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Shi G, Shaw GX, Zhu F, Tarasov SG, Ji X. Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Transition state analogs for high affinity binding. Bioorg Med Chem 2021; 29:115847. [PMID: 33199204 PMCID: PMC7855645 DOI: 10.1016/j.bmc.2020.115847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/20/2020] [Accepted: 11/02/2020] [Indexed: 11/22/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate biosynthesis pathway. It catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). HPPK is essential for microorganisms but absent in mammals; therefore, it is an attractive target for developing novel antimicrobial agents. Previously, based on our studies of the structure and mechanism of HPPK, we created first-generation bisubstrate inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed second-generation inhibitors by replacing the phosphate bridge with a linkage that contains a piperidine moiety. Here, we report third-generation inhibitors designed based on the piperidine-containing inhibitor, mimicking the transition state. We synthesized two such inhibitors, characterized their protein-binding and enzyme inhibition properties, and determined their crystal structures in complex with HPPK, advancing the development of such bisubstrate analog inhibitors.
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Affiliation(s)
- Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary X Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Fengxia Zhu
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA; School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huaiyin, Jiangsu Province, China(1)
| | - Sergey G Tarasov
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA.
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2
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Yogavel M, Nettleship JE, Sharma A, Harlos K, Jamwal A, Chaturvedi R, Sharma M, Jain V, Chhibber-Goel J, Sharma A. Structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase-dihydropteroate synthase from Plasmodium vivax sheds light on drug resistance. J Biol Chem 2018; 293:14962-14972. [PMID: 30104413 DOI: 10.1074/jbc.ra118.004558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/08/2018] [Indexed: 11/06/2022] Open
Abstract
The genomes of the malaria-causing Plasmodium parasites encode a protein fused of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) domains that catalyze sequential reactions in the folate biosynthetic pathway. Whereas higher organisms derive folate from their diet and lack the enzymes for its synthesis, most eubacteria and a number of lower eukaryotes including malaria parasites synthesize tetrahydrofolate via DHPS. Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) HPPK-DHPSs are currently targets of drugs like sulfadoxine (SDX). The SDX effectiveness as an antimalarial drug is increasingly diminished by the rise and spread of drug-resistant mutations. Here, we present the crystal structure of PvHPPK-DHPS in complex with four substrates/analogs, revealing the bifunctional PvHPPK-DHPS architecture in an unprecedented state of enzymatic activation. SDX's effect on HPPK-DHPS is due to 4-amino benzoic acid (pABA) mimicry, and the PvHPPK-DHPS structure sheds light on the SDX-binding cavity, as well as on mutations that effect SDX potency. We mapped five dominant drug resistance mutations in PvHPPK-DHPS: S382A, A383G, K512E/D, A553G, and V585A, most of which occur individually or in clusters proximal to the pABA-binding site. We found that these resistance mutations subtly alter the intricate enzyme/pABA/SDX interactions such that DHPS affinity for pABA is diminished only moderately, but its affinity for SDX is changed substantially. In conclusion, the PvHPPK-DHPS structure rationalizes and unravels the structural bases for SDX resistance mutations and highlights architectural features in HPPK-DHPSs from malaria parasites that can form the basis for developing next-generation anti-folate agents to combat malaria parasites.
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Affiliation(s)
- Manickam Yogavel
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India,
| | - Joanne E Nettleship
- the Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, and.,the Oxford Protein Production Facility, United Kingdom Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, United Kingdom
| | - Akansha Sharma
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Karl Harlos
- the Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, and
| | - Abhishek Jamwal
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Rini Chaturvedi
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Manmohan Sharma
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Vitul Jain
- the Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, and
| | - Jyoti Chhibber-Goel
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Amit Sharma
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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3
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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4
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Jongkon N, Gleeson D, Gleeson MP. Elucidation of the catalytic mechanism of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase using QM/MM calculations. Org Biomol Chem 2018; 16:6239-6249. [DOI: 10.1039/c8ob01428k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This account describes the application of QM/MM calculations to understand the reaction mechanism of HPPK, an important pharmacological target on the folate pathway for the treatment of diseases including anti-microbial resistance, malaria and cancer.
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Affiliation(s)
- Nathjanan Jongkon
- Department of Social and Applied Science
- College of Industrial Technology
- King Mongkut's University of Technology North Bangkok
- Bangkok 10800
- Thailand
| | - Duangkamol Gleeson
- Department of Chemistry
- Faculty of Science
- King Mongkut's Institute of Technology Ladkrabang
- Thailand
| | - M. Paul Gleeson
- Department of Biomedical Engineering
- Faculty of Engineering
- King Mongkut's Institute of Technology Ladkrabang
- Bangkok 10520
- Thailand
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5
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Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Microbiol Mol Biol Rev 2016; 81:81/1/e00040-16. [PMID: 28031352 DOI: 10.1128/mmbr.00040-16] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
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6
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Gao K, Jia Y, Yang M. A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP. Biochemistry 2016; 55:6931-6939. [PMID: 27951655 DOI: 10.1021/acs.biochem.6b00720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that, in its binary form, even bound by analogues of MgATP, loops 2 and 3 remain rather flexible; this raises questions about the putative large-scale induced-fit conformational change of the HPPK-MgATP binary complex. In this work, long-time all-atomic molecular dynamics simulations were conducted to investigate the loop dynamics in this complex. Our simulations show that, with loop 3 closed, multiple conformations of loop 2, including the open, semiopen, and closed forms, are all accessible to the binary complex. These results provide valuable structural insights into the details of conformational changes upon 6-hydroxymethyl-7,8-dihydropterin (HP) binding and biological activities of HPPK. Conformational network analysis and principal component analysis related to the loops are also discussed.
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Affiliation(s)
- Kaifu Gao
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Ya Jia
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
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7
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Dennis ML, Pitcher NP, Lee MD, DeBono AJ, Wang ZC, Harjani JR, Rahmani R, Cleary B, Peat TS, Baell JB, Swarbrick JD. Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli. J Med Chem 2016; 59:5248-63. [PMID: 27094768 DOI: 10.1021/acs.jmedchem.6b00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a member of the folate biosynthesis pathway found in prokaryotes and lower eukaryotes that catalyzes the pyrophosphoryl transfer from the ATP cofactor to a 6-hydroxymethyl-7,8-dihydropterin substrate. We report the chemical synthesis of a series of S-functionalized 8-mercaptoguanine (8MG) analogues as substrate site inhibitors of HPPK and quantify binding against the E. coli and S. aureus enzymes (EcHPPK and SaHPPK). The results demonstrate that analogues incorporating acetophenone-based substituents have comparable affinities for both enzymes. Preferential binding of benzyl-substituted 8MG derivatives to SaHPPK was reconciled when a cryptic pocket unique to SaHPPK was revealed by X-ray crystallography. Differential chemical shift perturbation analysis confirmed this to be a common mode of binding for this series to SaHPPK. One compound (41) displayed binding affinities of 120 nM and 1.76 μM for SaHPPK and EcHPPK, respectively, and represents a lead for the development of more potent and selective inhibitors of SaHPPK.
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Affiliation(s)
- Matthew L Dennis
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.,CSIRO Biosciences Program , Parkville, Victoria 3052, Australia
| | - Noel P Pitcher
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Michael D Lee
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Aaron J DeBono
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Zhong-Chang Wang
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing 210093, People's Republic of China
| | - Jitendra R Harjani
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Raphaël Rahmani
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Ben Cleary
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO Biosciences Program , Parkville, Victoria 3052, Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - James D Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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8
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Gao K, He H, Yang M, Yan H. Molecular dynamics simulations of the Escherichia coli HPPK apo-enzyme reveal a network of conformational transitions. Biochemistry 2015; 54:6734-42. [PMID: 26492157 DOI: 10.1021/acs.biochem.5b01012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that even when confined by crystal contacts, loops 2 and 3 remain rather flexible when the enzyme is in its apo form, raising questions about the putative large-scale induced-fit conformational change of HPPK. To investigate the loop dynamics in a crystal-free environment, we performed conventional molecular dynamics simulations of the apo-enzyme at two different temperatures (300 and 350 K). Our simulations show that the crystallographic B-factors considerably underestimate the loop dynamics; multiple conformations of loops 2 and 3, including the open, semi-open, and closed conformations that an enzyme must adopt throughout its catalytic cycle, are all accessible to the apo-enzyme. These results revise our previous view of the functional mechanism of conformational change upon MgATP binding and offer valuable structural insights into the workings of HPPK. In this paper, conformational network analysis and principal component analysis related to the loops are discussed to support the presented conclusions.
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Affiliation(s)
- Kaifu Gao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Hongqing He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
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9
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Dennis ML, Chhabra S, Wang ZC, Debono A, Dolezal O, Newman J, Pitcher NP, Rahmani R, Cleary B, Barlow N, Hattarki M, Graham B, Peat TS, Baell JB, Swarbrick JD. Structure-based design and development of functionalized Mercaptoguanine derivatives as inhibitors of the folate biosynthesis pathway enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Staphylococcus aureus. J Med Chem 2014; 57:9612-26. [PMID: 25357262 DOI: 10.1021/jm501417f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), an enzyme from the folate biosynthesis pathway, catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin and is a yet-to-be-drugged antimicrobial target. Building on our previous discovery that 8-mercaptoguanine (8MG) is an inhibitor of Staphylococcus aureus HPPK (SaHPPK), we have identified and characterized the binding of an S8-functionalized derivative (3). X-ray structures of both the SaHPPK/3/cofactor analogue ternary and the SaHPPK/cofactor analogue binary complexes have provided insight into cofactor recognition and key residues that move over 30 Å upon binding of 3, whereas NMR measurements reveal a partially plastic ternary complex active site. Synthesis and binding analysis of a set of analogues of 3 have identified an advanced new lead compound (11) displaying >20-fold higher affinity for SaHPPK than 8MG. A number of these exhibited low micromolar affinity for dihydropteroate synthase (DHPS), the adjacent, downstream enzyme to HPPK, and may thus represent promising new leads to bienzyme inhibitors.
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Affiliation(s)
- Matthew L Dennis
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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10
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Shaw GX, Li Y, Shi G, Wu Y, Cherry S, Needle D, Zhang D, Tropea JE, Waugh DS, Yan H, Ji X. Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis. FEBS J 2014; 281:4123-37. [PMID: 24975935 PMCID: PMC5600157 DOI: 10.1111/febs.12896] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Two valid targets for antibiotic development, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS), catalyze consecutive reactions in folate biosynthesis. In Francisella tularensis (Ft), these two activities are contained in a single protein, FtHPPK-DHPS. Although Pemble et al. (PLoS One 5, e14165) determined the structure of FtHPPK-DHPS, they were unable to measure the kinetic parameters of the enzyme. In this study, we elucidated the binding and inhibitory activities of two HPPK inhibitors (HP-18 and HP-26) against FtHPPK-DHPS, determined the structure of FtHPPK-DHPS in complex with HP-26, and measured the kinetic parameters for the dual enzymatic activities of FtHPPK-DHPS. The biochemical analyses showed that HP-18 and HP-26 have significant isozyme selectivity, and that FtHPPK-DHPS is unique in that the catalytic efficiency of its DHPS activity is only 1/260,000 of that of Escherichia coli DHPS. Sequence and structural analyses suggest that HP-26 is an excellent lead for developing therapeutic agents for tularemia, and that the very low DHPS activity is due, at least in part, to the lack of a key residue that interacts with the substrate p-aminobenzoic acid (pABA). A BLAST search of the genomes of ten F. tularensis strains indicated that the bacterium contains a single FtHPPK-DHPS. The marginal DHPS activity and the single copy existence of FtHPPK-DHPS in F. tularensis make this bacterium more vulnerable to DHPS inhibitors. Current sulfa drugs are ineffective against tularemia; new inhibitors targeting the unique pABA-binding pocket may be effective and less subject to resistance because any mutations introducing resistance may make the marginal DHPS activity unable to support the growth of F. tularensis. DATABASE The coordinates and structure factors have been deposited in the Protein Data Bank under accession code 4PZV.
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Affiliation(s)
- Gary X. Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Scott Cherry
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Danielle Needle
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Di Zhang
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
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11
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Yun MK, Hoagland D, Kumar G, Waddell MB, Rock CO, Lee RE, White SW. The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Bioorg Med Chem 2014; 22:2157-65. [PMID: 24613625 DOI: 10.1016/j.bmc.2014.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 01/19/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is an essential enzyme in the microbial folate biosynthetic pathway. This pathway has proven to be an excellent target for antimicrobial development, but widespread resistance to common therapeutics including the sulfa drugs has stimulated interest in HPPK as an alternative target in the pathway. A screen of a pterin-biased compound set identified several HPPK inhibitors that contain an aryl substituted 8-thioguanine scaffold, and structural analyses showed that these compounds engage the HPPK pterin-binding pocket and an induced cryptic pocket. A preliminary structure activity relationship profile was developed from biophysical and biochemical characterizations of derivative molecules. Also, a similarity search identified additional scaffolds that bind more tightly within the HPPK pterin pocket. These inhibitory scaffolds have the potential for rapid elaboration into novel lead antimicrobial agents.
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Affiliation(s)
- Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Daniel Hoagland
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gyanendra Kumar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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12
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Utility of the Biosynthetic Folate Pathway for Targets in Antimicrobial Discovery. Antibiotics (Basel) 2014; 3:1-28. [PMID: 27025730 PMCID: PMC4790348 DOI: 10.3390/antibiotics3010001] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 01/07/2023] Open
Abstract
The need for new antimicrobials is great in face of a growing pool of resistant pathogenic organisms. This review will address the potential for antimicrobial therapy based on polypharmacological activities within the currently utilized bacterial biosynthetic folate pathway. The folate metabolic pathway leads to synthesis of required precursors for cellular function and contains a critical node, dihydrofolate reductase (DHFR), which is shared between prokaryotes and eukaryotes. The DHFR enzyme is currently targeted by methotrexate in anti-cancer therapies, by trimethoprim for antibacterial uses, and by pyrimethamine for anti-protozoal applications. An additional anti-folate target is dihyropteroate synthase (DHPS), which is unique to prokaryotes as they cannot acquire folate through dietary means. It has been demonstrated as a primary target for the longest standing antibiotic class, the sulfonamides, which act synergistically with DHFR inhibitors. Investigations have revealed most DHPS enzymes possess the ability to utilize sulfa drugs metabolically, producing alternate products that presumably inhibit downstream enzymes requiring the produced dihydropteroate. Recent work has established an off-target effect of sulfonamide antibiotics on a eukaryotic enzyme, sepiapterin reductase, causing alterations in neurotransmitter synthesis. Given that inhibitors of both DHFR and DHPS are designed to mimic their cognate substrate, which contain shared substructures, it is reasonable to expect such “off-target” effects. These inhibitors are also likely to interact with the enzymatic neighbors in the folate pathway that bind products of the DHFR or DHPS enzymes and/or substrates of similar substructure. Computational studies designed to assess polypharmacology reiterate these conclusions. This leads to hypotheses exploring the vast utility of multiple members of the folate pathway for modulating cellular metabolism, and includes an appealing capacity for prokaryotic-specific polypharmacology for antimicrobial applications.
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13
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14
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He Y, Lu M, Lu HP. Single-molecule photon stamping FRET spectroscopy study of enzymatic conformational dynamics. Phys Chem Chem Phys 2013; 15:770-5. [PMID: 23085845 PMCID: PMC3657739 DOI: 10.1039/c2cp42944f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescence resonant energy transfer (FRET) from a donor to an acceptor via transition dipole-dipole interactions decreases the donor's fluorescent lifetime. The donor's fluorescent lifetime decreases as the FRET efficiency increases, following the equation: E(FRET) = 1 - τ(DA)/τ(D), where τ(D) and τ(DA) are the donor fluorescence lifetime without FRET and with FRET. Accordingly, the FRET time trajectories associated with single-molecule conformational dynamics can be recorded by measuring the donor's lifetime fluctuations. In this article, we report our work on the use of a Cy3/Cy5-labeled enzyme, HPPK to demonstrate probing single-molecule conformational dynamics in an enzymatic reaction by measuring single-molecule FRET donor lifetime time trajectories. Compared with single-molecule fluorescence intensity-based FRET measurements, single-molecule lifetime-based FRET measurements are independent of fluorescence intensity. The latter has an advantage in terms of eliminating the analysis background noise from the acceptor fluorescence detection leak through noise, excitation light intensity noise, or light scattering noise due to local environmental factors, for example, in a AFM-tip correlated single-molecule FRET measurements. Furthermore, lifetime-based FRET also supports simultaneous single-molecule fluorescence anisotropy.
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Affiliation(s)
- Yufan He
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA.
| | - Maolin Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA.
| | - H. Peter Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA.
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Shi G, Shaw G, Li Y, Wu Y, Yan H, Ji X. Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: new lead exhibits a distinct binding mode. Bioorg Med Chem 2012; 20:4303-9. [PMID: 22727779 PMCID: PMC3389233 DOI: 10.1016/j.bmc.2012.05.060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 05/16/2012] [Accepted: 05/24/2012] [Indexed: 11/22/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), a key enzyme in the folate biosynthesis pathway catalyzing the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin, is an attractive target for developing novel antimicrobial agents. Previously, we studied the mechanism of HPPK action, synthesized bisubstrate analog inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed a new generation of bisubstrate inhibitors by replacing the phosphate bridge with a piperidine-containing linkage. To further improve linker properties, we have synthesized a new compound, characterized its protein binding/inhibiting properties, and determined its structure in complex with HPPK. Surprisingly, this inhibitor exhibits a new binding mode in that the adenine base is flipped when compared to previously reported structures. Furthermore, the side chain of amino acid residue E77 is involved in protein-inhibitor interaction, forming hydrogen bonds with both 2' and 3' hydroxyl groups of the ribose moiety. Residue E77 is conserved among HPPK sequences, but interacts only indirectly with the bound MgATP via water molecules. Never observed before, the E77-ribose interaction is compatible only with the new inhibitor-binding mode. Therefore, this compound represents a new direction for further development.
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Affiliation(s)
- Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Gary Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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16
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Chhabra S, Dolezal O, Collins BM, Newman J, Simpson JS, Macreadie IG, Fernley R, Peat TS, Swarbrick JD. Structure of S. aureus HPPK and the discovery of a new substrate site inhibitor. PLoS One 2012; 7:e29444. [PMID: 22276115 PMCID: PMC3261883 DOI: 10.1371/journal.pone.0029444] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/28/2011] [Indexed: 12/17/2022] Open
Abstract
The first structural and biophysical data on the folate biosynthesis pathway enzyme and drug target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (SaHPPK), from the pathogen Staphylococcus aureus is presented. HPPK is the second essential enzyme in the pathway catalysing the pyrophosphoryl transfer from cofactor (ATP) to the substrate (6-hydroxymethyl-7,8-dihydropterin, HMDP). In-silico screening identified 8-mercaptoguanine which was shown to bind with an equilibrium dissociation constant, Kd, of ∼13 µM as measured by isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR). An IC50 of ∼41 µM was determined by means of a luminescent kinase assay. In contrast to the biological substrate, the inhibitor has no requirement for magnesium or the ATP cofactor for competitive binding to the substrate site. The 1.65 Å resolution crystal structure of the inhibited complex showed that it binds in the pterin site and shares many of the key intermolecular interactions of the substrate. Chemical shift and 15N heteronuclear NMR measurements reveal that the fast motion of the pterin-binding loop (L2) is partially dampened in the SaHPPK/HMDP/α,β-methylene adenosine 5′-triphosphate (AMPCPP) ternary complex, but the ATP loop (L3) remains mobile on the µs-ms timescale. In contrast, for the SaHPPK/8-mercaptoguanine/AMPCPP ternary complex, the loop L2 becomes rigid on the fast timescale and the L3 loop also becomes more ordered – an observation that correlates with the large entropic penalty associated with inhibitor binding as revealed by ITC. NMR data, including 15N-1H residual dipolar coupling measurements, indicate that the sulfur atom in the inhibitor is important for stabilizing and restricting important motions of the L2 and L3 catalytic loops in the inhibited ternary complex. This work describes a comprehensive analysis of a new HPPK inhibitor, and may provide a foundation for the development of novel antimicrobials targeting the folate biosynthetic pathway.
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Affiliation(s)
- Sandeep Chhabra
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Olan Dolezal
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Australia
| | - Janet Newman
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Jamie S. Simpson
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ian G. Macreadie
- School of Applied Sciences, RMIT University, Bundoora, Australia
| | - Ross Fernley
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - Thomas S. Peat
- CSIRO Division of Materials, Science and Engineering, Parkville, Australia
| | - James D. Swarbrick
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- * E-mail:
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17
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Shi G, Shaw G, Liang YH, Subburaman P, Li Y, Wu Y, Yan H, Ji X. Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties. Bioorg Med Chem 2012; 20:47-57. [PMID: 22169600 PMCID: PMC3257516 DOI: 10.1016/j.bmc.2011.11.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/08/2011] [Accepted: 11/16/2011] [Indexed: 11/20/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), a key enzyme in the folate biosynthetic pathway, catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin. The enzyme is essential for microorganisms, is absent from humans, and is not the target for any existing antibiotics. Therefore, HPPK is an attractive target for developing novel antimicrobial agents. Previously, we characterized the reaction trajectory of HPPK-catalyzed pyrophosphoryl transfer and synthesized a series of bisubstrate analog inhibitors of the enzyme by linking 6-hydroxymethylpterin to adenosine through 2, 3, or 4 phosphate groups. Here, we report a new generation of bisubstrate analog inhibitors. To improve protein binding and linker properties of such inhibitors, we have replaced the pterin moiety with 7,7-dimethyl-7,8-dihydropterin and the phosphate bridge with a piperidine linked thioether. We have synthesized the new inhibitors, measured their K(d) and IC(50) values, determined their crystal structures in complex with HPPK, and established their structure-activity relationship. 6-Carboxylic acid ethyl ester-7,7-dimethyl-7,8-dihydropterin, a novel intermediate that we developed recently for easy derivatization at position 6 of 7,7-dimethyl-7,8-dihydropterin, offers a much high yield for the synthesis of bisubstrate analogs than that of previously established procedure.
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Affiliation(s)
- Genbin Shi
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Gary Shaw
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yu-He Liang
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Priadarsini Subburaman
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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18
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Shi G, Ji X. New ways to derivatize at position 6 of 7,7-dimethyl-7,8-dihydropterin. Tetrahedron Lett 2011; 52:6174-6176. [DOI: 10.1016/j.tetlet.2011.09.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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He Y, Li Y, Mukherjee S, Wu Y, Yan H, Lu HP. Probing single-molecule enzyme active-site conformational state intermittent coherence. J Am Chem Soc 2011; 133:14389-95. [PMID: 21823644 PMCID: PMC3198842 DOI: 10.1021/ja204644y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule fluorescence resonance energy transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single-molecule intensity-time trajectories of enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multistep conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. The coherence frequency, identified by statistical results of the correlation function analysis from single-molecule FRET trajectories, increases with the increasing substrate concentrations. The intermittent coherence in conformational state changes at the enzymatic reaction active site is likely to be common and exist in other conformation regulated enzymatic reactions. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.
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Affiliation(s)
- Yufan He
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Saptarshi Mukherjee
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - H. Peter Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403
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20
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Yan H, Ji X. Role of protein conformational dynamics in the catalysis by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Protein Pept Lett 2011; 18:328-35. [PMID: 21222642 DOI: 10.2174/092986611794654003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 12/15/2010] [Indexed: 11/22/2022]
Abstract
Enzymatic catalysis has conflicting structural requirements of the enzyme. In order for the enzyme to form a Michaelis complex, the enzyme must be in an open conformation so that the substrate can get into its active center. On the other hand, in order to maximize the stabilization of the transition state of the enzymatic reaction, the enzyme must be in a closed conformation to maximize its interactions with the transition state. The conflicting structural requirements can be resolved by a flexible active center that can sample both open and closed conformational states. For a bisubstrate enzyme, the Michaelis complex consists of two substrates in addition to the enzyme. The enzyme must remain flexible upon the binding of the first substrate so that the second substrate can get into the active center. The active center is fully assembled and stabilized only when both substrates bind to the enzyme. However, the side-chain positions of the catalytic residues in the Michaelis complex are still not optimally aligned for the stabilization of the transition state, which lasts only approximately 10(-13) s. The instantaneous and optimal alignment of catalytic groups for the transition state stabilization requires a dynamic enzyme, not an enzyme which undergoes a large scale of movements but an enzyme which permits at least a small scale of adjustment of catalytic group positions. This review will summarize the structure, catalytic mechanism, and dynamic properties of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase and examine the role of protein conformational dynamics in the catalysis of a bisubstrate enzymatic reaction.
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Affiliation(s)
- Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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21
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Chhabra S, Newman J, Peat TS, Fernley RT, Caine J, Simpson JS, Swarbrick JD. Crystallization and preliminary X-ray analysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:575-8. [PMID: 20445263 PMCID: PMC2864696 DOI: 10.1107/s1744309110010857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 03/23/2010] [Indexed: 11/10/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the Mg(2+)-dependent transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HMDP), forming 6-hydroxymethyl-7,8-dihydropterin pyrophosphate, which is a critical step in the de novo folic acid-biosynthesis pathway. Diffraction-quality crystals of HPPK from the medically relevant species Staphylococcus aureus were grown in the presence of ammonium sulfate or sodium malonate and diffracted to better than 1.65 A resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 36.8, b = 76.6, c = 51.5 A, alpha = gamma = 90.0, beta = 100.2 degrees . The crystals contained two molecules per asymmetric unit, with a volume per protein weight (V(M)) of 2.04 A(3) Da(-1) and an estimated solvent content of 39.6%.
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Affiliation(s)
- Sandeep Chhabra
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Janet Newman
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thomas S. Peat
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Ross T. Fernley
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Joanne Caine
- CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Jamie S. Simpson
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - James D. Swarbrick
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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22
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Su L, Cukier RI. Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK. J Phys Chem B 2010; 113:16197-208. [PMID: 19924845 DOI: 10.1021/jp903861a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) catalyzes the transfer of pyrophosphate from ATP to HP (6-hydroxymethyl-7,8-dihydropterin). This first reaction in the folate biosynthetic pathway is a potential target for antimicrobial agents. A Hamiltonian replica exchange method (HREM) molecular dynamics (MD) approach is used, with the goal of improving conformational sampling, whereby multiple copies of the system are run without requiring a large number of system copies. For HPPK, the aim is to improve conformational sampling around the HP binding pocket and thereby find near-closed conformations (similar but not identical to the binding pocket of HP, as defined by the ternary crystal structure). Near-closed conformations may be better targets for the design of species-selective inhibitors. Well-populated, near-closed conformations of Escherichia coli HPPK (EcHPPK) and Yersinia pestis HPPK (YpHPPK) were found with HREM by focusing on the interactions involving loops 2 and 3 that are known to be the more flexible regions of HPPK. A small number of systems were found to be sufficient to enlarge the sample space substantially, on the basis of root-mean-square fluctuation measures, relative to the results of a conventional MD simulation. By clustering snapshots on the basis of some of the key residues that form the HP binding pocket, distinct HREM-generated conformations are found. Residue displacements mainly from loop 2 are responsible for the distinct conformers found, relative to the crystal structure, for both EcHPPK and YpHPPK. In contrast, the conventional MD simulations of EcHPPK and YpHPPK each lead essentially to one cluster, with use of the same clustering criterion as for the HREM. The shapes of the HREM near-closed binding pockets are qualitatively investigated and found to be different. Some of these conformations are distinguishable between EcHPPK and YpHPPK, indicating that there may be differing species-selective, near-closed conformations suited to HP binding.
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Affiliation(s)
- Li Su
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, USA
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23
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Lescop E, Lu Z, Liu Q, Xu H, Li G, Xia B, Yan H, Jin C. Dynamics of the conformational transitions in the assembling of the Michaelis complex of a bisubstrate enzyme: a (15)N relaxation study of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry 2009; 48:302-12. [PMID: 19108643 DOI: 10.1021/bi8016262] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), which follows an ordered bi-bi kinetic mechanism with ATP binding to the enzyme first. HPPK undergoes dramatic conformational changes during its catalytic cycle as revealed by X-ray crystallography, and the conformational changes are essential for the enzymatic catalysis as shown by site-directed mutagenesis and biochemical and crystallographic analysis of the mutants. However, the dynamic properties of the enzyme have not been measured experimentally. Here, we report a (15)N NMR relaxation study of the dynamic properties of Escherichia coli HPPK from the apo form to the binary substrate complex with MgATP (represented by MgAMPCPP, an ATP analogue) to the Michaelis complex (ternary substrate complex) with MgATP (represented by MgAMPCPP) and HP (represented by 7,7-dimethyl-6-hydroxypterin, an HP analogue). The results show that the binding of the nucleotide to HPPK does not cause major changes in the dynamic properties of the enzyme. Whereas enzymes are often more rigid when bound to the ligand or the substrate, the internal mobility of HPPK is not reduced and is even moderately increased in the binary complex, particularly in the catalytic loops. The internal mobility of the catalytic loops is significantly quenched upon the formation of the ternary complex, but some mobility remains. The enhanced motions in the catalytic loops of the binary substrate complex may be required for the assembling of the ternary complex. On the other hand, some degrees of mobility in the catalytic loops of the ternary complex may be required for the optimal stabilization of the transition state, which may need the instantaneous adjustment and alignment of the side-chain positions of catalytic residues. Such dynamic behaviors may be characteristic of bisubstrate enzymes.
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Affiliation(s)
- Ewen Lescop
- Beijing NMR Center, College of Life Sciences, Peking University, Beijing 100871, China
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24
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Chapter 15 The Structure and Mechanism of 6‐Hydroxymethyl‐7,8‐Dihydropterin Pyrophosphokinase. VITAMINS AND HORMONES 2008. [DOI: 10.1016/s0083-6729(08)00415-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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25
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Lawrence MC, Iliades P, Fernley RT, Berglez J, Pilling PA, Macreadie IG. The three-dimensional structure of the bifunctional 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase/dihydropteroate synthase of Saccharomyces cerevisiae. J Mol Biol 2005; 348:655-70. [PMID: 15826662 DOI: 10.1016/j.jmb.2005.03.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/03/2005] [Accepted: 03/04/2005] [Indexed: 11/16/2022]
Abstract
In Saccharomyces cerevisiae and other fungi, the enzymes dihydroneopterin aldolase, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) are encoded by a polycistronic gene that is translated into a single polypeptide having all three functions. These enzymatic functions are essential to both prokaryotes and lower eukaryotes, and catalyse sequential reactions in folate biosynthesis. Deletion or disruption of either function leads to cell death. These enzymes are absent from mammals and thus make ideal antimicrobial targets. DHPS is currently the target of antifolate therapy for a number of infectious diseases, and its activity is inhibited by sulfonamides and sulfones. These drugs are typically used as part of a synergistic cocktail with the 2,4-diaminopyrimidines that inhibit dihydrofolate reductase. A gene encoding the S.cerevisiae HPPK and DHPS enzymes has been cloned and expressed in Escherichia coli. A complex of the purified bifunctional polypeptide with a pterin monophosphate substrate analogue has been crystallized, and its structure solved by molecular replacement and refined to 2.3A resolution. The polypeptide consists of two structural domains, each of which closely resembles its respective monofunctional bacterial HPPK and DHPS counterpart. The mode of ligand binding is similar to that observed in the bacterial enzymes. The association between the domains within the polypeptide as well as the quaternary association of the polypeptide via its constituent DHPS domains provide insight into the assembly of the trifunctional enzyme in S.cerevisiae and probably other fungal species.
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Affiliation(s)
- Michael C Lawrence
- CSIRO Health Sciences and Nutrition, 343 Royal Parade, Parkville, Victoria 3052, Australia.
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26
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Affiliation(s)
- Ivan M Kompis
- ARPIDA Ltd, Dammstrasse 36, 4142 Münchenstein, Switzerland
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27
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Yang R, Lee MC, Yan H, Duan Y. Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP. Biophys J 2005; 89:95-106. [PMID: 15821168 PMCID: PMC1366583 DOI: 10.1529/biophysj.105.061556] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK.MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design.
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Affiliation(s)
- Rong Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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