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Deng L, Sun H, Hu W, Liao W, Zhou Z, Pan H. Synthesis, Crystal Structure, and DFT Study of a New Derivative of Pyrido[2,3-d]pyrimidine. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363221120197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Valdez N, Hughes C, Palmer SO, Sepulveda A, Dean FB, Escamilla Y, Bullard JM, Zhang Y. Rational Design of an Antimicrobial Peptide Based on Structural Insight into the Interaction of Pseudomonas aeruginosa Initiation Factor 1 with Its Cognate 30S Ribosomal Subunit. ACS Infect Dis 2021; 7:3161-3167. [PMID: 34709785 DOI: 10.1021/acsinfecdis.1c00256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial infections continue to represent a major worldwide health hazard following the emergence of drug-resistant pathogenic strains. Pseudomonas aeruginosa is an opportunistic pathogen causing nosocomial infections with increased morbidity and mortality. The increasing antibiotic resistance in P. aeruginosa has led to an unmet need for discovery of new antibiotic candidates. Bacterial protein synthesis is an essential metabolic process and a validated target for antibiotic development; however, the precise structural mechanism in P. aeruginosa remains unknown. In this work, the interaction of P. aeruginosa initiation factor 1 (IF1) with the 30S ribosomal subunit was studied by NMR, which enabled us to construct a structure of IF1-bound 30S complex. A short α-helix in IF1 was found to be critical for IF1 ribosomal binding and function. A peptide derived from this α-helix was tested and displayed a high ability to inhibit bacterial growth. These results provide a clue for rational design of new antimicrobials.
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Affiliation(s)
- Nicolette Valdez
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Casey Hughes
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Stephanie O. Palmer
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Alyssa Sepulveda
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Frank B. Dean
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Yaritza Escamilla
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - James M. Bullard
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
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3
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Devi P, Bishnoi A, Singh V. A Multicomponent Synthesis of 4H-Pyrido[1,2-a]pyrimidine-2-hydroxy-4-one Derivatives and Assessment of Their Antimicrobial Activity. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021020184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Riadi Y. UV Light-mediated regioselective methylsulfanyl discrimination via Pd-catalyzed cross-coupling reactions of 2,4-dimethylsulfanylpyrido[2,3-d]pyrimidines. J Sulphur Chem 2019. [DOI: 10.1080/17415993.2019.1590581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yassine Riadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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5
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Riadi Y, Lazar S, Guillaumet G. Regioselective palladium-catalyzed Suzuki–Miyaura coupling reaction of 2,4,6-trihalogenopyrido[2,3-d]pyrimidines. CR CHIM 2019. [DOI: 10.1016/j.crci.2019.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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6
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Zamacona R, Chavero PN, Medellin E, Hu Y, Hughes CA, Quach N, Keniry M, Bullard JM. Identification and Characterization of Chemical Compounds that Inhibit Leucyl-tRNA Synthetase from Pseudomonas aeruginosa. Curr Drug Discov Technol 2018; 17:119-130. [PMID: 30088448 DOI: 10.2174/1570163815666180808095600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/20/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic multi-drug resistance pathogen implicated as the causative agent in a high-percentage of nosocomial and community acquired bacterial infections. The gene encoding leucyl-tRNA synthetase (LeuRS) from P. aeruginosa was overexpressed in Escherichia coli and the resulting protein was characterized. METHODS LeuRS was kinetically evaluated and the KM values for interactions with leucine, ATP and tRNA were 6.5, 330, and 3.0 μM, respectively. LeuRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen over 2000 synthetic and natural chemical compounds. RESULTS The initial screen resulted in the identification of two inhibitory compounds, BT03C09 and BT03E07. IC50s against LeuRS observed for BT03C09 and BT03E07 were 23 and 15 μM, respectively. The minimum inhibitory concentrations (MIC) were determined against nine clinically relevant bacterial strains. In time-kill kinetic analysis, BT03C09 was observed to inhibit bacterial growth in a bacteriostatic manner, while BT03E07 acted as a bactericidal agent. Neither compound competed with leucine or ATP for binding LeuRS. Limited inhibition was observed in aminoacylation assays with the human mitochondrial form of LeuRS, however when tested in cultures of human cell line, BT03C09 was toxic at all concentration whereas BT03E07 only showed toxic effects at elevated concentrations. CONCLUSION Two compounds were identified as inhibitors of LeuRS in a screen of over 2000 natural and synthetic compounds. After characterization one compound (BT03E07) exhibited broad spectrum antibacterial activity while maintaining low toxicity against human mitochondrial LeuRS as well as against human cell cultures.
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Affiliation(s)
- Regina Zamacona
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Pamela N Chavero
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Eduardo Medellin
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Yanmei Hu
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States.,Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Casey A Hughes
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Nathalie Quach
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - Megan Keniry
- Biology Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
| | - James M Bullard
- Chemistry Department, The University of Texas-RGV, 1201 W. University Drive, Edinburg, TX 78541, United States
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7
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Corona A, Palmer SO, Zamacona R, Mendez B, Dean FB, Bullard JM. Discovery and Characterization of Chemical Compounds That Inhibit the Function of Aspartyl-tRNA Synthetase from Pseudomonas aeruginosa. SLAS DISCOVERY 2017; 23:294-301. [PMID: 29186665 DOI: 10.1177/2472555217744559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa, an opportunistic pathogen, is highly susceptible to developing resistance to multiple antibiotics. The gene encoding aspartyl-tRNA synthetase (AspRS) from P. aeruginosa was cloned and the resulting protein characterized. AspRS was kinetically evaluated, and the KM values for aspartic acid, ATP, and tRNA were 170, 495, and 0.5 μM, respectively. AspRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 1690 chemical compounds, resulting in the identification of two inhibitory compounds, BT02A02 and BT02C05. The minimum inhibitory concentrations (MICs) were determined against nine clinically relevant bacterial strains, including efflux pump mutant and hypersensitive strains of P. aeruginosa. The compounds displayed broad-spectrum antibacterial activity and inhibited growth of the efflux and hypersensitive strains with MICs of 16 μg/mL. Growth of wild-type strains were unaffected, indicating that efflux was likely responsible for this lack of activity. BT02A02 did not inhibit growth of human cell cultures at any concentration. However, BT02C05 did inhibit human cell cultures with a cytotoxicity concentration (CC50) of 61.6 μg/mL. The compounds did not compete with either aspartic acid or ATP for binding AspRS, indicating that the mechanism of action of the compound occurs outside the active site of aminoacylation.
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Affiliation(s)
- Araceli Corona
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | | | - Regina Zamacona
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Benjamin Mendez
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Frank B Dean
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - James M Bullard
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
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8
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Photochemical route for the synthesis of novel 2-monosubstituted pyrido[2,3-d]pyrimidines by palladium-catalyzed cross-coupling reactions. CHEMICAL PAPERS 2017. [DOI: 10.1007/s11696-017-0325-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Koo J, Kim J, Park SB. Gold-Catalyzed Unexpected Ring Transformation of Pyrimidodiazepine Derivatives. Org Lett 2017; 19:344-347. [DOI: 10.1021/acs.orglett.6b03520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jaeyoung Koo
- Department
of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Jonghoon Kim
- Department
of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Seung Bum Park
- Department
of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
- Department
of Chemistry, Seoul National University, Seoul 08826, Korea
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10
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Palmer SO, Hu Y, Keniry M, Bullard JM. Identification of Chemical Compounds That Inhibit Protein Synthesis in Pseudomonas aeruginosa. SLAS DISCOVERY 2016; 22:775-782. [PMID: 27872201 DOI: 10.1177/1087057116679591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Four inhibitory compounds were identified using a poly-uridylic acid (polyU) mRNA-directed aminoacylation/translation (A/T) protein synthesis system composed of phenylalanyl-tRNA synthetases (PheRS), ribosomes, and ribosomal factors from Pseudomonas aeruginosa in an in vitro screen of a synthetic compound library. The compounds were specific for inhibition of bacterial protein synthesis. In enzymatic assays, the compounds inhibited protein synthesis with IC50 values ranging from 20 to 60 μM. Minimum inhibitory concentrations (MICs) were determined in cultures for a panel of pathogenic organisms, including Enterococcus faecalis, Escherichia coli, Haemophilus influenzae, P. aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae. All the compounds were observed to have broad-spectrum activity and inhibited an efflux pump mutant strain of P. aeruginosa with MICs of 0.5-16 μg/mL. The molecular target of two compounds was determined to be PheRS. These two compounds were bacteriostatic against both Gram-positive and Gram-negative pathogens. In competition assays, they were not observed to compete with the natural substrates ATP or phenylalanine for active site binding. The other two compounds directly inhibited the ribosome and were bactericidal against both Gram-positive and Gram-negative pathogens. In cytotoxicity MTT testing in human cell lines, the compounds were shown to be from 2500- to 30,000-fold less active than the control staurosporine.
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Affiliation(s)
| | - Yanmei Hu
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Megan Keniry
- 2 Biology Department, The University of Texas-RGV, Edinburg, TX, USA
| | - James M Bullard
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
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11
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Hu Y, Bernal A, Bullard JM, Zhang Y. Solution structure of protein synthesis initiation factor 1 from Pseudomonas aeruginosa. Protein Sci 2016; 25:2290-2296. [PMID: 27636899 DOI: 10.1002/pro.3042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen and a primary cause of nosocomial infection in humans. The rate of antibiotic resistance in P. aeruginosa is increasing worldwide leading to an unmet need for discovery of new chemical compounds distinctly different from present antimicrobials. Protein synthesis is an essential metabolic process and a validated target for the development of new antibiotics. Initiation factor 1 from P. aeruginosa (Pa-IF1) is the smallest of the three initiation factors that act to establish the 30S initiation complex during initiation of protein biosynthesis. Here we report the characterization and solution NMR structure of Pa-IF1. Pa-IF1 consists of a five-stranded β-sheet with an unusual extended β-strand at the C-terminus and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5. The structure adopts a typical β-barrel fold and contains an oligomer-binding motif. A cluster of basic residues (K39, R41, K42, K64, R66, R70, and R72) located on the surface of strands β4 and β5 near the short α-helix may compose the binding interface with the 30S subunit.
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Affiliation(s)
- Yanmei Hu
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
| | - Alejandra Bernal
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
| | - James M Bullard
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas
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12
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Discovery and Analysis of Natural-Product Compounds Inhibiting Protein Synthesis in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2016; 60:4820-9. [PMID: 27246774 DOI: 10.1128/aac.00800-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 05/23/2016] [Indexed: 11/20/2022] Open
Abstract
Bacterial protein synthesis is the target for numerous natural and synthetic antibacterial agents. We have developed a poly(U) mRNA-directed aminoacylation/translation (A/T) protein synthesis system composed of phenylalanyl-tRNA synthetases (PheRS), ribosomes, and ribosomal factors from Pseudomonas aeruginosa This system has been used for high-throughput screening of a natural-compound library. Assays were developed for each component of the system to ascertain the specific target of inhibitory compounds. In high-throughput screens, 13 compounds were identified that inhibit protein synthesis with 50% inhibitory concentrations ranging from 0.3 to >80 μM. MICs were determined for the compounds against the growth of a panel of pathogenic organisms, including Enterococcus faecalis, Escherichia coli, Haemophilus influenzae, Moraxella catarrhalis, P. aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae Three of the compounds were observed to have broad-spectrum activity and inhibited a hypersensitive strain of P. aeruginosa with MICs of 8 to 16 μg/ml. The molecular target of each of the three compounds was determined to be PheRS. One compound was found to be bacteriostatic, and one compound was bactericidal against both Gram-positive and Gram-negative pathogens. The third compound was observed to be bacteriostatic against Gram-positive and bactericidal against Gram-negative bacteria. All three compounds were competitive with the substrate ATP; however, one compound was competitive, one was uncompetitive, and one noncompetitive with the amino acid substrate. Macromolecular synthesis assays confirm the compounds inhibit protein synthesis. The compounds were shown to be more than 25,000-fold less active than the control staurosporine in cytotoxicity MTT testing in human cell lines.
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13
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Behalo MS, Mele G. Synthesis and Evaluation of Pyrido[2,3-d]pyrimidine and 1,8-Naphthyridine Derivatives as Potential Antitumor Agents. J Heterocycl Chem 2016. [DOI: 10.1002/jhet.2581] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mohamed S. Behalo
- Chemistry Department, Faculty of Science; Benha University; 13518 Benha Egypt
| | - Giuseppe Mele
- Department of Engineering for Innovation; University of Salento; Lecce Italy
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14
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Kim H, Jo A, Ha J, Lee Y, Hwang YS, Park SB. A pyrazolo[1,5-a]pyridine-fused pyrimidine based novel fluorophore and its bioapplication to probing lipid droplets. Chem Commun (Camb) 2016; 52:7822-5. [DOI: 10.1039/c6cc02184k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrimidine-containing novel organic fluorophores were discovered and successively applied to monitor the lipid droplets in live cellular systems.
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Affiliation(s)
- Heejun Kim
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Ala Jo
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Jaeyoung Ha
- WCU Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Korea
| | - Youngjun Lee
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Yoon Soo Hwang
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Seung Bum Park
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
- WCU Department of Biophysics and Chemical Biology
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15
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Hu Y, Palmer SO, Munoz H, Bullard JM. High Throughput Screen Identifies Natural Product Inhibitor of Phenylalanyl-tRNA Synthetase from Pseudomonas aeruginosa and Streptococcus pneumoniae. Curr Drug Discov Technol 2015; 11:279-92. [PMID: 25601215 DOI: 10.2174/1570163812666150120154701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/14/2015] [Accepted: 01/15/2015] [Indexed: 11/22/2022]
Abstract
Pseudomonas aeruginosa and Streptococcus pneumoniae are causative agents in a wide range of infections. Genes encoding proteins corresponding to phenylalanyl-tRNA synthetase (PheRS) were cloned from both bacteria. The two forms of PheRS were kinetically evaluated and the K(m)'s for P. aeruginosa PheRS with its three substrates, phenylalanine, ATP and tRNA(Phe) were determined to be 48, 200, and 1.2 µM, respectively, while the K(m)'s for S. pneumoniae PheRS with respect to phenylalanine, ATP and tRNA(Phe) were 21, 225 and 0.94 µM, respectively. P. aeruginosa and S. pneumoniae PheRS were used to screen a natural compound library and a single compound was identified that inhibited the function of both enzymes. The compound inhibited P. aeruginosa and S. pneumoniae PheRS with IC50's of 2.3 and 4.9 µM, respectively. The compound had a K(I) of 0.83 and 0.98 µM against P. aeruginosa and S. pneumoniae PheRS, respectively. The minimum inhibitory concentration (MIC) of the compound was determined against a panel of Gram positive and negative bacteria including efflux pump mutants and hyper-sensitive strains. MICs against wild-type P. aeruginosa and S. pneumoniae cells in culture were determined to be 16 and 32 µg/ml, respectively. The mechanism of action of the compound was determined to be competitive with the amino acid, phenylalanine, and uncompetitive with ATP. There was no inhibition of cytoplasmic protein synthesis, however, partial inhibition of the human mitochondrial PheRS was observed.
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Affiliation(s)
| | | | | | - James M Bullard
- Chemistry Department, SCIE. 3.320, The University of Texas-Pan American, 1201 W. University Drive, Edinburg, TX 78541, USA.
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Khatri TT, Shah VH. One Pot Synthesis of Novel Cyanopyridones as an Intermediate of Bioactive Pyrido[2,3-d]Pyrimidines. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2014. [DOI: 10.5012/jkcs.2014.58.4.366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Palmer SO, Rangel EY, Hu Y, Tran AT, Bullard JM. Two homologous EF-G proteins from Pseudomonas aeruginosa exhibit distinct functions. PLoS One 2013; 8:e80252. [PMID: 24260360 PMCID: PMC3832671 DOI: 10.1371/journal.pone.0080252] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/11/2013] [Indexed: 11/28/2022] Open
Abstract
Genes encoding two proteins corresponding to elongation factor G (EF-G) were cloned from Pseudomonas aeruginosa. The proteins encoded by these genes are both members of the EFG I subfamily. The gene encoding one of the forms of EF-G is located in the str operon and the resulting protein is referred to as EF-G1A while the gene encoding the other form of EF-G is located in another part of the genome and the resulting protein is referred to as EF-G1B. These proteins were expressed and purified to 98% homogeneity. Sequence analysis indicated the two proteins are 90/84% similar/identical. In other organisms containing multiple forms of EF-G a lower degree of similarity is seen. When assayed in a poly(U)-directed poly-phenylalanine translation system, EF-G1B was 75-fold more active than EF-G1A. EF-G1A pre-incubate with ribosomes in the presence of the ribosome recycling factor (RRF) decreased polymerization of poly-phenylalanine upon addition of EF-G1B in poly(U)-directed translation suggesting a role for EF-G1A in uncoupling of the ribosome into its constituent subunits. Both forms of P. aeruginosa EF-G were active in ribosome dependent GTPase activity. The kinetic parameters (KM) for the interaction of EF-G1A and EF-G1B with GTP were 85 and 70 μM, respectively. However, EF-G1B exhibited a 5-fold greater turnover number (observed kcat) for the hydrolysis of GTP than EF-G1A; 0.2 s-1 vs. 0.04 s-1. These values resulted in specificity constants (kcatobs/KM) for EF-G1A and EF-G1B of 0.5 x 103 s-1 M-1 and 3.0 x 103 s-1 M-1, respectively. The antibiotic fusidic acid (FA) completely inhibited poly(U)-dependent protein synthesis containing P. aeruginosa EF-G1B, but the same protein synthesis system containing EF-G1A was not affected. Likewise, the activity of EF-G1B in ribosome dependent GTPase assays was completely inhibited by FA, while the activity of EF-G1A was not affected.
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Affiliation(s)
- Stephanie O. Palmer
- The University of Texas-Pan American, Edinburg, Texas, United States of America
| | - Edna Y. Rangel
- The University of Texas-Pan American, Edinburg, Texas, United States of America
| | - Yanmei Hu
- The University of Texas-Pan American, Edinburg, Texas, United States of America
| | - Alexis T. Tran
- The University of Texas-Pan American, Edinburg, Texas, United States of America
| | - James M. Bullard
- The University of Texas-Pan American, Edinburg, Texas, United States of America
- * E-mail:
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Kim H, Tung TT, Park SB. Privileged substructure-based diversity-oriented synthesis pathway for diverse pyrimidine-embedded polyheterocycles. Org Lett 2013; 15:5814-7. [PMID: 24175659 DOI: 10.1021/ol402872b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A new diversity-oriented synthesis pathway for the fabrication of a pyrimidine-embedded polyheterocycles library was developed for potential interactions with diverse biopolymers. Five different pyrimidine-embedded core skeletons were synthesized from ortho-alkynylpyrimidine carbaldehydes by a silver- or iodine-mediated tandem cyclization strategy. The resulting polyheterocycles possess diverse fused ring sizes and positions with potential functionalities for further modification.
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Affiliation(s)
- Heejun Kim
- Department of Chemistry and Department of Biophysics and Chemical Biology/Bio-MAX Institute, Seoul National University , Seoul 151-747, Korea
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Cloning and characterization of EF-Tu and EF-Ts from Pseudomonas aeruginosa. BIOMED RESEARCH INTERNATIONAL 2013; 2013:585748. [PMID: 23984384 PMCID: PMC3747624 DOI: 10.1155/2013/585748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/12/2013] [Indexed: 11/17/2022]
Abstract
We have cloned genes encoding elongation factors EF-Tu and EF-Ts from Pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. Sequence analysis indicated that P. aeruginosa EF-Tu and EF-Ts are 84% and 55% identical to E. coli counterparts, respectively. P. aeruginosa EF-Tu was active when assayed in GDP exchange assays. Kinetic parameters for the interaction of EF-Tu with GDP in the absence of EF-Ts were observed to be K M = 33 μM, k cat (obs) = 0.003 s(-1), and the specificity constant k cat (obs)/K M was 0.1 × 10(-3) s(-1) μM(-1). In the presence of EF-Ts, these values were shifted to K M = 2 μM, k cat (obs) = 0.005 s(-1), and the specificity constant k(cat)(obs)/K M was 2.5 × 10(-3) s(-1) μM(-1). The equilibrium dissociation constants governing the binding of EF-Tu to GDP (K GDP) were 30-75 nM and to GTP (K GTP) were 125-200 nM. EF-Ts stimulated the exchange of GDP by EF-Tu 10-fold. P. aeruginosa EF-Tu was active in forming a ternary complex with GTP and aminoacylated tRNA and was functional in poly(U)-dependent binding of Phe-tRNA(Phe) at the A-site of P. aeruginosa ribosomes. P. aeruginosa EF-Tu was active in poly(U)-programmed polyphenylalanine protein synthesis system composed of all P. aeruginosa components.
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Guiles JW, Toro A, Ochsner UA, Bullard JM. Development of 4H-pyridopyrimidines: a class of selective bacterial protein synthesis inhibitors. Org Med Chem Lett 2012; 2:5. [PMID: 22373064 PMCID: PMC3353862 DOI: 10.1186/2191-2858-2-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/16/2012] [Indexed: 11/27/2022] Open
Abstract
Background We have identified a series of compounds that inhibit protein synthesis in bacteria. Initial IC50's in aminoacylation/translation (A/T) assays ranged from 3 to14 μM. This series of compounds are variations on a 5,6,7,8-tetrahydropyrido[4,3-d]pyrimidin-4-ol scaffold (e.g., 4H-pyridopyrimidine). Methods Greater than 80 analogs were prepared to investigate the structure-activity relationship (SAR). Structural modifications included changes in the central ring and substituent modifications in its periphery focusing on the 2- and 6-positions. An A/T system was used to determine IC50 values for activity of the analogs in biochemical assays. Minimum inhibitory concentrations (MIC) were determined for each analog against cultures of Enterococcus faecalis, Moraxella catarrhalis, Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli tolC mutants and E. coli modified with PMBN. Results Modifications to the 2-(pyridin-2-yl) ring resulted in complete inactivation of the compounds. However, certain modifications at the 6-position resulted in increased antimicrobial potency. The optimized compounds inhibited the growth of E. faecalis, M. catarrhalis, H. influenzae, S. pneumoniae, S. aureus, E. coli tolC, mutants and E. coli modified with PMBN with MIC values of 4, ≤ 0.12, 1, 2, 4, 1, 1 μg/ml, respectively. IC50 values in biochemical assay were reduced to mid-nanomolar range. Conclusion 4H-pyridopyrimidine analogs demonstrate broad-spectrum inhibition of bacterial growth and modification of the compounds establishes SAR.
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