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Petrova YD, Wadda K, Nathubhai A, Yevglevskis M, Mitchell PJ, James TD, Threadgill MD, Woodman TJ, Lloyd MD. Identification of novel small-molecule inhibitors of α-methylacyl-CoA racemase (AMACR; P504S) and structure-activity relationships. Bioorg Chem 2019; 92:103264. [PMID: 31536955 DOI: 10.1016/j.bioorg.2019.103264] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S; EC 5.1.99.4) catalyses epimerization of 2-methylacyl-CoAs and is important for the degradation of branched-chain fatty acids and the pharmacological activation of ibuprofen and related drugs. It is also a novel drug target for prostate and other cancers. However, development of AMACR as a drug target has been hampered by the difficulties in assaying enzyme activity. Consequently, reported inhibitors have been rationally designed acyl-CoA esters, which are delivered as their carboxylate prodrugs. The novel colorimetric assay for AMACR based on the elimination of 2,4-dinitrophenolate was developed for high-throughput screening and 20,387 'drug-like compounds' were screened, with a throughput of 768 compounds assayed per day. Pyrazoloquinolines and pyrazolopyrimidines were identified as novel scaffolds and investigated as AMACR inhibitors. The most potent inhibitors have IC50 values of ~2 µM. The pyrazoloquinoline inhibitor 10a displayed uncompetitive inhibition, whilst 10j displayed mixed competitive inhibition. The pyrazolopyrimidine inhibitor 11k displayed uncompetitive inhibition. This is the first report of the identification of specific drug-like small-molecule AMACR inhibitors by high-throughput screening. Pyrazoloquinolines and pyrazolopyrimidines may also be useful as inhibitors of other CoA-utilizing enzymes.
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Affiliation(s)
- Yoana D Petrova
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Katty Wadda
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK; School of Pharmacy and Pharmaceutical Sciences, Sciences Complex, City Campus, Dale Building, Room 121, Sunderland SR1 3SD, UK(1)
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Paul J Mitchell
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Graves JL, Ewunkem AJ, Ward J, Staley C, Thomas MD, Rhinehardt KL, Han J, Harrison SH. Experimental evolution of gallium resistance in Escherichia coli. EVOLUTION MEDICINE AND PUBLIC HEALTH 2019; 2019:169-180. [PMID: 31890209 PMCID: PMC6928379 DOI: 10.1093/emph/eoz025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/29/2019] [Indexed: 12/26/2022]
Abstract
Background and Objectives Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. Methodology Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. Results By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. Conclusions This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. Lay summary We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.
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Affiliation(s)
- Joseph L Graves
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
| | - Akamu J Ewunkem
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
| | - Jason Ward
- High School Science Teacher, Davie Public High School, Davie, NC, USA
| | | | - Misty D Thomas
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
| | - Kristen L Rhinehardt
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University & UNC Greensboro, Greensboro, NC, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
| | - Jian Han
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
| | - Scott H Harrison
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
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Ahmad S, Murtaza UA, Raza S, Azam SS. Blocking the catalytic mechanism of MurC ligase enzyme from Acinetobacter baumannii: An in Silico guided study towards the discovery of natural antibiotics. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Kahler CM, Sarkar-Tyson M, Kibble EA, Stubbs KA, Vrielink A. Enzyme targets for drug design of new anti-virulence therapeutics. Curr Opin Struct Biol 2018; 53:140-150. [PMID: 30223251 DOI: 10.1016/j.sbi.2018.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/19/2022]
Abstract
Society has benefitted greatly from the use of antibiotics. Unfortunately, the misuse of these valuable molecules has resulted in increased levels of antibiotic resistance, a major global and public health issue. This resistance and the reliance on a small number of biological targets for the development of antibiotics emphasizes the need for new targets. A critical aspect guiding the development of new antimicrobials through a rational structure-guided approach is to understand the molecular structures of specific biological targets of interest. Here we give an overview of the structures of bacterial virulence enzyme targets involved in protein folding, peptidoglycan biosynthesis and cell wall modification. These include enzymes of the thiol-disulphide oxidoreductase pathway (DSB enzymes), peptidyl-proly cis/trans isomerases (Mips), enzymes from the Mur pathway and enzymes involved in lipopolysaccharide modification (EptA and ArnT). We also present progress towards inhibitor design of these targets for the development of novel anti-virulence therapeutic agents.
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Affiliation(s)
- Charlene M Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Emily A Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia; Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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Abdallah AEM, Elgemeie GH. Design, synthesis, docking, and antimicrobial evaluation of some novel pyrazolo[1,5- a] pyrimidines and their corresponding cycloalkane ring-fused derivatives as purine analogs. Drug Des Devel Ther 2018; 12:1785-1798. [PMID: 29950813 PMCID: PMC6018852 DOI: 10.2147/dddt.s159310] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Over the years, pyrazolopyrimidine derivatives have been recognized as having antimicrobial activities. Recently, we reported different synthetic methods to prepare pyrazolopyrimidine derivatives as anticancer and antimicrobial agents. The studies showed that our previously reported 5-aminopyrazoles 2 act as a building block for the preparation of a variety of interesting pyrazolopyrimidines as purine analogs. Purpose The objective of this study was to describe the direct new method for preparation of novel pyrazolo[1,5-a]pyrimidine derivatives and their corresponding cycloalkane ring-fused derivatives. Also, the new compounds were tested in vitro for their antibacterial and antifungal activity properties. Methods Pyrazolo[1,5-a]pyrimidine derivatives were prepared by the reaction of our previously reported 5-aminopyrazoles 2 with suitable sodium salts of (hydroxymethylene) cycloalkanones and sodium salts of unsaturated ketones. Results The structures of the new compounds were characterized according to their mass spectroscopy, 1H NMR, IR and elemental analyses. Compounds 8b, 10e, 10i, and 10n were the most active compounds against Gram-positive and Gram-negative bacterial species. Compound 10i with two moieties of 4-Br-C6H4 revealed increased reactivity compared with ampicillin as standard reference. Conclusion About twenty two novel pyrazolo[1,5-a]pyrimidine derivatives and their corresponding cycloalkane ring-fused derivatives were prepared through the reaction of 5-aminopyrazoles 2 with different sodium salts of (hydroxymethylene) cycloalkanones and sodium salts of unsaturated ketones. The antibacterial and antifungal activities of the newly synthesized compounds were evaluated and revealed that compounds 8b, 10e, 10i, and 10n were the most active compounds against Gram-positive and Gram-negative bacterial strains.
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Affiliation(s)
- Amira EM Abdallah
- Department of Chemistry, Faculty of Science, Helwan University, Helwan, Cairo, Egypt
| | - Galal H Elgemeie
- Department of Chemistry, Faculty of Science, Helwan University, Helwan, Cairo, Egypt
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Mutant Alleles of lptD Increase the Permeability of Pseudomonas aeruginosa and Define Determinants of Intrinsic Resistance to Antibiotics. Antimicrob Agents Chemother 2015; 60:845-54. [PMID: 26596941 DOI: 10.1128/aac.01747-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/15/2015] [Indexed: 01/11/2023] Open
Abstract
Gram-negative bacteria provide a particular challenge to antibacterial drug discovery due to their cell envelope structure. Compound entry is impeded by the lipopolysaccharide (LPS) of the outer membrane (OM), and those molecules that overcome this barrier are often expelled by multidrug efflux pumps. Understanding how efflux and permeability affect the ability of a compound to reach its target is paramount to translating in vitro biochemical potency to cellular bioactivity. Herein, a suite of Pseudomonas aeruginosa strains were constructed in either a wild-type or efflux-null background in which mutations were engineered in LptD, the final protein involved in LPS transport to the OM. These mutants were demonstrated to be defective in LPS transport, resulting in compromised barrier function. Using isogenic strain sets harboring these newly created alleles, we were able to define the contributions of permeability and efflux to the intrinsic resistance of P. aeruginosa to a variety of antibiotics. These strains will be useful in the design and optimization of future antibiotics against Gram-negative pathogens.
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Transposon Mutagenesis Paired with Deep Sequencing of Caulobacter crescentus under Uranium Stress Reveals Genes Essential for Detoxification and Stress Tolerance. J Bacteriol 2015. [PMID: 26195598 DOI: 10.1128/jb.00382-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The ubiquitous aquatic bacterium Caulobacter crescentus is highly resistant to uranium (U) and facilitates U biomineralization and thus holds promise as an agent of U bioremediation. To gain an understanding of how C. crescentus tolerates U, we employed transposon (Tn) mutagenesis paired with deep sequencing (Tn-seq) in a global screen for genomic elements required for U resistance. Of the 3,879 annotated genes in the C. crescentus genome, 37 were found to be specifically associated with fitness under U stress, 15 of which were subsequently tested through mutational analysis. Systematic deletion analysis revealed that mutants lacking outer membrane transporters (rsaFa and rsaFb), a stress-responsive transcription factor (cztR), or a ppGpp synthetase/hydrolase (spoT) exhibited a significantly lower survival rate under U stress. RsaFa and RsaFb, which are homologues of TolC in Escherichia coli, have previously been shown to mediate S-layer export. Transcriptional analysis revealed upregulation of rsaFa and rsaFb by 4- and 10-fold, respectively, in the presence of U. We additionally show that rsaFa mutants accumulated higher levels of U than the wild type, with no significant increase in oxidative stress levels. Our results suggest a function for RsaFa and RsaFb in U efflux and/or maintenance of membrane integrity during U stress. In addition, we present data implicating CztR and SpoT in resistance to U stress. Together, our findings reveal novel gene targets that are key to understanding the molecular mechanisms of U resistance in C. crescentus. IMPORTANCE Caulobacter crescentus is an aerobic bacterium that is highly resistant to uranium (U) and has great potential to be used in U bioremediation, but its mechanisms of U resistance are poorly understood. We conducted a Tn-seq screen to identify genes specifically required for U resistance in C. crescentus. The genes that we identified have previously remained elusive using other omics approaches and thus provide significant insight into the mechanisms of U resistance by C. crescentus. In particular, we show that outer membrane transporters RsaFa and RsaFb, previously known as part of the S-layer export machinery, may confer U resistance by U efflux and/or by maintaining membrane integrity during U stress.
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