolin derivative, AS-1934, is an effective treatment for Helicobacter pylori infection. Helicobacter 2018; 23:e12470. [PMID: 29488678 DOI: 10.1111/hel.12470] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infection causes various gastrointestinal diseases including gastric cancer. Hence, eradication of this infection could prevent these diseases. The most popular first-line treatment protocol to eradicate H. pylori is termed "triple therapy" and consists of a proton pump inhibitor (PPI), clarithromycin, and amoxicillin or metronidazole. However, the antibiotics used to treat H. pylori infection are hindered by the antibiotics-resistant bacteria and by their antimicrobial activity against intestinal bacteria, leading to side effects. Therefore, an alternative treatment with fewer adverse side effects is urgently required to improve the overall eradication rate of H. pylori. OBJECTIVE The aim of this study was to assess the effectiveness and mechanism of action of an antitumor agent, intervenolin, and its derivatives as an agent for the treatment of H. pylori infection. RESULTS We demonstrate that intervenolin, and its derivatives showed selective anti-H. pylori activity, including antibiotic-resistant strains, without any effect on intestinal bacteria. We showed that dihydroorotate dehydrogenase, a key enzyme for de novo pyrimidine biosynthesis, is a target and treatment with intervenolin or its derivatives decreased the protein and mRNA levels of H. pylori urease, which protects H. pylori against acidic conditions in the stomach. Using a mouse model of H. pylori infection, oral monotherapy with the intervenolin derivative AS-1934 had a stronger anti-H. pylori effect than the triple therapy commonly used worldwide to eradicate H. pylori. CONCLUSION AS-1934 has potential advantages over current treatment options for H. pylori infection.
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Affiliation(s)
- Tomokazu Ohishi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan
| | - Tohru Masuda
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan
| | - Hikaru Abe
- Institute of Microbial Chemistry (BIKAKEN), Laboratory of Synthetic Organic Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo, Japan
| | - Chigusa Hayashi
- Institute of Microbial Chemistry (BIKAKEN), Laboratory of Microbiology, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo, Japan
| | - Hayamitsu Adachi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan
| | - Shun-Ichi Ohba
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan
| | - Masayuki Igarashi
- Institute of Microbial Chemistry (BIKAKEN), Laboratory of Microbiology, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo, Japan
| | - Takumi Watanabe
- Institute of Microbial Chemistry (BIKAKEN), Laboratory of Synthetic Organic Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo, Japan
| | - Hitomi Mimuro
- Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.,Division of Infectious Disease, Department of Infection Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Eri Amalia
- Department of Biomedical Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki-shi, Nagasaki, Japan
| | - Kota Mochizuki
- Department of Immunogenetics, Institute of Tropical Medicine, Nagasaki University, Nagasaki-shi, Nagasaki, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki-shi, Nagasaki, Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN), Laboratory of Synthetic Organic Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo, Japan
| | - Manabu Kawada
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, Numazu-shi, Shizuoka, Japan.,Institute of Microbial Chemistry (BIKAKEN), Laboratory of Oncology, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo, Japan
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13
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Ohishi T, Inaoka DK, Kita K, Kawada M. Dihydroorotate Dehydrogenase as a Target for the Development of Novel Helicobacter pylori-Specific Antimicrobials. Chem Pharm Bull (Tokyo) 2018; 66:239-242. [PMID: 29491257 DOI: 10.1248/cpb.c17-00796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Helicobacter pylori (H. pylori) infection is the world's most common bacterial infection, affecting approximately 50% of the global population. H. pylori is the strongest known risk factor for stomach diseases, including cancer. Hence, treatment for H. pylori infection can help reduce the risk of these diseases. However, the emergence of drug-resistant strains of H. pylori and the occurrence of adverse effects resulting from current therapies have complicated the successful eradication of H. pylori infection. Although various antibiotics that target several bacterial enzymes have been discovered, dihydroorotate dehydrogenase (DHODH) may hold potential for the development of novel anti-H. pylori agents with reduced toxicity and side effects. Here we review the existing literature that has focused on strategies for developing novel therapeutic agents that target the DHODH of H. pylori.
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Affiliation(s)
- Tomokazu Ohishi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation
| | | | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University
| | - Manabu Kawada
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation.,Institute of Microbial Chemistry (BIKAKEN), Laboratory of Oncology, Microbial Chemistry Research Foundation
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14
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Bu FZ, Tan XJ, Xing DX, Wang C. Design, synthesis, crystal structure and in vitro cytotoxic properties of a novel Schiff base derived from indole and biphenyl. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:546-555. [DOI: 10.1107/s2053229617009044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/16/2017] [Indexed: 03/18/2023]
Abstract
A novel and potentially active dihydroorotate dehydrogenase (DHODH) inhibitor, namely 3-({(E)-[(E)-1-(biphenyl-4-yl)ethylidene]hydrazinylidene}methyl)-1H-indole (BEHI) acetonitrile disolvate, C23H19N3·2CH3CN, has been designed and synthesized. The structure of BEHI was characterized by elemental analysis, Q-TOF (quadrupole time-of-flight) MS, NMR, UV–Vis and single-crystal X-ray diffraction. The antitumour activity of the target molecule was evaluated by the MTT method. Results indicated that BEHI exhibited rather potent cytotoxic activity against human A549 (IC50 = 20.5 µM) and mouse breast 4T1 (IC50 = 18.5 µM) cancer cell lines. Meanwhile, to rationalize its potencies in the target, BEHI was docked into DHODH and the interactions with the active site residues were analyzed. Single-crystal structure analysis indicated that hydrogen bonds are present only between BEHI and acetonitrile solvent molecules in the asymmetric unit. The interplay of weak π–π stacking and weak C(N)—H...π interactions between neighbouring BEHI molecules play crucial roles in the formation of the final supramolecular frameworks.
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15
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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]
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16
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The Open Form Inducer Approach for Structure-Based Drug Design. PLoS One 2016; 11:e0167078. [PMID: 27893848 PMCID: PMC5125662 DOI: 10.1371/journal.pone.0167078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/08/2016] [Indexed: 01/07/2023] Open
Abstract
Many open form (OF) structures of drug targets were obtained a posteriori by analysis of co-crystals with inhibitors. Therefore, obtaining the OF structure of a drug target a priori will accelerate development of potent inhibitors. In addition to its small active site, Trypanosoma cruzi dihydroorotate dehydrogenase (TcDHODH) is fully functional in its monomeric form, making drug design approaches targeting the active site and protein-protein interactions unrealistic. Therefore, a novel a priori approach was developed to determination the TcDHODH active site in OF. This approach consists of generating an "OF inducer" (predicted in silico) to bind the target and cause steric repulsion with flexible regions proximal to the active site that force it open. We provide the first proof-of-concept of this approach by predicting and crystallizing TcDHODH in complex with an OF inducer, thereby obtaining the OF a priori with its subsequent use in designing potent and selective inhibitors. Fourteen co-crystal structures of TcDHODH with the designed inhibitors are presented herein. This approach has potential to encourage drug design against diseases where the molecular targets are such difficult proteins possessing small AS volume. This approach can be extended to study open/close conformation of proteins in general, the identification of allosteric pockets and inhibitors for other drug targets where conventional drug design approaches are not applicable, as well as the effective exploitation of the increasing number of protein structures deposited in Protein Data Bank.
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17
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Li J, Wu D, Xu X, huang J, Shao X, Li Z. Design, synthesis and inhibitory activity against human dihydroorotate dehydrogenase ( h DHODH) of 1,3-benzoazole derivatives bearing amide units. Bioorg Med Chem Lett 2016; 26:3064-3066. [DOI: 10.1016/j.bmcl.2016.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/12/2016] [Accepted: 05/04/2016] [Indexed: 01/26/2023]
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18
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Guo Q, Wei Y, Xia B, Jin Y, Liu C, Pan X, Shi J, Zhu F, Li J, Qian L, Liu X, Cheng Z, Jin S, Lin J, Wu W. Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa. Sci Rep 2016; 6:19141. [PMID: 26751736 PMCID: PMC4707474 DOI: 10.1038/srep19141] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
The rising antibiotic resistance of bacteria imposes a severe threat on human health. Inhibition of bacterial virulence is an alternative approach to develop new antimicrobials. Molecules targeting antibiotic resistant enzymes have been used in combination with cognate antibiotics. It might be ideal that a molecule can simultaneously suppress virulence factors and antibiotic resistance. Here we combined genetic and computer-aided inhibitor screening to search for such molecules against the bacterial pathogen Pseudomonas aeruginosa. To identify target proteins that control both virulence and antibiotic resistance, we screened for mutants with defective cytotoxicity and biofilm formation from 93 transposon insertion mutants previously reported with increased antibiotic susceptibility. A pyrD mutant displayed defects in cytotoxicity, biofilm formation, quorum sensing and virulence in an acute mouse pneumonia model. Next, we employed a computer-aided screening to identify potential inhibitors of the PyrD protein, a dihydroorotate dehydrogenase (DHODase) involved in pyrimidine biosynthesis. One of the predicted inhibitors was able to suppress the enzymatic activity of PyrD as well as bacterial cytotoxicity, biofilm formation and antibiotic resistance. A single administration of the compound reduced the bacterial colonization in the acute mouse pneumonia model. Therefore, we have developed a strategy to identify novel treatment targets and antimicrobial molecules.
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Affiliation(s)
- Qiaoyun Guo
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yu Wei
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Bin Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jing Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Feng Zhu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jinlong Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Lei Qian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
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19
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Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method. PLoS One 2015; 10:e0125829. [PMID: 25961853 PMCID: PMC4427443 DOI: 10.1371/journal.pone.0125829] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 03/26/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives. METHODOLOGY/PRINCIPAL FINDINGS Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. CONCLUSIONS/SIGNIFICANCE FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.
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20
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Alka K, Windle HJ, Cornally D, Ryan BJ, Henehan GTM. A short chain NAD(H)-dependent alcohol dehydrogenase (HpSCADH) from Helicobacter pylori: a role in growth under neutral and acidic conditions. Int J Biochem Cell Biol 2013; 45:1347-55. [PMID: 23583739 DOI: 10.1016/j.biocel.2013.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 03/27/2013] [Accepted: 04/03/2013] [Indexed: 11/18/2022]
Abstract
Toxic aldehydes produced by alcohol dehydrogenases have been implicated in the pathogenesis of Helicobacter pylori-related damage to the gastric mucosa. Despite this, the enzymes that might be responsible for producing such aldehydes have not been fully described. It was, therefore, of considerable interest to characterize the alcohol oxidizing enzymes in this pathogen. Previous work in this laboratory characterized two such H. pylori enzymes that had broad specificity for a range of aromatic alcohol substrates. However, an enzyme with specificity for aliphatic alcohols is likely to be required in order that H. pylori can metabolize the wide range of substrates encountered in the gastric mucosa. In this study we describe HpSCADH, an alcohol dehydrogenase from H. pylori 26695 with broad specificity for aliphatic alcohols. HpSCADH was classified in the cD1e subfamily of classical short chain alcohol dehydrogenases. The enzyme was a monomer of approximately 29kDa with a preference for NAD(+) as cofactor. Pyrazole was found to be a competitive inhibitor of HpSCADH. The physiological role of this enzyme was explored by construction of an HpSCADH isogenic mutant. At pH 7.0 the mutant showed reduced growth which became more pronounced when the pH was lowered to 5.0. When pyrazole was added to wild type H. pylori cells it caused growth profiles to be reduced to match those of the isogenic mutant suggesting that HpSCADH inhibition alone was responsible for growth impairment. Taken together, the data relating to the alcohol metabolizing enzymes of this pathogen indicate that they play an important role in H. pylori growth and adaptation to acidic environments. The therapeutic potential of targeting H. pylori alcohol dehydrogenases is discussed.
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Affiliation(s)
- Kumari Alka
- School of Food Science and Environmental Health, Dublin Institute of Technology, Marlborough Street, Dublin 1, Ireland
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21
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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.
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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
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22
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3D-QSAR studies on a series of dihydroorotate dehydrogenase inhibitors: analogues of the active metabolite of leflunomide. Int J Mol Sci 2011; 12:2982-93. [PMID: 21686163 PMCID: PMC3116169 DOI: 10.3390/ijms12052982] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 03/31/2011] [Accepted: 04/28/2011] [Indexed: 01/05/2023] Open
Abstract
The active metabolite of the novel immunosuppressive agent leflunomide has been shown to inhibit the enzyme dihydroorotate dehydrogenase (DHODH). This enzyme catalyzes the fourth step in de novo pyrimidine biosynthesis. Self-organizing molecular field analysis (SOMFA), a simple three-dimensional quantitative structure-activity relationship (3D-QSAR) method is used to study the correlation between the molecular properties and the biological activities of a series of analogues of the active metabolite. The statistical results, cross-validated r(CV) (2) (0.664) and non cross-validated r(2) (0.687), show a good predictive ability. The final SOMFA model provides a better understanding of DHODH inhibitor-enzyme interactions, and may be useful for further modification and improvement of inhibitors of this important enzyme.
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23
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Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery. Eur J Med Chem 2010; 45:5899-909. [DOI: 10.1016/j.ejmech.2010.09.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Revised: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 11/22/2022]
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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]
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25
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Duckworth MJ, Okoli AS, Mendz GL. Novel Helicobacter pylori therapeutic targets: the unusual suspects. Expert Rev Anti Infect Ther 2009; 7:835-67. [PMID: 19735225 DOI: 10.1586/eri.09.61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the current status of the discovery and development of anti-Helicobacter therapies requires an overview of the searches for therapeutic targets performed to date. A summary is given of the very substantial body of work conducted in the quest to find Helicobacter pylori genes that could be suitable candidates for therapeutic intervention. The products of most of these genes perform metabolic functions, and others have roles in growth, cell motility and colonization. The genes identified as potential targets have been organized into three categories according to their degree of characterization. A short description and evaluation is provided of the main candidates in each category. Investigations of potential therapeutic targets have generated a wealth of information about the physiology and genetics of H. pylori, and its interactions with the host, but have yielded little by way of new therapies.
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Affiliation(s)
- Megan J Duckworth
- School of Medicine, Sydney, The University of Notre Dame Australia, 160 Oxford Street, Darlinghurst, NSW 2010, Australia.
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Deng X, Gujjar R, El Mazouni F, Kaminsky W, Malmquist NA, Goldsmith EJ, Rathod PK, Phillips MA. Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds. J Biol Chem 2009; 284:26999-7009. [PMID: 19640844 DOI: 10.1074/jbc.m109.028589] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.
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Affiliation(s)
- Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9041, USA
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27
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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: 173] [Impact Index Per Article: 11.5] [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.
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Affiliation(s)
- Ramesh Gujjar
- Department of Chemistry and Global Health and Department of Medicine, University of Washington, Seattle, Washington 98195, USA
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28
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Davies M, Heikkilä T, McConkey GA, Fishwick CWG, Parsons MR, Johnson AP. Structure-Based Design, Synthesis, and Characterization of Inhibitors of Human and Plasmodium falciparum Dihydroorotate Dehydrogenases. J Med Chem 2009; 52:2683-93. [DOI: 10.1021/jm800963t] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Matthew Davies
- School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Timo Heikkilä
- School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Glenn A. McConkey
- School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Colin W. G. Fishwick
- School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Mark R. Parsons
- School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - A. Peter Johnson
- School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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29
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Patel V, Booker M, Kramer M, Ross L, Celatka CA, Kennedy LM, Dvorin JD, Duraisingh MT, Sliz P, Wirth DF, Clardy J. Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biol Chem 2008; 283:35078-85. [PMID: 18842591 PMCID: PMC2596402 DOI: 10.1074/jbc.m804990200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 10/06/2008] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum causes the most deadly form of malaria and accounts for over one million deaths annually. The malaria parasite is unable to salvage pyrimidines and relies on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHOD), a mitochondrially localized flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive antimalarial chemotherapeutic target. Using a target-based high throughput screen, we have identified a series of potent, species-specific inhibitors of P. falciparum DHOD (pfDHOD) that are also efficacious against three cultured strains (3D7, HB3, and Dd2) of P. falciparum. The primary antimalarial mechanism of action of these compounds was confirmed to be inhibition of pfDHOD through a secondary assay with transgenic malaria parasites, and the structural basis for enzyme inhibition was explored through in silico structure-based docking and site-directed mutagenesis. Compound-mediated cytotoxicity was not observed with human dermal fibroblasts or renal epithelial cells. These data validate pfDHOD as an antimalarial drug target and provide chemical scaffolds with which to begin medicinal chemistry efforts.
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Affiliation(s)
- Vishal Patel
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Michael Booker
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Martin Kramer
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Leila Ross
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Cassandra A. Celatka
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Leah M. Kennedy
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Jeffrey D. Dvorin
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Manoj T. Duraisingh
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Piotr Sliz
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Dyann F. Wirth
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
| | - Jon Clardy
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard Medical School, Boston,
Massachusetts 02115, the Department
of Immunology and Infectious Disease, Harvard School of Public Health, Boston,
Massachusetts 02115, Drug and
Biomaterial Research and Development, Genzyme Corporation, Waltham,
Massachusetts 02451, Division of
Infectious Diseases, Children's Hospital Boston, Boston, Massachusetts 02115,
and the Department of Pediatrics, Harvard
Medical School, Boston, Massachusetts 02115
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30
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Inaoka DK, Sakamoto K, Shimizu H, Shiba T, Kurisu G, Nara T, Aoki T, Kita K, Harada S. Structures of Trypanosoma cruzi Dihydroorotate Dehydrogenase Complexed with Substrates and Products: Atomic Resolution Insights into Mechanisms of Dihydroorotate Oxidation and Fumarate Reduction. Biochemistry 2008; 47:10881-91. [DOI: 10.1021/bi800413r] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Kimitoshi Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Hironari Shimizu
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Tomoo Shiba
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Genji Kurisu
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Takeshi Nara
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Takashi Aoki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Shigeharu Harada
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
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31
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Walse B, Dufe VT, Svensson B, Fritzson I, Dahlberg L, Khairoullina A, Wellmar U, Al-Karadaghi S. The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites. Biochemistry 2008; 47:8929-36. [PMID: 18672895 DOI: 10.1021/bi8003318] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inhibitors of dihydroorotate dehydrogenase (DHODH) have been suggested for the treatment of rheumatoid arthritis, psoriasis, autoimmune diseases, Plasmodium, and bacterial and fungal infections. Here we present the structures of N-terminally truncated (residues Met30-Arg396) DHODH in complex with two inhibitors: a brequinar analogue (6) and a novel inhibitor (a fenamic acid derivative) (7), as well as the first structure of the enzyme to be characterized without any bound inhibitor. It is shown that 7 uses the "standard" brequinar binding mode and, in addition, interacts with Tyr356, a residue conserved in most class 2 DHODH proteins. Compared to the inhibitor-free structure, some of the amino acid side chains in the tunnel in which brequinar binds and which was suggested to be the binding site of ubiquinone undergo changes in conformation upon inhibitor binding. Using our data, the loop regions of residues Leu68-Arg72 and Asn212-Leu224, which were disordered in previously studied human DHODH structures, could be built into the electron density. The first of these loops, which is located at the entrance to the inhibitor-binding pocket, shows different conformations in the three structures, suggesting that it may interfere with inhibitor/cofactor binding. The second loop has been suggested to control the access of dihydroorotate to the active site of the enzyme and may be an important player in the enzymatic reaction. These observations provide new insights into the dynamic features of the DHODH reaction and suggest new approaches to the design of inhibitors against DHODH.
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Affiliation(s)
- Björn Walse
- SARomics AB, P.O. Box 724, SE-220 07 Lund, Sweden.
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32
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Heikkilä T, Ramsey C, Davies M, Galtier C, Stead AMW, Johnson AP, Fishwick CWG, Boa AN, McConkey GA. Design and Synthesis of Potent Inhibitors of the Malaria Parasite Dihydroorotate Dehydrogenase. J Med Chem 2006; 50:186-91. [PMID: 17228860 DOI: 10.1021/jm060687j] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyrimidine biosynthesis presents an attractive drug target in malaria parasites due to the absence of a pyrimidine salvage pathway. A set of compounds designed to inhibit the Plasmodium falciparum pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (PfDHODH) was synthesized. PfDHODH-specific inhibitors with low nanomolar binding affinities were identified that bind in the N-terminal hydrophobic channel of dihydroorotate dehydrogenase, the presumed site of ubiquinone binding during oxidation of dihydroorotate to orotate. These compounds also prevented growth of cultured parasites at low micromolar concentrations. Models that suggest the mode of inhibitor binding is based on shape complementarity, matching hydrophobic regions of inhibitor and enzyme, and interaction of inhibitors with amino acid residues F188, H185, and R265 are supported by mutagenesis data. These results further highlight PfDHODH as a promising new target for chemotherapeutic intervention in prevention of malaria and provide better understanding of the factors that determine specificity over human dihydroorotate dehydrogenase.
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Affiliation(s)
- Timo Heikkilä
- School of Chemistry and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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33
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Cordeiro AT, Feliciano PR, Nonato MC. Crystallization and preliminary X-ray diffraction analysis of Leishmania major dihydroorotate dehydrogenase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1049-51. [PMID: 17012810 PMCID: PMC2225193 DOI: 10.1107/s1744309106038966] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 09/22/2006] [Indexed: 11/10/2022]
Abstract
Dihydroorotate dehydrogenases (DHODHs) are flavin-containing enzymes that catalyze the oxidation of L-dihydroorotate to orotate, the fourth step in the de novo pyrimidine nucleotide synthesis pathway. In this study, DHODH from Leishmania major has been crystallized by the vapour-diffusion technique using lithium sulfate as the precipitating agent. The crystals belong to space group P6(1), with unit-cell parameters a = 143.7, c = 69.8 A. X-ray diffraction data were collected to 2.0 A resolution using an in-house rotating-anode generator. Analysis of the solvent content and the self-rotation function indicate the presence of two molecules in the asymmetric unit. The structure has been solved by the molecular-replacement technique.
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Affiliation(s)
- Artur T. Cordeiro
- Laboratório de Cristalografia de Proteínas, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Ribeirão Preto, SP 14040-903, Brazil
| | - Patricia R. Feliciano
- Laboratório de Cristalografia de Proteínas, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Ribeirão Preto, SP 14040-903, Brazil
| | - M. Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Ribeirão Preto, SP 14040-903, Brazil
- Correspondence e-mail:
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34
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Hurt DE, Sutton AE, Clardy J. Brequinar derivatives and species-specific drug design for dihydroorotate dehydrogenase. Bioorg Med Chem Lett 2006; 16:1610-5. [PMID: 16406782 DOI: 10.1016/j.bmcl.2005.12.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 12/07/2005] [Accepted: 12/07/2005] [Indexed: 10/25/2022]
Abstract
Therapeutic agents brequinar sodium and leflunomide (Arava) work by binding in a hydrophobic tunnel formed by a highly variable N-terminus of family 2 dihydroorotate dehydrogenase (DHODH). The X-ray crystallographic structure of an analog of brequinar bound to human DHODH was determined. In silico screening of a library of compounds suggested another subset of brequinar analogs that do not inhibit human DHODH as potentially effective inhibitors of Plasmodium falciparum DHODH.
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Affiliation(s)
- Darrell E Hurt
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
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35
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Fuh Wong F, Chang EM, Chen TH, Chiang KC, Yeh MY. Regioselectivity in 1,3-Dipolar Cycloaddition of 3-(4-Ethoxyphenyl)-4-cyanosydnone with Propargylic Esters. HETEROCYCLES 2006. [DOI: 10.3987/com-06-10714] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Heikkilä T, Thirumalairajan S, Davies M, Parsons MR, McConkey AG, Fishwick CWG, Johnson AP. The first de novo designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. Bioorg Med Chem Lett 2005; 16:88-92. [PMID: 16236496 DOI: 10.1016/j.bmcl.2005.09.045] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 09/17/2005] [Accepted: 09/19/2005] [Indexed: 11/28/2022]
Abstract
The de novo molecular design program SPROUT has been applied to the X-ray crystal structures of Plasmodium and human dihydroorotate dehydrogenase, respectively. The resulting design templates were used to prepare a series of molecules which, in keeping with predictions, showed useful levels of species-selective enzyme inhibition.
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Affiliation(s)
- Timo Heikkilä
- School of Chemistry, University of Leeds, Leeds, England LS2 9JT, UK
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37
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Thiele I, Vo TD, Price ND, Palsson BØ. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 2005; 187:5818-30. [PMID: 16077130 PMCID: PMC1196094 DOI: 10.1128/jb.187.16.5818-5830.2005] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 04/19/2005] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori is a human gastric pathogen infecting almost half of the world population. Herein, we present an updated version of the metabolic reconstruction of H. pylori strain 26695 based on the revised genome annotation and new experimental data. This reconstruction, iIT341 GSM/GPR, represents a detailed review of the current literature about H. pylori as it integrates biochemical and genomic data in a comprehensive framework. In total, it accounts for 341 metabolic genes, 476 intracellular reactions, 78 exchange reactions, and 485 metabolites. Novel features of iIT341 GSM/GPR include (i) gene-protein-reaction associations, (ii) elementally and charge-balanced reactions, (iii) more accurate descriptions of isoprenoid and lipopolysaccharide metabolism, and (iv) quantitative assessments of the supporting data for each reaction. This metabolic reconstruction was used to carry out in silico deletion studies to identify essential and conditionally essential genes in H. pylori. A total of 128 essential and 75 conditionally essential metabolic genes were identified. Predicted growth phenotypes of single knockouts were validated using published experimental data. In addition, in silico double-deletion studies identified a total of 47 synthetic lethal mutants involving 67 different metabolic genes in rich medium.
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Affiliation(s)
- Ines Thiele
- Department of Bioengineering, University of California-San Diego, 9500 Gilman Dr. 0412, La Jolla, CA 92093-0412, USA
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38
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Baldwin J, Michnoff CH, Malmquist NA, White J, Roth MG, Rathod PK, Phillips MA. High-throughput screening for potent and selective inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biol Chem 2005; 280:21847-53. [PMID: 15795226 DOI: 10.1074/jbc.m501100200] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum is the causative agent of the most serious and fatal malarial infections, and it has developed resistance to commonly employed chemotherapeutics. The de novo pyrimidine biosynthesis enzymes offer potential as targets for drug design, because, unlike the host, the parasite does not have pyrimidine salvage pathways. Dihydroorotate dehydrogenase (DHODH) is a flavin-dependent mitochondrial enzyme that catalyzes the fourth reaction in this essential pathway. Coenzyme Q (CoQ) is utilized as the oxidant. Potent and species-selective inhibitors of malarial DHODH were identified by high-throughput screening of a chemical library, which contained 220,000 drug-like molecules. These novel inhibitors represent a diverse range of chemical scaffolds, including a series of halogenated phenyl benzamide/naphthamides and urea-based compounds containing napthyl or quinolinyl substituents. Inhibitors in these classes with IC(50) values below 600 nm were purified by high pressure liquid chromatography, characterized by mass spectroscopy, and subjected to kinetic analysis against the parasite and human enzymes. The most active compound is a competitive inhibitor of CoQ with an IC(50) against malarial DHODH of 16 nm, and it is 12,500-fold less active against the human enzyme. Site-directed mutagenesis of residues in the CoQ-binding site significantly reduced inhibitor potency. The structural basis for the species selective enzyme inhibition is explained by the variable amino acid sequence in this binding site, making DHODH a particularly strong candidate for the development of new anti-malarial compounds.
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Affiliation(s)
- Jeffrey Baldwin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
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39
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Boa AN, Canavan SP, Hirst PR, Ramsey C, Stead AMW, McConkey GA. Synthesis of brequinar analogue inhibitors of malaria parasite dihydroorotate dehydrogenase. Bioorg Med Chem 2005; 13:1945-67. [PMID: 15727850 DOI: 10.1016/j.bmc.2005.01.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Accepted: 01/12/2005] [Indexed: 10/25/2022]
Abstract
A series of 2-phenyl quinoline-4-carboxylic acid derivatives related to brequinar, an inhibitor of human dihydroorotate dehydrogenase (DHODH), has been prepared and evaluated as inhibitors of DHODH from the malaria parasite Plasmodium falciparum. Brequinar was essentially inactive against PfDHODH (IC(50) 880 microM) whereas several members of the series inhibited PfDHODH. Unexpectedly, replacement of the carboxylic acid required for brequinar to inhibit hDHODH was not essential in the diisopropylamides that inhibited PfDHODH.
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Affiliation(s)
- Andrew N Boa
- Department of Chemistry, University of Hull, Cottingham Road, Hull HU6 7RX, UK.
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40
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Chimenti F, Bizzarri B, Manna F, Bolasco A, Secci D, Chimenti P, Granese A, Rivanera D, Lilli D, Scaltrito MM, Brenciaglia MI. Synthesis and in vitro selective anti-Helicobacter pylori activity of pyrazoline derivatives. Bioorg Med Chem Lett 2005; 15:603-7. [PMID: 15664821 DOI: 10.1016/j.bmcl.2004.11.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Revised: 11/15/2004] [Accepted: 11/17/2004] [Indexed: 10/26/2022]
Abstract
In order to develop new anti-Helicobacter pylori agents, a series of N1-substituted 3,5-diphenyl pyrazolines P1-P13 was prepared and evaluated for their antibacterial activity. All synthesized compounds showed little or no activity against different species of Gram-positive and Gram-negative bacteria of clinical relevance and against various strains of pathogenic fungi. The same derivatives exhibited a significant degree of activity against a range of H. pylori strains, including those resistant to the reference compound metronidazole. Among the prepared compounds those with an N1-acetyl group and a 4-methoxy substituent in the 5-phenyl ring showed the best activity against H. pylori metronidazole resistant strains in the 1-4 microg/mL MIC range.
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Affiliation(s)
- F Chimenti
- Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università 'La Sapienza', P.le A. Moro 5, 00185 Rome, Italy
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41
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Hansen M, Le Nours J, Johansson E, Antal T, Ullrich A, Löffler M, Larsen S. Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain. Protein Sci 2004; 13:1031-42. [PMID: 15044733 PMCID: PMC2280058 DOI: 10.1110/ps.03533004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The flavin enzyme dihydroorotate dehydrogenase (DHOD; EC 1.3.99.11) catalyzes the oxidation of dihydroorotate to orotate, the fourth step in the de novo pyrimidine biosynthesis of UMP. The enzyme is a promising target for drug design in different biological and clinical applications for cancer and arthritis. The first crystal structure of the class 2 dihydroorotate dehydrogenase from rat has been determined in complex with its two inhibitors brequinar and atovaquone. These inhibitors have shown promising results as anti-proliferative, immunosuppressive, and antiparasitic agents. A unique feature of the class 2 DHODs is their N-terminal extension, which folds into a separate domain comprising two alpha-helices. This domain serves as the binding site for the two inhibitors and the respiratory quinones acting as the second substrate for the class 2 DHODs. The orientation of the first N-terminal helix is very different in the two complexes of rat DHOD (DHODR). Binding of atovaquone causes a 12 A movement of the first residue in the first alpha-helix. Based on the information from the two structures of DHODR, a model for binding of the quinone and the residues important for the interactions could be defined. His 56 and Arg 136, which are fully conserved in all class 2 DHODs, seem to play a key role in the interaction with the electron acceptor. The differences between the membrane-bound rat DHOD and membrane-associated class 2 DHODs exemplified by the Escherichia coli DHOD has been investigated by GRID computations of the hydrophobic probes predicted to interact with the membrane.
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Affiliation(s)
- Majbritt Hansen
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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42
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Baldwin J, Farajallah AM, Malmquist NA, Rathod PK, Phillips MA. Malarial dihydroorotate dehydrogenase. Substrate and inhibitor specificity. J Biol Chem 2002; 277:41827-34. [PMID: 12189151 DOI: 10.1074/jbc.m206854200] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The malarial parasite relies on de novo pyrimidine biosynthesis to maintain its pyrimidine pools, and unlike the human host cell it is unable to scavenge preformed pyrimidines. Dihydroorotate dehydrogenase (DHODH) catalyzes the oxidation of dihydroorotate (DHO) to produce orotate, a key step in pyrimidine biosynthesis. The enzyme is located in the outer membrane of the mitochondria of the malarial parasite. To characterize the biochemical properties of the malarial enzyme, an N-terminally truncated version of P. falciparum DHODH has been expressed as a soluble, active enzyme in E. coli. The recombinant enzyme binds 0.9 molar equivalents of the cofactor FMN and it has a pH maximum of 8.0 (k(cat) 8 s(-1), K(m)(app) DHO (40-80 microm)). The substrate specificity of the ubiquinone cofactor (CoQ(n)) that is required for the oxidation of FMN in the second step of the reaction was also determined. The isoprenoid (n) length of CoQ(n) was a determinant of reaction efficiency; CoQ(4), CoQ(6) and decylubiquinone (CoQ(D)) were efficiently utilized in the reaction, however cofactors lacking an isoprenoid tail (CoQ(0) and vitamin K(3)) showed decreased catalytic efficiency resulting from a 4 to 7-fold increase in K(m)(app). Five potent inhibitors of mammalian DHODH, Redoxal, dichloroallyl lawsone (DCL), and three analogs of A77 1726 were tested as inhibitors of the malarial enzyme. All five compounds were poor inhibitors of the malarial enzyme, with IC(50)'s ranging from 0.1-1.0 mm. The IC(50) values for inhibition of the malarial enzyme are 10(2)-10(4)-fold higher than the values reported for the mammalian enzyme, demonstrating that inhibitor binding to DHODH is species specific. These studies provide direct evidence that the malarial DHODH active site is different from the host enzyme, and that it is an attractive target for the development of new anti-malarial agents.
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Affiliation(s)
- Jeffrey Baldwin
- Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas, 75390-9041, USA
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43
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Haque TS, Tadesse S, Marcinkeviciene J, Rogers MJ, Sizemore C, Kopcho LM, Amsler K, Ecret LD, Zhan DL, Hobbs F, Slee A, Trainor GL, Stern AM, Copeland RA, Combs AP. Parallel synthesis of potent, pyrazole-based inhibitors of Helicobacter pylori dihydroorotate dehydrogenase. J Med Chem 2002; 45:4669-78. [PMID: 12361393 DOI: 10.1021/jm020112w] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification of several potent pyrazole-based inhibitors of bacterial dihydroorotate dehydrogenase (DHODase) via a directed parallel synthetic approach is described below. The initial pyrazole-containing lead compounds were optimized for potency against Helicobacter pylori DHODase. Using three successive focused libraries, inhibitors were rapidly identified with the following characteristics: K(i) < 10 nM against H. pylori DHODase, sub-microg/mL H. pylori minimum inhibitory concentration activity, low molecular weight, and >10 000-fold selectivity over human DHODase.
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Affiliation(s)
- Tasir S Haque
- Department of Medicinal Chemistry, Bristol-Myers Squibb Company, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880, USA.
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44
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Nørager S, Jensen KF, Björnberg O, Larsen S. E. coli dihydroorotate dehydrogenase reveals structural and functional distinctions between different classes of dihydroorotate dehydrogenases. Structure 2002; 10:1211-23. [PMID: 12220493 DOI: 10.1016/s0969-2126(02)00831-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The flavoenzymes dihydroorotate dehydrogenases (DHODs) catalyze the fourth and only redox step in the de novo biosynthesis of UMP. Enzymes belonging to class 2, according to their amino acid sequence, are characterized by having a serine residue as the catalytic base and a longer N terminus. The structure of class 2 E. coli DHOD, determined by MAD phasing, showed that the N-terminal extension forms a separate domain. The catalytic serine residue has an environment differing from the equivalent cysteine in class 1 DHODs. Significant differences between the two classes of DHODs were identified by comparison of the E. coli DHOD with the other known DHOD structures, and differences with the class 2 human DHOD explain the variation in their inhibitors.
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Affiliation(s)
- Sofie Nørager
- Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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45
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Ando R, Kawamura M, Chiba N. 3-(Arylacetylamino)-N-methylbenzamides: a novel class of selective anti-Helicobacter pylori agents. J Med Chem 2001; 44:4468-74. [PMID: 11728192 DOI: 10.1021/jm010307o] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
After chemical modification preceded by the random screening of our chemical library, a novel class of selective anti-Helicobacter pylori agents was generated. Consequently, the 3-(arylacetylamino)-N-methylbenzamides, which were quite easy to prepare, showed potent inhibitory activity against Helicobacter pylori but exhibited no inhibitory activity against other sorts of bacteria and fungi, e.g., Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Bacteroides fragilis, and Candida albicans. These compounds showed potent anti-H. pylori activity under acidic conditions, whereas amoxicillin and clarithromycin decreased activity. The 3-(3-arylpropionylamino)-N-methylbenzamides, 3-(aryloxyacetylamino)-N-methylbenzamides, and (3-methylcarbamoylphenyl)carbamic acid 1-arylmethyl esters also exhibited potent anti-H. pylori activity. Finally, we selected 7n (BAS-118) as a candidate compound for further evaluation.
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Affiliation(s)
- R Ando
- Research Laboratory, Pharmaceuticals Research Division, Mitsubishi Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan.
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46
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Palfey BA, Björnberg O, Jensen KF. Specific inhibition of a family 1A dihydroorotate dehydrogenase by benzoate pyrimidine analogues. J Med Chem 2001; 44:2861-4. [PMID: 11520193 DOI: 10.1021/jm015535x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) catalyze the conversion of dihydroorotate to orotate in de novo pyrimidine biosynthesis. We have found that 3,4-dihydroxybenzoate and 3,5-dihydroxybenzoate are competitive inhibitors vs dihydroorotate with the prototypical family 1A DHOD from Lactococcus lactis. The dissociation constants of these compounds, determined by spectral titrations, were similar to the dissociation constant of orotate, the enzymatic reaction product, suggesting that hydroxybenzoates could be developed into useful drugs for treating infections by certain protozoan parasites.
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Affiliation(s)
- B A Palfey
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, 48109-0606, USA.
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47
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Björnberg O, Jordan DB, Palfey BA, Jensen KF. Dihydrooxonate is a substrate of dihydroorotate dehydrogenase (DHOD) providing evidence for involvement of cysteine and serine residues in base catalysis. Arch Biochem Biophys 2001; 391:286-94. [PMID: 11437361 DOI: 10.1006/abbi.2001.2409] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The flavoprotein dihydroorotate dehydrogenase (DHOD) catalyzes the oxidation of dihydroorotate to orotate. Dihydrooxonate is an analogue of dihydroorotate in which the C5 carbon is substituted by a nitrogen atom. We have investigated dihydrooxonate as a substrate of three DHODs, each representing a distinct evolutionary class of the enzyme, namely the two family 1 enzymes from Lactococcus lactis, DHODA and DHODB, and the enzyme from Escherichia coli, which, like the human enzyme, belongs to family 2. Dihydrooxonate was accepted as a substrate although much less efficiently than dihydroorotate. The first half-reaction was rate limiting according to pre-steady-state and steady-state kinetics with different electron acceptors. Cysteine and serine have been implicated as active site base residues, which promote substrate oxidation in family 1 and family 2 DHODs, respectively. Mutants of DHODA (C130A) and E. coli DHOD (S175A) have extremely low activity in standard assays with dihydroorotate as substrate, but with dihydrooxonate the mutants display considerable and increasing activity above pH 8.0. Thus, the absence of the active site base residue in the enzymes seems to be compensated for by a lower pK(a) of the 5-position in the substrate. Oxonate, the oxidation product of dihydrooxonate, was a competitive inhibitor versus dihydroorotate, and DHODA was the most sensitive of the three enzymes. DHODA was reinvestigated with respect to product inhibition by orotate. The results suggest a classical one-site ping-pong mechanism with fumarate as electron acceptor, while the kinetics with ferricyanide is highly dependent on the detailed reaction conditions.
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Affiliation(s)
- O Björnberg
- Department of Biological Chemistry, University of Copenhagen, Denmark
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48
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Chalker AF, Minehart HW, Hughes NJ, Koretke KK, Lonetto MA, Brinkman KK, Warren PV, Lupas A, Stanhope MJ, Brown JR, Hoffman PS. Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis. J Bacteriol 2001; 183:1259-68. [PMID: 11157938 PMCID: PMC94999 DOI: 10.1128/jb.183.4.1259-1268.2001] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2000] [Accepted: 11/17/2000] [Indexed: 12/12/2022] Open
Abstract
A comparative genomic approach was used to identify Helicobacter pylori 26695 open reading frames (ORFs) which are conserved in H. pylori J99 but highly diverged in other eubacteria. A survey of selected pathways of central intermediary metabolism was also carried out, and genes with a potentially selective role in H. pylori were identified. Forty-five ORFs identified in these two analyses were screened using a rapid vector-free allelic replacement mutagenesis technique, and 33 were shown to be essential in vitro. Notably, 13 ORFs gave essentiality results which are unexpected in view of their known or proposed functions, and phylogenetic analysis was used to investigate the annotation of 7 such ORFs which are highly diverged. We propose that the products of a number of these H. pylori-specific essential genes may be suitable targets for novel anti-H. pylori therapies.
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Affiliation(s)
- A F Chalker
- Department of Anti-Infective Research, SmithKline Beecham Pharmaceuticals, Collegeville, Pennsylvania 19426, USA.
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