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Halogenated Pyrrolopyrimidines with Low MIC on Staphylococcus aureus and Synergistic Effects with an Antimicrobial Peptide. Antibiotics (Basel) 2022; 11:antibiotics11080984. [PMID: 35892374 PMCID: PMC9330635 DOI: 10.3390/antibiotics11080984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Currently, there is a world-wide rise in antibiotic resistance causing burdens to individuals and public healthcare systems. At the same time drug development is lagging behind. Therefore, finding new ways of treating bacterial infections either by identifying new agents or combinations of drugs is of utmost importance. Additionally, if combination therapy is based on agents with different modes of action, resistance is less likely to develop. The synthesis of 21 fused pyrimidines and a structure-activity relationship study identified two 6-aryl-7H-pyrrolo [2,3-d] pyrimidin-4-amines with potent activity towards Staphylococcus aureus. The MIC-value was found to be highly dependent on a bromo or iodo substitution in the 4-benzylamine group and a hydroxyl in the meta or para position of the 6-aryl unit. The most active bromo and iodo derivatives had MIC of 8 mg/L. Interestingly, the most potent compounds experienced a four-fold lower MIC-value when they were combined with the antimicrobial peptide betatide giving MIC of 1–2 mg/L. The front runner bromo derivative also has a low activity towards 50 human kinases, including thymidylate monophosphate kinase, a putative antibacterial target.
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2
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Reed JM, Gardner SG, Mishra NN, Bayer AS, Somerville GA. Metabolic interventions for the prevention and treatment of daptomycin non-susceptibility in Staphylococcus aureus. J Antimicrob Chemother 2020; 74:2274-2283. [PMID: 31074482 DOI: 10.1093/jac/dkz194] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/03/2019] [Accepted: 04/07/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A major developing problem in the treatment of Staphylococcus aureus infections is the emergence of resistance during treatment with daptomycin. Previous metabolomic analyses of isogenic S. aureus strains prior to and after evolution into a daptomycin non-susceptible (DapNS) state provided important metabolic information about this transition (e.g. perturbations of the tricarboxylic acid cycle). OBJECTIVES To assess the significance of these metabolic changes, in vitro susceptibility to daptomycin was determined in daptomycin-susceptible (DapS) and DapNSS. aureus strains cultivated with metabolic inhibitors targeting these changes. METHODS Only inhibitors that are approved for use in humans were chosen (i.e. fosfomycin, valproate, trimetazidine and 6-mercaptopurine) to assess the importance of metabolic pathways for daptomycin non-susceptibility. The ability of these inhibitors to forestall the emergence of DapNS strains was also assessed. RESULTS The combination of daptomycin and fosfomycin synergistically killed both DapS and DapNS strains in vitro and enhanced the in vivo outcome against a DapNS strain in experimental endocarditis. Interestingly, fosfomycin acts on the peptidoglycan biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA); however, it also had a significant effect on the enzymatic activity of enolase, an essential enzyme in S. aureus. While fosfomycin acted synergistically with daptomycin, it failed to prevent the in vitro evolution of daptomycin non-susceptibility. In contrast, trimetazidine, an anti-angina drug that stimulates glucose oxidation, abolished the ability of DapSS. aureus strains to transition to a DapNS state. CONCLUSIONS These data reveal that metabolic adaptations associated with DapNS strains can be targeted to prevent the emergence of and/or reverse pre-existing resistance to daptomycin.
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Affiliation(s)
- Joseph M Reed
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905, USA
| | - Stewart G Gardner
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905, USA
| | - Nagendra N Mishra
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.,Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.,Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0905, USA
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3
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Chaudhary SK, Iyyappan Y, Elayappan M, Jeyakanthan J, Sekar K. Insights into product release dynamics through structural analyses of thymidylate kinase. Int J Biol Macromol 2018; 123:637-647. [PMID: 30447376 DOI: 10.1016/j.ijbiomac.2018.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 01/06/2023]
Abstract
Several studies on enzyme catalysis have pointed out that the product release event could be a rate limiting step. In this study, we have compared the release event of two products, Adenosine di-phosphate (ADP) and Thymidine di-phosphate (TDP) from the active-site of human and Thermus thermophilus thymidine mono-phosphate kinase (TMPK), referred to as hTMPK and ttTMPK, respectively. TMPK catalyses the conversion of Thymidine mono-phosphate (TMP) to TDP using ATP as phosphoryl donor in the presence of Mg2+ ion. Most of the earlier studies on this enzyme have focused on understanding substrate binding and catalysis, but the critical product release event remains elusive. Competitive binding experiments of the substrates and the products using ttTMPK apo crystals have indicated that the substrate (TMP) can replace the bound product (TDP), even in the presence of an ADP molecule. Further, the existing random accelerated molecular dynamics (RAMD) simulation program was modified to study the release of both the products simultaneously from the active site. The RAMD simulations on product-bound structures of both ttTMPK and hTMPK, revealed that while several exit patterns of the products are permissible, the sequential exit mode is the most preferred pattern for both ttTMPK and hTMPK enzymes. Additionally, the product release from the hTMPK was found to be faster and more directional as compared to ttTMPK. Structural investigation revealed that the critical changes in the residue composition in the LID-region of ttTMPK and hTMPK have an effect on the product release and can be attributed to the observed differences during product release event. Understanding of these dissimilarities is of considerable utility in designing potent inhibitors or prodrugs that can distinguish between eukaryotic and prokaryotic homologues of thymidylate kinase.
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Affiliation(s)
| | - Yuvaraj Iyyappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Mohanapriya Elayappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India
| | | | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.
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4
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Chaudhary SK, Jeyakanthan J, Sekar K. Structural and functional roles of dynamically correlated residues in thymidylate kinase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:341-354. [PMID: 29652261 DOI: 10.1107/s2059798318002267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/07/2018] [Indexed: 11/10/2022]
Abstract
Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg2+. In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP-TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism.
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Affiliation(s)
| | | | - Kanagaraj Sekar
- Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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5
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Insights into the structure-function relationship of Brugia malayi thymidylate kinase (BmTMK). Int J Biol Macromol 2016; 88:565-71. [PMID: 27044348 DOI: 10.1016/j.ijbiomac.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 11/23/2022]
Abstract
Lymphatic filariasis is a debilitating disease caused by lymph dwelling nematodal parasites like Wuchereria bancrofti, Brugia malayi and Brugia timori. Thymidylate kinase of B. malayi is a key enzyme in the de novo and salvage pathways for thymidine 5'-triphosphate (dTTP) synthesis. Therefore, B. malayi thymidylate kinase (BmTMK) is an essential enzyme for DNA biosynthesis and an important drug target to rein in filariasis. In the present study, the structural and functional changes associated with recombinant BmTMK, in the presence of protein denaturant GdnHCl, urea and pH were studied. GdnHCl and urea induced unfolding of BmTMK is non-cooperative and influence the functional property of the enzyme much lower than their Cm values. The study delineate that BmTMK is more prone to ionic perturbation. The dimeric assembly of BmTMK is an absolute requirement for enzymatic acitivity and any subtle change in dimeric conformation due to denaturation leads to loss of enzymatic activity. The pH induced changes on structure and activity suggests that selective modification of active site microenvironment pertains to difference in activity profile. This study also envisages that chemical moieties which acts by modulating oligomeric assembly, could be used for better designing of inhibitors against BmTMK enzyme.
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6
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Russell JH, Ostermeier M. The thymidylate kinase genes from Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus confer 3'-azido-3'-deoxythymidine resistance to Escherichia coli. FEMS Microbiol Lett 2014; 361:158-65. [PMID: 25310917 DOI: 10.1111/1574-6968.12627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 11/27/2022] Open
Abstract
The case number of invasive multidrug-resistant bacteria cultured from both hospital and community acquired infections is increasing at an alarming rate. Identifying the mechanisms bacteria use to escape the current antimicrobial treatments is essential to containing potential outbreaks and developing new antimicrobial therapies. Many bacteria naturally encode nonessential resistance genes on their chromosome enabling their survival and/or persistence in the presence of antibiotics using enzymes and efflux pumps. This study investigates the ability of an evolutionarily conserved essential gene to provide resistance against antimicrobial compounds. An Escherichia coli chromosomally encoded thymidylate kinase (tmk) conditional lethal strain was developed to investigate tmk alleles from relevant nosocomial pathogens. The thymidylate kinase conditional lethal strain harboring a plasmid with a tmk gene from Mycobacterium tuberculosis, methicillin-resistant Staphylococcus aureus (MRSA), or Pseudomonas aeruginosa downstream of an inducible promoter was examined for survival against increasing concentrations of 3'-azido-3'-deoxythymidine (AZT). The results indicate that M. tuberculosis and MRSA thymidylate kinases are deficient in cellular activity toward AZT monophosphate.
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Affiliation(s)
- Jay H Russell
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
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7
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Doharey PK, Suthar MK, Verma A, Kumar V, Yadav S, Balaramnavar VM, Rathaur S, Saxena AK, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Brugia malayi thymidylate kinase. Acta Trop 2014; 133:83-92. [PMID: 24556140 DOI: 10.1016/j.actatropica.2014.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 02/03/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of deoxythymidine triphosphate, which is an essential component for DNA synthesis. The gene encoding thymidylate kinase of Brugia malayi was amplified by PCR and expressed in Escherichia coli. The native molecular weight of recombinant B. malayi thymidylate kinase (rBmTMK) was estimated to be ∼52kDa by gel filtration chromatography, suggesting a homodimeric structure. rBmTMK activity required divalent cation and Mg(2+) was found to be the most effective cation. The enzyme was sensitive to pH and temperature, it showed maximum activity at pH 7.4 and 37°C. The Km values for dTMP and ATP were 17 and 66μM, respectively. The turnover number kcat was found to be 38.09s(-1), a value indicating the higher catalytic efficiency of the filarial enzyme. The nucleoside analogues 5-bromo-2'-deoxyuridine (5-BrdU), 5-chloro-2'-deoxyuridine (5-CldU) and 3'-azido-3'-deoxythymidine (AZT) showed specific inhibitory effect on the enzyme activity and these effects were in good association with binding interactions and the scoring functions as compared to human TMK. Differences in kinetic properties and structural differences in the substrate binding site of BmTMK model with respect to human TMK can serve as basis for designing specific inhibitors against parasitic enzyme.
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8
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Kotaiah Y, Nagaraju K, Harikrishna N, Venkata Rao C, Yamini L, Vijjulatha M. Synthesis, docking and evaluation of antioxidant and antimicrobial activities of novel 1,2,4-triazolo[3,4-b][1,3,4]thiadiazol-6-yl)selenopheno[2,3-d]pyrimidines. Eur J Med Chem 2014; 75:195-202. [DOI: 10.1016/j.ejmech.2014.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 01/02/2014] [Accepted: 01/03/2014] [Indexed: 11/29/2022]
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9
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Mikoulinskaia GV, Taran SA, Skoblov YS, Feofanov SA. The study of the bacteriophage T5 deoxynucleoside monophosphate kinase active site by site-directed mutagenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013. [DOI: 10.1134/s1068162013060071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Keating TA, Newman JV, Olivier NB, Otterson LG, Andrews B, Boriack-Sjodin PA, Breen JN, Doig P, Dumas J, Gangl E, Green OM, Guler SY, Hentemann MF, Joseph-McCarthy D, Kawatkar S, Kutschke A, Loch JT, McKenzie AR, Pradeepan S, Prasad S, Martínez-Botella G. In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound. ACS Chem Biol 2012; 7:1866-72. [PMID: 22908966 DOI: 10.1021/cb300316n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is an urgent need for new antibacterials that pinpoint novel targets and thereby avoid existing resistance mechanisms. We have created novel synthetic antibacterials through structure-based drug design that specifically target bacterial thymidylate kinase (TMK), a nucleotide kinase essential in the DNA synthesis pathway. A high-resolution structure shows compound TK-666 binding partly in the thymidine monophosphate substrate site, but also forming new induced-fit interactions that give picomolar affinity. TK-666 has potent, broad-spectrum Gram-positive microbiological activity (including activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus), bactericidal action with rapid killing kinetics, excellent target selectivity over the human ortholog, and low resistance rates. We demonstrate in vivo efficacy against S. aureus in a murine infected-thigh model. This work presents the first validation of TMK as a compelling antibacterial target and provides a rationale for pursuing novel clinical candidates for treating Gram-positive infections through TMK.
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Affiliation(s)
- Thomas A. Keating
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Joseph V. Newman
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nelson B. Olivier
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Linda G. Otterson
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Beth Andrews
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - P. Ann Boriack-Sjodin
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - John N. Breen
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Peter Doig
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Jacques Dumas
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Eric Gangl
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Oluyinka M. Green
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Satenig Y. Guler
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Martin F. Hentemann
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Diane Joseph-McCarthy
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Sameer Kawatkar
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Amy Kutschke
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - James T. Loch
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Andrew R. McKenzie
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Selvi Pradeepan
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Swati Prasad
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Gabriel Martínez-Botella
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
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11
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Martínez-Botella G, Breen JN, Duffy JES, Dumas J, Geng B, Gowers IK, Green OM, Guler S, Hentemann MF, Hernandez-Juan FA, Joseph-McCarthy D, Kawatkar S, Larsen NA, Lazari O, Loch JT, Macritchie JA, McKenzie AR, Newman JV, Olivier NB, Otterson LG, Owens AP, Read J, Sheppard DW, Keating TA. Discovery of Selective and Potent Inhibitors of Gram-Positive Bacterial Thymidylate Kinase (TMK). J Med Chem 2012; 55:10010-21. [DOI: 10.1021/jm3011806] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Martínez-Botella
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - John N. Breen
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Jacques Dumas
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Bolin Geng
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Ian K. Gowers
- BioFocus, Chesterford Research Park, Saffron Walden
CB10 1XL, U.K
| | - Oluyinka M. Green
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Satenig Guler
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Martin F. Hentemann
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Diane Joseph-McCarthy
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Sameer Kawatkar
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nicholas A. Larsen
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Ovadia Lazari
- BioFocus, Chesterford Research Park, Saffron Walden
CB10 1XL, U.K
| | - James T. Loch
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Andrew R. McKenzie
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Joseph V. Newman
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nelson B. Olivier
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Linda G. Otterson
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Andrew P. Owens
- BioFocus, Chesterford Research Park, Saffron Walden
CB10 1XL, U.K
| | - Jon Read
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Thomas A. Keating
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
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12
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Carbocyclic thymidine derivatives efficiently inhibit Plasmodium falciparum thymidylate kinase (PfTMK). Parasitol Int 2012; 61:501-3. [PMID: 22425904 DOI: 10.1016/j.parint.2012.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/02/2012] [Accepted: 03/02/2012] [Indexed: 11/20/2022]
Abstract
During the course of our research into new anti-malaria drugs, Plasmodium falciparum thymidylate kinase (PfTMK) has emerged as an important drug target because of its unique substrate specificity. Compared with human thymidylate kinase (HsTMK), PfTMK shows broader substrate specificity, which includes both purine and pyrimidine nucleotides. PfTMK accepts both 2'-deoxyguanosine monophosphate (dGMP) and thymidine monosphosphate (TMP) as substrates. We have evaluated the inhibitory activity of seven carbocyclic thymidine analogs and report the first structure-activity relationship for these inhibitors against PfTMK. The 2',3' dideoxycarbocyclic derivative of thymidine showed the most potent inhibition of the enzyme. The K(i)(dTMP) and K(i)(dGMP) values were 20 and 7 μM respectively. Thus, further modifications of carbocyclic thymidine analogs represent a good strategy for developing more powerful thymidylate kinase inhibitors.
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13
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Choi JY, Plummer MS, Starr J, Desbonnet CR, Soutter H, Chang J, Miller JR, Dillman K, Miller AA, Roush WR. Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation. J Med Chem 2012; 55:852-70. [PMID: 22243413 DOI: 10.1021/jm201349f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of an essential component, thymidine triphosphate, in DNA replication. All reported TMK inhibitors are thymidine analogues, which might retard their development as potent therapeutics due to cell permeability and off-target activity against human TMK. A small molecule hit (1, IC(50) = 58 μM), which has reasonable inhibition potency against Pseudomonas aeruginosa TMK (PaTMK), was identified by the analysis of the binding mode of thymidine or TP(5)A in a PaTMK homology model. This hit (1) was cocrystallized with PaTMK, and several potent PaTMK inhibitors (leads, 46, 47, 48, and 56, IC(50) = 100-200 nM) were synthesized using computer-aided design approaches including virtual synthesis/screening, which was used to guide the design of inhibitors. The binding mode of the optimized leads in PaTMK overlaps with that of other bacterial TMKs but not with human TMK, which shares few common features with the bacterial enzymes. Therefore, the optimized TMK inhibitors described here should be useful for the development of antibacterial agents targeting TMK without undesired off-target effects. In addition, an inhibition mechanism associated with the LID loop, which mimics the process of phosphate transfer from ATP to dTMP, was proposed based on X-ray cocrystal structures, homology models, and structure-activity relationship results.
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Affiliation(s)
- Jun Yong Choi
- Department of Chemistry, Scripps Florida, Jupiter, Florida 33458, United States
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14
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Structural basis for the efficient phosphorylation of AZT-MP (3'-azido-3'-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase. Biochem J 2010; 428:499-509. [PMID: 20353400 DOI: 10.1042/bj20091880] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plasmodium falciparum is the causative agent of malaria, a disease where new drug targets are required due to increasing resistance to current anti-malarials. TMPK (thymidylate kinase) is a good candidate as it is essential for the synthesis of dTTP, a critical precursor of DNA and has been much studied due to its role in prodrug activation and as a drug target. Type I TMPKs, such as the human enzyme, phosphorylate the substrate AZT (3'-azido-3'-deoxythymidine)-MP (monophosphate) inefficiently compared with type II TMPKs (e.g. Escherichia coli TMPK). In the present paper we report that eukaryotic PfTMPK (P. falciparum TMPK) presents sequence features of a type I enzyme yet the kinetic parameters for AZT-MP phosphorylation are similar to those of the highly efficient E. coli enzyme. Structural information shows that this is explained by a different juxtaposition of the P-loop and the azide of AZT-MP. Subsequent formation of the transition state requires no further movement of the PfTMPK P-loop, with no steric conflicts for the azide moiety, allowing efficient phosphate transfer. Likewise, we present results that confirm the ability of the enzyme to uniquely accept dGMP as a substrate and shed light on the basis for its wider substrate specificity. Information resulting from two ternary complexes (dTMP-ADP and AZT-MP-ADP) and a binary complex with the transition state analogue AP5dT [P1-(5'-adenosyl)-P5-(5'-thymidyl) pentaphosphate] all reveal significant differences with the human enzyme, notably in the lid region and in the P-loop which may be exploited in the rational design of Plasmodium-specific TMPK inhibitors with therapeutic potential.
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Lulli G, Messina E, Archetti F, Lanzeni S. A Mathematical Model for Optimal Functional Disruption of Biochemical Networks. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s10852-009-9118-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Mutational, inhibitory and microcalorimetric analyses of Plasmodium falciparum TMP kinase. Implications for drug discovery. Parasitology 2009; 136:11-25. [PMID: 19126267 DOI: 10.1017/s0031182008005301] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) can tolerate a range of substrates, which distinguishes it from other thymidylate kinases. The enzyme not only phosphorylates TMP and dUMP but can also tolerate bulkier purines, namely, dGMP, GMP, and dIMP. In order to probe the flexibility of PfTMK in accommodating ligands of various sizes, we developed 6 mutant enzymes and subjected these to thermodynamic, inhibitory and catalytic evaluation. Kinase activity was markedly affected by introducing a larger lysine residue instead of A111. The lack of the hydroxyl group after inducing mutation of Y107F affected enzyme activity, and had a more severe impact on dGMP kinase activity. PfTMK can be inhibited by both purine and pyrimidine nucleosides, raising the possibility of developing highly selective drugs. Thermodynamic analysis revealed that enthalpic forces govern both purine and pyrimidine nucleoside monophosphate binding, and the binding affinity of both substrates was highly comparable. The heat produced due to dGMP binding is lower than that attributable to TMP. This indicates that additional interactions occur with TMP, which may be lost with larger dGMP. Targeting PfTMK not only affects thymidine nucleotide synthesis but may also affect purine nucleotides, and thus the enzyme represents an attractive antimicrobial target.
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Crystal structure of poxvirus thymidylate kinase: an unexpected dimerization has implications for antiviral therapy. Proc Natl Acad Sci U S A 2008; 105:16900-5. [PMID: 18971333 DOI: 10.1073/pnas.0804525105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike most DNA viruses, poxviruses replicate in the cytoplasm of host cells. They encode enzymes needed for genome replication and transcription, including their own thymidine and thymidylate kinases. Some herpes viruses encode only 1 enzyme catalyzing both reactions, a peculiarity used for prodrug activation to obtain maximum specificity. We have solved the crystal structures of vaccinia virus thymidylate kinase bound to TDP or brivudin monophosphate. Although the viral and human enzymes have similar sequences (42% identity), they differ in their homodimeric association and active-site geometry. The vaccinia TMP kinase dimer arrangement is orthogonal and not antiparallel as in human enzyme. This different monomer orientation is related to the presence of a canal connecting the edge of the dimer interface to the TMP base binding pocket. Consequently, the pox enzyme accommodates nucleotides with bulkier bases, like brivudin monophosphate and dGMP; these are efficiently phosphorylated and stabilize the enzyme. The brivudin monophosphate-bound structure explains the structural basis for this specificity, opening the way to the rational development of specific antipox agents that may also be suitable for poxvirus TMP kinase gene-based chemotherapy of cancer.
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Carnrot C, Wang L, Topalis D, Eriksson S. Mechanisms of substrate selectivity for Bacillus anthracis thymidylate kinase. Protein Sci 2008; 17:1486-93. [PMID: 18523102 DOI: 10.1110/ps.034199.107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacillus anthracis is well known in connection with biological warfare. The search for new drug targets and antibiotics is highly motivated because of upcoming multiresistant strains. Thymidylate kinase is an ideal target since this enzyme is at the junction of the de novo and salvage synthesis of dTTP, an essential precursor for DNA synthesis. Here the expression and characterization of thymidylate kinase from B. anthracis (Ba-TMPK) is presented. The enzyme phosphorylated deoxythymidine-5'-monophosphate (dTMP) efficiently with K (m) and V (max) values of 33 microM and 48 micromol mg(-1) min(-1), respectively. The efficiency of deoxyuridine-5'-monophosphate phosphorylation was approximately 10% of that of dTMP. Several dTMP analogs were tested, and D-FMAUMP (2'-fluoroarabinosyl-5-methyldeoxyuridine-5'-monophosphate) was selectively phosphorylated with an efficiency of 172% of that of D-dTMP, but L-FMAUMP was a poor substrate as were 5-fluorodeoxyuridine-5'-monophosphate (5FdUMP) and 2',3'-dideoxy-2',3'-didehydrothymidine-5'-monophosphate (d4TMP). No activity could be detected with 3'-azidothymidine-5'-monophosphate (AZTMP). The corresponding nucleosides known as efficient anticancer and antiviral compounds were also tested, and d-FMAU was a strong inhibitor with an IC(50) value of 10 microM, while other nucleosides--L-FMAU, dThd, 5-FdUrd, d4T, and AZT, and 2'-arabinosylthymidine--were poor inhibitors. A structure model was built for Ba-TMPK based on the Staphylococcus aureus TMPK structure. Docking with various substrates suggested mechanisms explaining the differences in substrate selectivity of the human and the bacterial TMPKs. These results may serve as a start point for development of new antibacterial agents.
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Affiliation(s)
- Cecilia Carnrot
- Department of Anatomy, Physiology and Biochemistry, The Swedish University of Agricultural Sciences, The Biomedical Centre, S-751 23 Uppsala, Sweden
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Mitsakos V, Dobson RC, Pearce FG, Devenish SR, Evans GL, Burgess BR, Perugini MA, Gerrard JA, Hutton CA. Inhibiting dihydrodipicolinate synthase across species: Towards specificity for pathogens? Bioorg Med Chem Lett 2008; 18:842-4. [DOI: 10.1016/j.bmcl.2007.11.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/07/2007] [Accepted: 11/08/2007] [Indexed: 01/28/2023]
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El Omari K, Dhaliwal B, Lockyer M, Charles I, Hawkins AR, Stammers DK. Structure of Staphylococcus aureus guanylate monophosphate kinase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:949-53. [PMID: 17012781 PMCID: PMC2225188 DOI: 10.1107/s174430910603613x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 09/06/2006] [Indexed: 05/12/2023]
Abstract
Nucleotide monophosphate kinases (NMPKs) are potential antimicrobial drug targets owing to their role in supplying DNA and RNA precursors. The present work reports the crystal structure of Staphylococcus aureus guanylate monophosphate kinase (SaGMK) at 1.9 A resolution. The structure shows that unlike most GMKs SaGMK is dimeric, confirming the role of the extended C-terminus in dimer formation as first observed for Escherichia coli GMK (EcGMK). One of the two SaGMK dimers within the crystal asymmetric unit has two monomers in different conformations: an open form with a bound sulfate ion (mimicking the beta-phosphate of ATP) and a closed form with bound GMP and sulfate ion. GMP-induced domain movements in SaGMK can thus be defined by comparison of these conformational states. Like other GMKs, the binding of GMP firstly triggers a partial closure of the enzyme, diminishing the distance between the GMP-binding and ATP-binding sites. In addition, the closed structure shows the presence of a potassium ion in contact with the guanine ring of GMP. The potassium ion appears to form an integral part of the GMP-binding site, as the Tyr36 side chain has significantly moved to form a metal ion-ligand coordination involving the lone pair of the side-chain O atom. The potassium-binding site might also be exploited in the design of novel inhibitors.
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Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Balvinder Dhaliwal
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Michael Lockyer
- Arrow Therapeutics, Britannia House, 7 Trinity Street, London SE1 1DA, England
| | - Ian Charles
- Arrow Therapeutics, Britannia House, 7 Trinity Street, London SE1 1DA, England
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Catherine Cookson Building, Medical School, Framlington Place, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne NE2 4HH, England
| | - David K. Stammers
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
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