1
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Wurihan W, Wang Y, Yeung S, Zou Y, Lai Z, Fondell JD, Li WV, Zhong G, Fan H. Expression activation of over 70% of Chlamydia trachomatis genes during the first hour of infection. Infect Immun 2024; 92:e0053923. [PMID: 38299827 PMCID: PMC10929459 DOI: 10.1128/iai.00539-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The obligate intracellular bacterium Chlamydia has a unique developmental cycle that alternates between two contrasting cell types. With a hardy envelope and highly condensed genome, the small elementary body (EB) maintains limited metabolic activities yet survives in extracellular environments and is infectious. After entering host cells, EBs differentiate into larger and proliferating reticulate bodies (RBs). Progeny EBs are derived from RBs in late developmental stages and eventually exit host cells. How expression of the chlamydial genome consisting of nearly 1,000 genes governs the chlamydial developmental cycle is unclear. A previous microarray study identified only 29 Chlamydia trachomatis immediate early genes, defined as genes with increased expression during the first hour postinoculation in cultured cells. In this study, we performed more sensitive RNA sequencing (RNA-Seq) analysis for C. trachomatis cultures with high multiplicities of infection. Remarkably, we observed well over 700 C. trachomatis genes that underwent 2- to 900-fold activation within 1 hour postinoculation. Quantitative reverse transcription real-time PCR analysis was further used to validate the activated expression of a large subset of the genes identified by RNA-Seq. Importantly, our results demonstrate that the immediate early transcriptome is over 20 times more extensive than previously realized. Gene ontology analysis indicates that the activated expression spans all functional categories. We conclude that over 70% of C. trachomatis genes are activated in EBs almost immediately upon entry into host cells, thus implicating their importance in initiating rapid differentiation into RBs and establishing an intracellular niche conducive with chlamydial development and growth.
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Affiliation(s)
- Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Sydney Yeung
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Joseph D. Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Wei Vivian Li
- Department of Statistics, University of California Riverside, Riverside, California, USA
| | - Guangming Zhong
- Department of Microbiology and Immunology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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2
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Lu B, Qiao Q, Park ER, Wang Y, Gilleran JA, Pan M, Pilch DS, Wu X, Roberge JY, Fan H. Acylpyrazoline-Based Third-Generation Selective Antichlamydial Compounds with Enhanced Potency. ACS OMEGA 2023; 8:6597-6607. [PMID: 36844602 PMCID: PMC9947980 DOI: 10.1021/acsomega.2c06992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Chlamydiae are obligate intracellular Gram-negative bacteria and widespread pathogens in humans and animals. Broad-spectrum antibiotics are currently used to treat chlamydial infections. However, broad-spectrum drugs also kill beneficial bacteria. Recently, two generations of benzal acylhydrazones have been shown to selectively inhibit chlamydiae without toxicity to human cells and lactobacilli, which are dominating, beneficial bacteria in the vagina of reproductive-age women. Here, we report the identification of two acylpyrazoline-based third-generation selective antichlamydials (SACs). With minimal inhibitory concentrations (MIC) and minimal bactericidal concentrations (MBC) of 10-25 μM against Chlamydia trachomatis and Chlamydia muridarum, these new antichlamydials are 2- to 5-fold more potent over the benzal acylhydrazone-based second-generation selective antichlamydial lead SF3. Both acylpyrazoline-based SACs are well tolerated by Lactobacillus, Escherichia coli, Klebsiella, and Salmonella as well as host cells. These third-generation selective antichlamydials merit further evaluation for therapeutic application.
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Affiliation(s)
- Bin Lu
- Department
of Parasitology, Central South University
Xiangya Medical School, Changsha, Hunan 410013, China
- Department
of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Qi Qiao
- Molecular
Design and Synthesis Core, RUBRIC, Office for Research, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Elizabeth R. Park
- Molecular
Design and Synthesis Core, RUBRIC, Office for Research, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Chemistry and Chemical Biology, Rutgers,
The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Yuxuan Wang
- Department
of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - John A. Gilleran
- Molecular
Design and Synthesis Core, RUBRIC, Office for Research, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Matthew Pan
- Department
of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Daniel S. Pilch
- Department
of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Xiang Wu
- Department
of Parasitology, Central South University
Xiangya Medical School, Changsha, Hunan 410013, China
| | - Jacques Y. Roberge
- Molecular
Design and Synthesis Core, RUBRIC, Office for Research, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Huizhou Fan
- Department
of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
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3
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de Campos LJ, Seleem MA, Feng J, Pires de Oliveira KM, de Andrade Dos Santos JV, Hayer S, Clayton JB, Kathi S, Fisher DJ, Ouellette SP, Conda-Sheridan M. Design, Biological Evaluation, and Computer-Aided Analysis of Dihydrothiazepines as Selective Antichlamydial Agents. J Med Chem 2023; 66:2116-2142. [PMID: 36696579 PMCID: PMC10056257 DOI: 10.1021/acs.jmedchem.2c01894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chlamydia trachomatis (CT) causes the most prevalent sexually transmitted bacterial disease in the United States. The lack of drug selectivity is one of the main challenges of the current antichlamydial pharmacotherapy. The metabolic needs of CT are controlled, among others, by cylindrical proteases and their chaperones (e.g., ClpX). It has been shown that dihydrothiazepines can disrupt CT-ClpXP. Based on this precedent, we synthesized a dihydrothiazepine library and characterized its antichlamydial activity using a modified semi-high-throughput screening assay. Then, we demonstrated their ability to inhibit ClpX ATPase activity in vitro, supporting ClpX as a target. Further, our lead compound displayed a promising selectivity profile against CT, acceptable cytotoxicity, no mutagenic potential, and good in vitro stability. A two-dimensional quantitative structure-activity relationship (2D QSAR) model was generated as a support tool in the identification of more potent antichlamydial molecules. This study suggests dihydrothiazepines are a promising starting point for the development of new and selective antichlamydial drugs.
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Affiliation(s)
- Luana Janaína de Campos
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Mohamed A Seleem
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jiachen Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Kelly Mari Pires de Oliveira
- Faculty of Biological and Environmental Science, Federal University of Grande Dourados, Dourados, MS 79804-970, Brazil
| | | | - Shivdeep Hayer
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, United States
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, United States
- Department of Food Science and Technology, University of Nebraska─Lincoln, Lincoln, Nebraska 68588, United States
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Nebraska Food for Health Center, University of Nebraska─Lincoln, Lincoln, Nebraska 68508, United States
| | - Sharvath Kathi
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Derek J Fisher
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Scot P Ouellette
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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4
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Kadian LK, Arora M, Prasad CP, Pramanik R, Chauhan SS. Signaling pathways and their potential therapeutic utility in esophageal squamous cell carcinoma. Clin Transl Oncol 2022; 24:1014-1032. [PMID: 34990001 DOI: 10.1007/s12094-021-02763-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
Esophageal cancer is a complex gastrointestinal malignancy with an extremely poor outcome. Approximately 80% of cases of this malignancy in Asian countries including India are of squamous cell origin, termed Esophageal Squamous Cell Carcinoma (ESCC).The five-year survival rate in ESCC patients is less than 20%. Neo-adjuvant chemo-radiotherapy (NACRT) followed by surgical resection remains the major therapeutic strategy for patients with operable ESCC. However, resistance to NACRT and local recurrence after initial treatment are the leading cause of dismal outcomes in these patients. Therefore, an alternative strategy to promote response to the therapy and reduce the post-operative disease recurrence is highly needed. At the molecular level, wide variations have been observed in tumor characteristics among different populations, nevertheless, several common molecular features have been identified which orchestrate disease progression and clinical outcome in the malignancy. Therefore, determination of candidate molecular pathways for targeted therapy remains the mainstream idea of focus in ESCC research. In this review, we have discussed the key signaling pathways associated with ESCC, i.e., Notch, Wnt, and Nrf2 pathways, and their crosstalk during disease progression. We further discuss the recent developments of novel agents to target these pathways in the context of targeted cancer therapy. In-depth research of the signaling pathways, gene signatures, and a combinatorial approach may help in discovering targeted therapy for ESCC.
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Affiliation(s)
- L K Kadian
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - M Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - C P Prasad
- Department of Medical Oncology (Lab), Dr. B. R. Ambedkar-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - R Pramanik
- Department of Medical Oncology, Dr. B. R. Ambedkar-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - S S Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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5
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Huang Y, Wurihan W, Lu B, Zou Y, Wang Y, Weldon K, Fondell JD, Lai Z, Wu X, Fan H. Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor. Front Microbiol 2022; 12:812448. [PMID: 35046926 PMCID: PMC8762339 DOI: 10.3389/fmicb.2021.812448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.
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Affiliation(s)
- Yehong Huang
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Bin Lu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Joseph D Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
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6
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Li X, Jiang Q, Yang X. Discovery of Inhibitors for Mycobacterium Tuberculosis Peptide Deformylase Based on Virtual Screening in Silico. Mol Inform 2021; 41:e2100002. [PMID: 34708566 DOI: 10.1002/minf.202100002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/21/2021] [Indexed: 01/02/2023]
Abstract
Tuberculosis has been the serious disease threatening human health and public safety due to the emergence of MDR and XDR-TB. Mycobacterium tuberculosis peptide deformylase (MtPDF) is a valuable target for antituberculotics. In order to discover new potential inhibitor candidates of MtPDF as leads for antituberculotics, Discovery Studio (DS) 2019 was used to perform molecular docking for virtual screening in silico with the bioactive compound library-I (L1700) against MtPDF. Six compounds with high docking scores and favourable ligand-protein interactions by LibDock and CDOCKER were selected for the evaluation of the inhibition potencies against MtPDF and Mycobacterium smegmatis. GST-6×His tagged MtPDF was recombinant expressed and purified firstly by Glutathione Sepharose 4B, and secondly by Ni Sepharose 6 FF after the cleavage of human rhinovirus 3C protease. These compounds showed IC50 values from 0.5 μmol/L to 112 μmol/L against MtPDF, among which CUDC-101 bearing hydroxamic acid exhibited IC50 of 0.5 μmol/L on MtPDF and MIC against Mycobacterium smegmatis of 32 μg/mL, and Ixazomib Citrate with IC50 of 63 μmol/L and MIC of 16 μg/mL. CUDC-101 and Ixazomib Citrate are promising as the potential leads for antituberculotics.
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Affiliation(s)
- Xinpeng Li
- Key Laboratory of Medical Laboratory Diagnostics of the, Ministry of Education of China, Chongqing Medical University, Chongqing, China
| | - Qihua Jiang
- College of pharmacy, Chongqing Medical University, Chongqing, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the, Ministry of Education of China, Chongqing Medical University, Chongqing, China
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7
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Abstract
Chlamydia trachomatis is an obligate intracellular bacterium whose unique developmental cycle consists of an infectious elementary body and a replicative reticulate body. Progression of this developmental cycle requires temporal control of the transcriptome. In addition to the three chlamydial sigma factors (σ66, σ28, and σ54) that recognize promoter sequences of genes, chlamydial transcription factors are expected to play crucial roles in transcriptional regulation. Here, we investigate the function of GrgA, a Chlamydia-specific transcription factor, in C. trachomatis transcriptomic expression. We show that 10 to 30 min of GrgA overexpression induces 13 genes, which likely comprise the direct regulon of GrgA. Significantly, σ66-dependent genes that code for two important transcription repressors are components of the direct regulon. One of these repressors is Euo, which prevents the expression of late genes during early phases. The other is HrcA, which regulates molecular chaperone expression and controls stress response. The direct regulon also includes a σ28-dependent gene that codes for the putative virulence factor PmpI. Furthermore, overexpression of GrgA leads to decreased expression of almost all tRNAs. Transcriptomic studies suggest that GrgA, Euo, and HrcA have distinct but overlapping indirect regulons. These findings, together with temporal expression patterns of grgA, euo, and hrcA, indicate that a transcriptional regulatory network of these three transcription factors plays critical roles in C. trachomatis growth and development. IMPORTANCEChlamydia trachomatis is the most prevalent sexually transmitted bacterial pathogen worldwide and is a leading cause of preventable blindness in underdeveloped areas as well as some developed countries. Chlamydia carries genes that encode a limited number of known transcription factors. While Euo is thought to be critical for early chlamydial development, the functions of GrgA and HrcA in the developmental cycle are unclear. Activation of euo and hrcA immediately following GrgA overexpression indicates that GrgA functions as a master transcriptional regulator. In addition, by broadly inhibiting tRNA expression, GrgA serves as a key regulator of chlamydial protein synthesis. Furthermore, by upregulating pmpI, GrgA may act as an upstream virulence determinant. Finally, genes coregulated by GrgA, Euo, and HrcA likely play critical roles in chlamydial growth and developmental control.
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8
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Wurihan W, Weber AM, Gong Z, Lou Z, Sun S, Zhou J, Fan H. GrgA overexpression inhibits Chlamydia trachomatis growth through sigma 66- and sigma 28-dependent mechanisms. Microb Pathog 2021; 156:104917. [PMID: 33940135 PMCID: PMC8187326 DOI: 10.1016/j.micpath.2021.104917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/21/2023]
Abstract
The obligate intracellular bacterium Chlamydia trachomatis is an important human pathogen with a biphasic developmental cycle comprised of an infectious elementary body (EB) and a replicative reticulate body (RB). Whereas σ66, the primary sigma factor, is necessary for transcription of most chlamydial genes throughout the developmental cycle, σ28 is required for expression of some late genes. We previously showed that the Chlamydia-specific transcription factor GrgA physically interacts with both of these sigma factors and activates transcription from σ66- and σ28-dependent promoters in vitro. Here, we investigated the organismal functions of GrgA. We show that overexpression of GrgA slows EB-to-RB conversion, decreases RB proliferation, and reduces progeny EB production. In contrast, overexpression of a GrgA variant without the σ28-binding domain shows significantly less severe inhibitory effects, while overexpression of a variant without the σ66-binding domain demonstrates no adverse effects. These findings indicate that GrgA plays important roles in the expression regulation of both σ66-dependent genes and σ28-dependent genes during the chlamydial developmental cycle.
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Affiliation(s)
- Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Alec M Weber
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zheng Gong
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zhongzi Lou
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Samantha Sun
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jizhang Zhou
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA.
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9
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Zhang H, Vellappan S, Tang MM, Bao X, Fan H. GrgA as a potential target of selective antichlamydials. PLoS One 2019; 14:e0212874. [PMID: 30822328 PMCID: PMC6396966 DOI: 10.1371/journal.pone.0212874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/11/2019] [Indexed: 01/16/2023] Open
Abstract
Chlamydia is a common pathogen that can causes serious complications in the reproductive system and eyes. Lack of vaccine and other effective prophylactic measures coupled with the largely asymptomatic nature and unrare clinical treatment failure calls for development of new antichlamydials, particularly selective antichlamydials without adverse effects on humans and the beneficial microbiota. We previously reported that benzal-N-acylhydrazones (BAH) can inhibit chlamydiae without detectable adverse effects on host cells and beneficial lactobacilli that dominate the human vaginal microbiota among reproductive-age women. However, the antichlamydial mechanism of BAH is not known. Whereas 4 single nucleotide polymorphisms (i.e., SNP1-4) were identified in a rare Chlamydia variant with a low level of BAH resistance, termed MCR, previous studies failed to establish a causal effect of any particular SNP(s). In the present work, we performed recombination to segregate the four SNPs. Susceptibility tests indicate that the R51G GrgA allele is both necessary and sufficient for the low level of BAH resistance. Thus, the Chlamydia-specific transcription factor GrgA either is a direct target of BAH or regulates BAH susceptibility. We further confirm an extremely low rate of BAH resistance in Chlamydia. Our findings warrant exploration of GrgA as a therapeutic and prophylactic target for chlamydial infections.
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Affiliation(s)
- Huirong Zhang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
| | - Sangeevan Vellappan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
- The George H. Cook Undergraduate Honors Scholars Program, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - M. Matt Tang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
- Graduate Program in Physiology and Integrative Biology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Xiaofeng Bao
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, United States of America
- Graduate Program in Physiology and Integrative Biology, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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10
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Ahmadvand S, Elahifard M, Jabbarzadeh M, Mirzanejad A, Pflughoeft K, Abbasi B, Abbasi B. Bacteriostatic Effects of Apatite-Covered Ag/AgBr/TiO2 Nanocomposite in the Dark: Anomaly in Bacterial Motility. J Phys Chem B 2019; 123:787-791. [DOI: 10.1021/acs.jpcb.8b10710] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Mohammadreza Elahifard
- Chemical Engineering Department, Faculty of Engineering, Ardakan University, Ardakan 89518-95491, Iran
| | - Mehdi Jabbarzadeh
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Amir Mirzanejad
- Chemical Engineering Department, Faculty of Engineering, Ardakan University, Ardakan 89518-95491, Iran
| | | | - Bahman Abbasi
- Department of Mechanical Engineering, Oregon State University, Corvallis, Oregon 97333, United States
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11
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MacDonald A, Priess M, Curran J, Guess J, Farutin V, Oosterom I, Chu CL, Cochran E, Zhang L, Getchell K, Lolkema M, Schultes BC, Krause S. Necuparanib, A Multitargeting Heparan Sulfate Mimetic, Targets Tumor and Stromal Compartments in Pancreatic Cancer. Mol Cancer Ther 2018; 18:245-256. [PMID: 30401693 DOI: 10.1158/1535-7163.mct-18-0417] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/06/2018] [Accepted: 11/02/2018] [Indexed: 11/16/2022]
Abstract
Pancreatic cancer has an abysmal 5-year survival rate of 8%, making it a deadly disease with a need for novel therapies. Here we describe a multitargeting heparin-based mimetic, necuparanib, and its antitumor activity in both in vitro and in vivo models of pancreatic cancer. Necuparanib reduced tumor cell proliferation and invasion in a three-dimensional (3D) culture model; in vivo, it extended survival and reduced metastasis. Furthermore, proteomic analysis demonstrated that necuparanib altered the expression levels of multiple proteins involved in cancer-driving pathways including organ development, angiogenesis, proliferation, genomic stability, cellular energetics, and invasion and metastasis. One protein family known to be involved in invasion and metastasis and altered by necuparanib treatment was the matrix metalloprotease (MMP) family. Necuparanib reduced metalloproteinase 1 (MMP1) and increased tissue inhibitor of metalloproteinase 3 (TIMP3) protein levels and was found to increase RNA expression of TIMP3. MMP enzymatic activity was also found to be reduced in the 3D model. Finally, we confirmed necuparanib's in vivo activity by analyzing plasma samples of patients enrolled in a phase I/II study in patients with metastatic pancreatic cancer; treatment with necuparanib plus standard of care significantly increased TIMP3 plasma protein levels. Together, these results demonstrate necuparanib acts as a broad multitargeting therapeutic with in vitro and in vivo anti-invasive and antimetastatic activity.
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Affiliation(s)
| | | | | | - Jamey Guess
- Momenta Pharmaceuticals, Inc. Cambridge, Massachusetts
| | | | - Ilse Oosterom
- Erasmus Medical Center Cancer Center, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Chia Lin Chu
- Momenta Pharmaceuticals, Inc. Cambridge, Massachusetts
| | | | - Lynn Zhang
- Momenta Pharmaceuticals, Inc. Cambridge, Massachusetts
| | | | - Martijn Lolkema
- Erasmus Medical Center Cancer Center, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Silva Krause
- Momenta Pharmaceuticals, Inc. Cambridge, Massachusetts.
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12
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Li JL, Yang N, Huang L, Chen D, Zhao Y, Tang MM, Fan H, Bao X. Pyocyanin Inhibits Chlamydia Infection by Disabling Infectivity of the Elementary Body and Disrupting Intracellular Growth. Antimicrob Agents Chemother 2018; 62:e02260-17. [PMID: 29610203 PMCID: PMC5971585 DOI: 10.1128/aac.02260-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular bacterium Chlamydia is a widespread human pathogen that causes serious problems, including (but not limited to) infertility and blindness. Our search for novel antichlamydial metabolites from marine-derived microorganisms led to the isolation of pyocyanin, a small compound from Pseudomonas aeruginosa Pyocyanin is an effective antichlamydial for all three Chlamydia spp. tested. It has a 50% inhibitory concentration (IC50) of 0.019 to 0.028 μM, which is comparable to the IC50 of tetracycline. At concentrations as low as 0.0039 μM, pyocyanin disables infectivity of the chlamydial elementary body (EB). At 0.5 μM or higher concentrations, the continuous presence of pyocyanin also inhibits chlamydial growth in the inclusion during later stages of the developmental cycle. Oxidative stress, a major known antimicrobial mechanism of pyocyanin, appears to be responsible only for the inhibition of bacterial growth and not for the disinfection of EBs. Pyocyanin is well-tolerated by probiotic vaginal Lactobacillus spp. Our findings suggest that pyocyanin is of therapeutic value for chlamydial infections and can serve as a valuable chemical probe for studying chlamydial biology.
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Affiliation(s)
- Jian Lin Li
- School of Pharmacy, Nantong University, Nantong, China
| | - Ningjing Yang
- School of Pharmacy, Nantong University, Nantong, China
| | - Lei Huang
- School of Pharmacy, Nantong University, Nantong, China
- Department of Pharmacy, The First People's Hospital of Yanchen, Yanchen, China
| | - Dandan Chen
- Department of Pharmacy, The Second People's Hospital of Nantong, Nantong, China
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong, China
| | - M Matt Tang
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| | - Huizhou Fan
- Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| | - Xiaofeng Bao
- School of Pharmacy, Nantong University, Nantong, China
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13
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Chen H, Ni M, Bao X, Wang C, Liu L, Chang W, Li J. The Diverse Reactivity of Homopropargylic Amines as “Masked” 1C Synthons for the Aza-Friedel-Crafts Alkylation of Indoles. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hao Chen
- The State Key Laboratory and Institute of Elemento-Organic Chemistry; College of Chemistry; Nankai University; Weijin Road 94# 300071 Tianjin China
| | - Min Ni
- School of Pharmacy; Nantong University; 226001 Nantong China
| | - Xiaofeng Bao
- School of Pharmacy; Nantong University; 226001 Nantong China
| | - Chan Wang
- The State Key Laboratory and Institute of Elemento-Organic Chemistry; College of Chemistry; Nankai University; Weijin Road 94# 300071 Tianjin China
| | - Lingyan Liu
- The State Key Laboratory and Institute of Elemento-Organic Chemistry; College of Chemistry; Nankai University; Weijin Road 94# 300071 Tianjin China
| | - Weixing Chang
- The State Key Laboratory and Institute of Elemento-Organic Chemistry; College of Chemistry; Nankai University; Weijin Road 94# 300071 Tianjin China
| | - Jing Li
- The State Key Laboratory and Institute of Elemento-Organic Chemistry; College of Chemistry; Nankai University; Weijin Road 94# 300071 Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); 300071 Tianjin China
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14
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Resveratrol Inhibits Propagation of Chlamydia trachomatis in McCoy Cells. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4064071. [PMID: 29318147 PMCID: PMC5727650 DOI: 10.1155/2017/4064071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022]
Abstract
Resveratrol (RESV), an antifungal compound from grapes and other plants, has a distinct ability to inhibit the Chlamydia (C.) trachomatis developmental cycle in McCoy cells, a classic cell line used for chlamydial research. Inoculation of C. trachomatis with increasing amounts of RESV (from 12.5 to 100 μM) gave a dose-dependent reduction in the number of infected McCoy cells visualized by using monoclonal antibodies against chlamydial lipopolysaccharide. A similar trend has been observed with immunoassay for major outer membrane protein (MOMP). Furthermore, there was a step-wise reduction in the number of C. trachomatis infective progenies caused by the increasing concentrations of RESV. The ability of RESV to arrest C. trachomatis growth in McCoy cells was confirmed by a nucleic acid amplification protocol which revealed dose-dependent changes in mRNAs for different genes of chlamydial developmental cycle (euo, incA, and omcB). Although the precise nature of the antichlamydial activity of RESV is yet to be determined and evaluated in future studies, the observed effect of RESV on C. trachomatis infection was not related to its potential effect on attachment/entry of the pathogen into eukaryotic cells or RESV toxicity to McCoy cells. Similar inhibitory effect was shown for C. pneumoniae and C. muridarum.
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15
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Good JAD, Kulén M, Silver J, Krishnan KS, Bahnan W, Núñez-Otero C, Nilsson I, Wede E, de Groot E, Gylfe Å, Bergström S, Almqvist F. Thiazolino 2-Pyridone Amide Isosteres As Inhibitors of Chlamydia trachomatis Infectivity. J Med Chem 2017; 60:9393-9399. [DOI: 10.1021/acs.jmedchem.7b00716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- James A. D. Good
- Department
of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Martina Kulén
- Department
of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Jim Silver
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department
of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - K. Syam Krishnan
- Department
of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Wael Bahnan
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department
of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Carlos Núñez-Otero
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
- Clinical
microbiology, Umeå University, 901 85 Umeå, Sweden
| | - Ingela Nilsson
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department
of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Emma Wede
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department
of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Esmee de Groot
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department
of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Åsa Gylfe
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
- Clinical
microbiology, Umeå University, 901 85 Umeå, Sweden
| | - Sven Bergström
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
- Department
of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Fredrik Almqvist
- Department
of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå
Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
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16
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Zhang H, Kunadia A, Lin Y, Fondell JD, Seidel D, Fan H. Identification of a strong and specific antichlamydial N-acylhydrazone. PLoS One 2017; 12:e0185783. [PMID: 28973037 PMCID: PMC5626472 DOI: 10.1371/journal.pone.0185783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/19/2017] [Indexed: 12/02/2022] Open
Abstract
Sexually transmitted Chlamydia trachomatis is an extremely common infection and often leads to serious complications including infertility and pelvic inflammatory syndrome. Several broad-spectrum antibiotics are currently used to treat C. trachomatis. Although effective, they also kill beneficial vaginal lactobacilli. Two N-acylhydrazones, CF0001 and CF0002, have been shown previously to inhibit chlamydial growth without toxicity to human cells and Lactobacillus spp. Of particular significance, the rate of random mutation leading to resistance of these inhibitors appears to be extremely low. Here, we report three analogs of CF0001 and CF0002 with significantly stronger inhibitory effects on chlamydiae. Even though the new compounds (termed SF1, SF2 and SF3) displayed slightly decreased inhibition efficiencies for a rare Chlamydia variant selected for CF0001 resistance (Chlamydia muridarum MCR), they completely overcame the resistance when used at concentrations of 75–100 μM. Importantly, SF1, SF2 and SF3 did not shown any toxic effect on lactobacilli, whereas SF3 was also well tolerated by human host cells. An effort to isolate SF3-resistant variants was unsuccessful. By comparison, variants resistant to rifampin or spectinomycin were obtained from smaller numbers of chlamydiae. Our findings suggest that SF3 utilizes an antichlamydial mechanism similar to that of CF0001 and CF0002, and will be more difficult for chlamydiae to develop resistance to, potentially making it a more effective antichlamydial agent.
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Affiliation(s)
- Huirong Zhang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Anuj Kunadia
- Department of Chemistry and Chemical Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Yingfu Lin
- Department of Chemistry and Chemical Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Joseph D. Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Daniel Seidel
- Department of Chemistry and Chemical Biology, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail: (DS); (HF)
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail: (DS); (HF)
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17
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Kayastha S, Horvath D, Gilberg E, Gütschow M, Bajorath J, Varnek A. Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps. J Chem Inf Model 2017; 57:1218-1232. [DOI: 10.1021/acs.jcim.7b00128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shilva Kayastha
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Laboratoire
de Chemoinformatique, UMR 7140, Université de Strasbourg, 1 rue
Blaise Pascal, Strasbourg 67000, France
| | - Dragos Horvath
- Laboratoire
de Chemoinformatique, UMR 7140, Université de Strasbourg, 1 rue
Blaise Pascal, Strasbourg 67000, France
| | - Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Alexandre Varnek
- Laboratoire
de Chemoinformatique, UMR 7140, Université de Strasbourg, 1 rue
Blaise Pascal, Strasbourg 67000, France
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18
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Bao X, Gylfe A, Sturdevant GL, Gong Z, Xu S, Caldwell HD, Elofsson M, Fan H. Benzylidene acylhydrazides inhibit chlamydial growth in a type III secretion- and iron chelation-independent manner. J Bacteriol 2014; 196:2989-3001. [PMID: 24914180 PMCID: PMC4135636 DOI: 10.1128/jb.01677-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/04/2014] [Indexed: 11/20/2022] Open
Abstract
Chlamydiae are widespread Gram-negative pathogens of humans and animals. Salicylidene acylhydrazides, developed as inhibitors of type III secretion system (T3SS) in Yersinia spp., have an inhibitory effect on chlamydial infection. However, these inhibitors also have the capacity to chelate iron, and it is possible that their antichlamydial effects are caused by iron starvation. Therefore, we have explored the modification of salicylidene acylhydrazides with the goal to uncouple the antichlamydial effect from iron starvation. We discovered that benzylidene acylhydrazides, which cannot chelate iron, inhibit chlamydial growth. Biochemical and genetic analyses suggest that the derivative compounds inhibit chlamydiae through a T3SS-independent mechanism. Four single nucleotide polymorphisms were identified in a Chlamydia muridarum variant resistant to benzylidene acylhydrazides, but it may be necessary to segregate the mutations to differentiate their roles in the resistance phenotype. Benzylidene acylhydrazides are well tolerated by host cells and probiotic vaginal Lactobacillus species and are therefore of potential therapeutic value.
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Affiliation(s)
- Xiaofeng Bao
- Department of Pharmacology, Rutgers University Robert Wood Johnson Medical School, Piscataway, New Jersey, USA Department of Pharmacology, Nantong University School of Pharmacy, Nantong, People's Republic of China
| | - Asa Gylfe
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Gail L Sturdevant
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Zheng Gong
- Department of Pharmacology, Rutgers University Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Shuang Xu
- Department of Pharmacology, Rutgers University Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Harlan D Caldwell
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | | | - Huizhou Fan
- Department of Pharmacology, Rutgers University Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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19
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Puri AW, Bogyo M. Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses. Biochemistry 2013; 52:5985-96. [PMID: 23937332 DOI: 10.1021/bi400854d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Elucidating the molecular and biochemical details of bacterial infections can be challenging because of the many complex interactions that exist between a pathogen and its host. Consequently, many tools have been developed to aid the study of bacterial pathogenesis. Small molecules are a valuable complement to traditional genetic techniques because they can be used to rapidly perturb genetically intractable systems and to monitor post-translationally regulated processes. Activity-based probes are a subset of small molecules that covalently label an enzyme of interest based on its catalytic mechanism. These tools allow monitoring of enzyme activation within the context of a native biological system and can be used to dissect the biochemical details of enzyme function. This review describes the development and application of activity-based probes for examining aspects of bacterial infection on both sides of the host-pathogen interface.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical and Systems Biology, ‡Department of Microbiology and Immunology, and §Department of Pathology, Stanford University School of Medicine , 300 Pasteur Drive, Stanford, California 94305, United States
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20
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Mutations in hemG mediate resistance to salicylidene acylhydrazides, demonstrating a novel link between protoporphyrinogen oxidase (HemG) and Chlamydia trachomatis infectivity. J Bacteriol 2013; 195:4221-30. [PMID: 23852872 DOI: 10.1128/jb.00506-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Salicylidene acylhydrazides (SAHs) inhibit the type III secretion system (T3S) of Yersinia and other Gram-negative bacteria. In addition, SAHs restrict the growth and development of Chlamydia species. However, since the inhibition of Chlamydia growth by SAH is suppressed by the addition of excess iron and since SAHs have an iron-chelating capacity, their role as specific T3S inhibitors is unclear. We investigated here whether SAHs exhibit a function on C. trachomatis that goes beyond iron chelation. We found that the iron-saturated SAH INP0341 (IS-INP0341) specifically affects C. trachomatis infectivity with reduced generation of infectious elementary body (EB) progeny. Selection and isolation of spontaneous SAH-resistant mutant strains revealed that mutations in hemG suppressed the reduced infectivity caused by IS-INP0341 treatment. Structural modeling of C. trachomatis HemG predicts that the acquired mutations are located in the active site of the enzyme, suggesting that IS-INP0341 inhibits this domain of HemG and that protoporphyrinogen oxidase (HemG) and heme metabolism are important for C. trachomatis infectivity.
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21
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Weiling H, Xiaowen Y, Chunmei L, Jianping X. Function and evolution of ubiquitous bacterial signaling adapter phosphopeptide recognition domain FHA. Cell Signal 2013. [DOI: 10.1016/j.cellsig.2012.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Exploration of chlamydial type III secretion system reconstitution in Escherichia coli. PLoS One 2012; 7:e50833. [PMID: 23239989 PMCID: PMC3519817 DOI: 10.1371/journal.pone.0050833] [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: 08/17/2012] [Accepted: 10/25/2012] [Indexed: 11/23/2022] Open
Abstract
Background Type III secretion system is a virulent factor for many pathogens, and is thought to play multiple roles in the development cycle and pathogenesis of chlamydia, an important human pathogen. However, due to the obligate intracellular parasitical nature of chlamydiae and a lack of convenient genetic methodology for the organisms, very limited approaches are available to study the chlamydial type III secretion system. In this study, we explored the reconstitution of a chlamydial type III secretion in Escherichia coli. Results We successfully cloned all 6 genomic DNA clusters of the chlamydial type III secretion system into three bacterial plasmids. 5 of the 6 clusters were found to direct mRNA synthesis from their own promoters in Escherichia coli transformed with the three plasmids. Cluster 5 failed to express mRNA using its own promoters. However, fusion of cluster 5 to cluster 6 resulted in the expression of cluster 5 mRNA. Although only two of the type III secretion system proteins were detected transformed E. coli due to limited antibody availability, type III secretion system-like structures were detected in ultrathin sections in a small proportion of transformed E. coli. Conclusions We have successfully generated E. coli expressing all genes of the chlamydial type III secretion system. This serves as a foundation for optimal expression and assembly of the recombinant chlamydial type III secretion system, which may be extremely useful for the characterization of the chlamydial type III secretion system and for studying its role in chlamydial pathogenicity.
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23
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Choi JY, Park HJ, Lee YJ, Byun J, Youn YS, Choi JH, Woo SY, Kang JL. Upregulation of Mer receptor tyrosine kinase signaling attenuated lipopolysaccharide-induced lung inflammation. J Pharmacol Exp Ther 2012. [PMID: 23197771 DOI: 10.1124/jpet.112.199778] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mer receptor tyrosine kinase (Mer) signaling plays a central role in the intrinsic inhibition of the inflammatory response to Toll-like receptor activation. Previously, we found that lung Mer protein expression decreased after lipopolysaccharide (LPS) treatment due to enhanced Mer cleavage. The purpose of the present study was to examine whether pharmacologically restored membrane-bound Mer expression upregulates the Mer signaling pathways and suppresses lung inflammatory responses. Pretreatment with the ADAM17 (a disintegrin and metalloproteinase-17) inhibitor TAPI-0 (tumor necrosis factor alpha protease inhibitor-0) reduced LPS-induced production of soluble Mer protein in bronchoalveolar lavage (BAL) fluid, restored membrane-bound Mer expression, and increased Mer activation in alveolar macrophages and lungs after LPS treatment. TAPI-0 also enhanced Mer downstream signaling, including phosphorylation of protein kinase b, focal adhesion kinase, and signal transducer and activator of transcription 1. As expected from enhanced Mer signaling, TAPI-0 also augmented suppressor of cytokine signaling-1 and -3 mRNA and protein levels and inhibited nuclear factor κB activation at 4 and 24 hours after LPS treatment. TAPI-0 suppressed LPS-induced inflammatory cell accumulation, total protein level elevation in BAL fluid, and production of inflammatory mediators, including tumor necrosis factor-α, interleukin-1β, and macrophage inflammatory protein-2. Additionally, the effects of TAPI-0 on the activation of Mer signaling and the production of inflammatory responses could be reversed by cotreatment with specific Mer-neutralizing antibody. Restored Mer protein expression by treatment with TAPI-0 efficiently prevents the inflammatory cascade during acute lung injury.
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Affiliation(s)
- Ji-Yeon Choi
- Department of Physiology, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
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24
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Tandem photoaffinity labeling-bioorthogonal conjugation in medicinal chemistry. Bioorg Med Chem 2012; 20:6237-47. [PMID: 23026086 DOI: 10.1016/j.bmc.2012.09.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/30/2012] [Accepted: 09/05/2012] [Indexed: 12/24/2022]
Abstract
Photoaffinity labeling has a longstanding history as a powerful biochemical technique. However, photoaffinity labeling has significantly evolved over the past decade principally due to its coupling with bioorthogonal/click chemistry reactions. This review aims to highlight tandem photoaffinity labeling-bioorthogonal conjugation as a chemical approach in medicinal chemistry and chemical biology. In particular, recent examples of using this strategy for affinity-based protein profiling (AfBPP), drug target identification, binding ensemble profiling, studying endogenous biological molecules, and imaging applications will be presented. Additionally, recent advances in the development of 'all-in-one' compact moieties possessing a photoreactive group and clickable handle will be discussed.
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25
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Meyer BS, Rademann J. Extra- and intracellular imaging of human matrix metalloprotease 11 (hMMP-11) with a cell-penetrating FRET substrate. J Biol Chem 2012; 287:37857-67. [PMID: 22927434 DOI: 10.1074/jbc.m112.371500] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Matrix metalloprotease 11 (MMP-11), a protease associated with invasion and aggressiveness of cancerous tissue, was postulated as a prognostic marker for pancreatic, breast, and colon cancer patients. Expression analysis, however, did not reveal localization and regulation of this protease. Thus, cellular tools for the visualization of MMP-11 are highly desirable to monitor presence and activity and to elucidate the functional role of MMP-11. Therefore, fluorescein-Dabcyl-labeled Foerster resonance energy transfer (FRET) substrates were developed. The design focused on enhanced peptide binding to human MMP-11, employing an unusual amino acid for the specificity pocket P1'. The addition of several arginines resulted in a cell-permeable FRET substrate SM-P124 (Ac-GRRRK(Dabcyl)-GGAANC(MeOBn)RMGG-fluorescein). In vitro evaluation of SM-P124 with human MMP-11 showed a 25-fold increase of affinity (k(cat)/K(m) = 9.16 × 10(3) m(-1) s(-1), K(m) = 8 μm) compared with previously published substrates. Incubation of pancreatic adenocarcinoma cell line MIA PaCa-2 and mamma adenocarcinoma cell line MCF-7 with the substrate SM-P124 (5 μm) indicated intra- and extracellular MMP-11 activity. A negative control cell line (Jurkat) showed no fluorescent signal either intra- or extracellularly. Negative control FRET substrate SM-P123 produced only insignificant extracellular fluorescence without any intracellular fluorescence. SM-P124 therefore enabled intra- and extracellular tracking of MMP-11-overexpressing cancers such as pancreatic and breast adenocarcinoma and might contribute to the understanding of the activation pathways leading to MMP-11-mediated invasive processes.
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Affiliation(s)
- B Sina Meyer
- Department of Organic Chemistry, Freie Universität Berlin, Berlin 14195, Germany
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26
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Lee YJ, Lee SH, Youn YS, Choi JY, Song KS, Cho MS, Kang JL. Preventing cleavage of Mer promotes efferocytosis and suppresses acute lung injury in bleomycin treated mice. Toxicol Appl Pharmacol 2012; 263:61-72. [PMID: 22687607 DOI: 10.1016/j.taap.2012.05.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/01/2012] [Accepted: 05/31/2012] [Indexed: 12/31/2022]
Abstract
Mer receptor tyrosine kinase (Mer) regulates macrophage activation and promotes apoptotic cell clearance. Mer activation is regulated through proteolytic cleavage of the extracellular domain. To determine if membrane-bound Mer is cleaved during bleomycin-induced lung injury, and, if so, how preventing the cleavage of Mer enhances apoptotic cell uptake and down-regulates pulmonary immune responses. During bleomycin-induced acute lung injury in mice, membrane-bound Mer expression decreased, but production of soluble Mer and activity as well as expression of disintegrin and metalloproteinase 17 (ADAM17) were enhanced . Treatment with the ADAM inhibitor TAPI-0 restored Mer expression and diminished soluble Mer production. Furthermore, TAPI-0 increased Mer activation in alveolar macrophages and lung tissue resulting in enhanced apoptotic cell clearance in vivo and ex vivo by alveolar macrophages. Suppression of bleomycin-induced pro-inflammatory mediators, but enhancement of hepatocyte growth factor induction were seen after TAPI-0 treatment. Additional bleomycin-induced inflammatory responses reduced by TAPI-0 treatment included inflammatory cell recruitment into the lungs, levels of total protein and lactate dehydrogenase activity in bronchoalveolar lavage fluid, as well as caspase-3 and caspase-9 activity and alveolar epithelial cell apoptosis in lung tissue. Importantly, the effects of TAPI-0 on bleomycin-induced inflammation and apoptosis were reversed by coadministration of specific Mer-neutralizing antibodies. These findings suggest that restored membrane-bound Mer expression by TAPI-0 treatment may help resolve lung inflammation and apoptosis after bleomycin treatment.
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Affiliation(s)
- Ye-Ji Lee
- Department of Physiology, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
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27
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Yasir M, Pachikara ND, Bao X, Pan Z, Fan H. Regulation of chlamydial infection by host autophagy and vacuolar ATPase-bearing organelles. Infect Immun 2011; 79:4019-28. [PMID: 21807906 PMCID: PMC3187247 DOI: 10.1128/iai.05308-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 07/20/2011] [Indexed: 11/20/2022] Open
Abstract
As arguably the most successful parasite, Chlamydia is an obligate intracellular bacterium replicating inside a vacuole of eukaryotic host cells. The chlamydial vacuole does not fuse with the defense cell organelle lysosome. We previously showed that chlamydial infection increases markers of autophagy, an innate antimicrobial activity requiring lysosomal function. However, the work presented here demonstrates that p62, an autophagy protein that is degraded in lysosomes, either remained unchanged or increased in chlamydia-infected human epithelial, mouse fibroblast, and mouse macrophage cell lines. In addition, the activities of three lysosomal enzymes analyzed were diminished in chlamydia-infected macrophages. Bafilomycin A1 (BafA), a specific inhibitor of vacuolar ATPase (vATPase) required for lysosomal function, increased the growth of the human pathogen Chlamydia trachomatis (L2) in wild-type murine fibroblasts and macrophages but inhibited growth in the autophagy-deficient ATG5(-/-) fibroblasts. BafA exhibited only slight inhibition or no effect on L2 growth in multiple human genital epithelial cell lines. In contrast to L2, the mouse pathogen Chlamydia muridarum (MoPn) was consistently inhibited by BafA in all cell lines examined, regardless of species origin and autophagy status. Finally, L2 but not MoPn grew more efficiently in the ATG5(-/-) cells than in wild-type cells. These results suggest that there are two types of vATPase-bearing organelles that regulate chlamydial infection: one supports chlamydial infection, while the other plays a defensive role through autophagy when cells are artificially infected with certain chlamydiae that have not been adapted to the host species.
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Affiliation(s)
| | | | | | - Zui Pan
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, New Jersey 08854
| | - Huizhou Fan
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, New Jersey 08854
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28
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Bao X, Pachikara ND, Oey CB, Balakrishnan A, Westblade LF, Tan M, Chase T, Nickels BE, Fan H. Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis. MICROBIOLOGY-SGM 2011; 157:2569-2581. [PMID: 21719536 PMCID: PMC3352175 DOI: 10.1099/mic.0.049668-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chlamydia trachomatis, an obligate intracellular bacterium, is a highly prevalent human pathogen. Hydroxamic-acid-based matrix metalloprotease inhibitors can effectively inhibit the pathogen both in vitro and in vivo, and have exhibited therapeutic potential. Here, we provide genome sequencing data indicating that peptide deformylase (PDF) is the sole target of the inhibitors in this organism. We further report molecular mechanisms that control chlamydial PDF (cPDF) expression and inhibition efficiency. In particular, we identify the σ66-dependent promoter that controls cPDF gene expression and demonstrate that point mutations in this promoter lead to resistance by increasing cPDF transcription. Furthermore, we show that substitution of two amino acids near the active site of the enzyme alters enzyme kinetics and protein stability.
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Affiliation(s)
- Xiaofeng Bao
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
| | - Niseema D Pachikara
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
| | - Christopher B Oey
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
| | - Amit Balakrishnan
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
| | - Lars F Westblade
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ming Tan
- Department of Microbiology and Molecular Genetics, and Department of Medicine, University of California, Irvine, CA 92697, USA
| | - Theodore Chase
- Department of Biochemistry and Microbiology, School of Environmental and Biological Science, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huizhou Fan
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
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29
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Oey CB, Bao X, Lewis C, Kerrigan JE, Fan H. High tolerance to mutations in a Chlamydia trachomatis peptide deformylase loop. World J Biol Chem 2011; 2:90-7. [PMID: 21666811 PMCID: PMC3110899 DOI: 10.4331/wjbc.v2.i5.90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 04/27/2011] [Accepted: 05/04/2011] [Indexed: 02/05/2023] Open
Abstract
AIM: To determine if and how a loop region in the peptide deformylase (PDF) of Chlamydia trachomatis regulates enzyme function.
METHODS: Molecular dynamics simulation was used to study a structural model of the chlamydial PDF (cPDF) and predict the temperature factor per residue for the protein backbone atoms. Site-directed mutagenesis was performed to construct cPDF variants. Catalytic properties of the resulting variants were determined by an enzyme assay using formyl-Met-Ala-Ser as a substrate.
RESULTS: In silico analysis predicted a significant increase in atomic motion in the DGELV sequence (residues 68-72) of a loop region in a cPDF mutant, which is resistant to PDF inhibitors due to two amino acid substitutions near the active site, as compared to wild-type cPDF. The D68R and D68R/E70R cPDF variants demonstrated significantly increased catalytic efficiency. The E70R mutant showed only slightly decreased efficiency. Although deletion of residues 68-72 resulted in a nearly threefold loss in substrate binding, this deficiency was compensated for by increased catalytic efficiency.
CONCLUSION: Movement of the DGELV loop region is involved in a rate-limiting conformational change of the enzyme during catalysis. However, there is no stringent sequence requirement for this region for cPDF enzyme activity.
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Affiliation(s)
- Christopher B Oey
- Christopher B Oey, Xiaofeng Bao, Christal Lewis, Huizhou Fan, Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, United States
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30
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Che X, Hu J, Wang L, Zhu Z, Xu Q, Lv J, Fu Z, Sun Y, Sun J, Lin G, Lu R, Yao Z. Expression, purification, and activity assay of peptide deformylase from Escherichia coli and Staphylococcus aureus. Mol Cell Biochem 2011; 357:47-54. [PMID: 21603885 DOI: 10.1007/s11010-011-0874-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 05/06/2011] [Indexed: 10/18/2022]
Abstract
Peptide deformylase (PDF) is considered an attractive target for screening novel antibiotics. The PDF from Escherichia coli and Staphylococcus aureus are representative of the gram-negative species type of PDF (type I PDF) and the gram-positive species type of PDF (type II PDF), respectively. They could be used for screening broad-spectrum antibiotics. Herein, we cloned the def gene by PCR, inserted it into plasmid pET-22b-def, and transformed the plasmid into E. coli BL21 (DE3) cells, then the cells were induced by IPTG to express PDF. E. coli Ni(2+)-PDF was extracted and purified by ion-exchange chromatography and gel filtration chromatography. S. aureus PDFs were extracted and purified using the MagExtractor kit. The nickel form of S. aureus PDF was obtained by adding NiCl(2) to all reagents used for purification. Iron-enriched S. aureus PDF was obtained by adding FeCl(3) to the growth medium for E. coli BL21 (DE3) cells and adding FeCl(3) and catalase to all reagents used for purification. The activities of PDFs were analyzed, compared, and grouped according to the experimental conditions that produced optimal activity, and we used actinonin as an inhibitor of PDF and calculated the IC(50) value. We obtained high expression of E. coli and S. aureus PDF with high activity and stability. The function of PDFs was inhibited by actinonin in a dose-dependent manner. Results may be helpful for future mechanistic investigations of PDF as well as high-throughput screening for other PDF inhibitors.
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Affiliation(s)
- Xuchun Che
- Department of Immunology, Tianjin Medical University, Tianjin 300070, China
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31
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Kalesh KA, Shi H, Ge J, Yao SQ. The use of click chemistry in the emerging field of catalomics. Org Biomol Chem 2010; 8:1749-62. [DOI: 10.1039/b923331h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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32
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Fmt bypass in Pseudomonas aeruginosa causes induction of MexXY efflux pump expression. Antimicrob Agents Chemother 2009; 53:5015-21. [PMID: 19786597 DOI: 10.1128/aac.00253-09] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intrinsic resistance of P. aeruginosa PAO1 to the peptide deformylase inhibitor (PDF-I) LBM415 was mediated by the MexAB-OprM and MexXY-OprM efflux pumps, the latter of which was strongly induced by LBM415. Single-step exposure of PAO1 deleted for mexAB-oprM (therefore lacking both MexAB-OprM and MexXY-OprM functions) to PDF-Is selected for nfxB mutants, which express the MexCD-OprJ efflux pump, indicating that these compounds are also substrates for this pump. Selection of resistant mutants by use of levels of LBM415 greater than that accommodated by efflux yielded two additional groups of mutations, in the methionyl-tRNA(fmet) formyltransferase (fmt) and folD genes. Both mechanisms are known to impose an in vitro growth deficit (also observed here), presumably due to impairment of protein synthesis. We surmised that this inherent impairment of protein synthesis would upregulate expression of mexXY in a fashion similar to upregulation by LBM415 or by ribosome inhibitory compounds. Transcriptional profiling and/or mexX::lux promoter fusion analysis revealed that fmt and folD mutants were strongly upregulated for mexXY and another gene known to be required for upregulation of the pump, PA5471. Complementation of the fmt mutation in trans reversed this constitutive expression. This supports the notion that MexXY has a natural physiological function responding to impairment of ribosome function or protein synthesis and that fmt mutation (Fmt bypass) and folD mutation generate the intracellular mexXY-inducing signal.
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33
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Puri AW, Bogyo M. Using small molecules to dissect mechanisms of microbial pathogenesis. ACS Chem Biol 2009; 4:603-16. [PMID: 19606820 DOI: 10.1021/cb9001409] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the ways in which pathogens invade and neutralize their hosts is of great interest from both an academic and a clinical perspective. However, in many cases genetic tools are unavailable or insufficient to fully characterize the detailed mechanisms of pathogenesis. Small molecule approaches are particularly powerful due to their ability to modulate specific biological functions in a highly controlled manner and their potential to broadly target conserved processes across species. Recently, two approaches that make use of small molecules, activity-based protein profiling and high-throughput phenotypic screening, have begun to find applications in the study of pathways involved in pathogenesis. In this Review we highlight ways in which these techniques have been applied to examine bacterial and parasitic pathogenesis and discuss possible ways in which these efforts can be expanded in the near future.
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Affiliation(s)
| | - Matthew Bogyo
- Chemical and Systems Biology
- Pathology
- Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, California 94305
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34
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Yang ZR. Predict prokaryotic proteins through detecting N-formylmethionine residues in protein sequences using support vector machine. Biosystems 2009; 97:141-5. [PMID: 19505530 DOI: 10.1016/j.biosystems.2009.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 05/18/2009] [Accepted: 05/26/2009] [Indexed: 12/19/2022]
Abstract
Identifying prokaryotes in silico is commonly based on DNA sequences. In experiments where DNA sequences may not be immediately available, we need to have a different approach to detect prokaryotes based on RNA or protein sequences. N-formylmethionine (fMet) is known as a typical characteristic of prokaryotes. A web tool has been implemented here for predicting prokaryotes through detecting the N-formylmethionine residues in protein sequences. The predictor is constructed using support vector machine. An online predictor has been implemented using Python. The implemented predictor is able to achieve the total prediction accuracy 80% with the specificity 80% and the sensitivity 81%.
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Affiliation(s)
- Zheng Rong Yang
- School of Biosciences, University of Exeter, Hatherly Building, Exeter, UK.
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35
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Pachikara N, Zhang H, Pan Z, Jin S, Fan H. Productive Chlamydia trachomatis lymphogranuloma venereum 434 infection in cells with augmented or inactivated autophagic activities. FEMS Microbiol Lett 2009; 292:240-9. [PMID: 19187200 DOI: 10.1111/j.1574-6968.2009.01494.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Autophagy, a eukaryotic cellular activity leading to the degradation of cellular components, serves as a defense mechanism against facultative intracellular bacteria as well as a growth niche for the obligate intracellular bacterium Coxiella burnetii. We here demonstrate that the obligate intracellular bacterial pathogen Chlamydia trachomatis lymphogranuloma venereum strongly induced autophagy in the middle of the chlamydial developmental cycle (24 h after infection), a time point with maximal level of chlamydial replication, but not during the early stages with low overall chlamydial metabolism (before 8 h). No autophagy induction was evident in cells exposed to heat- and UV-inactivated elementary bodies (EBs, the infectious form of Chlamydia) or to inocula from which EBs had been removed before inoculation. Blocking chlamydial development with chloramphenicol also prevented autophagy induction in cells infected with infectious EBs. It appears that autophagy is activated primarily in response to the metabolic stress consequent to chlamydial replication. However, autophagy-defective ATG5(-/-) cells supported chlamydial development as efficiently as autophagy-proficient ATG5(+/+) cells.
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Affiliation(s)
- Niseema Pachikara
- Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
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36
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Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem 2008; 77:383-414. [PMID: 18366325 DOI: 10.1146/annurev.biochem.75.101304.124125] [Citation(s) in RCA: 933] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequencing projects have provided researchers with a complete inventory of the predicted proteins produced by eukaryotic and prokaryotic organisms. Assignment of functions to these proteins represents one of the principal challenges for the field of proteomics. Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomic strategy to characterize enzyme function directly in native biological systems on a global scale. Here, we review the basic technology of ABPP, the enzyme classes addressable by this method, and the biological discoveries attributable to its application.
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Affiliation(s)
- Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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37
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Jacobsen FE, Lewis JA, Cohen SM. The design of inhibitors for medicinally relevant metalloproteins. ChemMedChem 2008; 2:152-71. [PMID: 17163561 DOI: 10.1002/cmdc.200600204] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A number of metalloproteins are important medicinal targets for conditions ranging from pathogenic infections to cancer. Many but not all of these metalloproteins contain a zinc(II) ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In this review several metalloproteins of interest are discussed, including matrix metalloproteinases (MMPs), histone deacetylases (HDACs), anthrax lethal factor (LF), and others. Different strategies that have been employed to design effective inhibitors against these proteins are described, with an effort to highlight the strengths and drawbacks of each approach. An emphasis is placed on examining the bioinorganic chemistry of these metal active sites and how a better understanding of the coordination chemistry in these systems may lead to improved inhibitors. It is hoped that this review will help inspire medicinal, biological, and inorganic chemists to tackle this important problem by considering all aspects of metalloprotein inhibitor design.
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Affiliation(s)
- Faith E Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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38
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Antczak C, Radu C, Djaballah H. A profiling platform for the identification of selective metalloprotease inhibitors. ACTA ACUST UNITED AC 2008; 13:285-94. [PMID: 18349423 DOI: 10.1177/1087057108315877] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although proteases represent an estimated 5% to 10% of potential drug targets, inhibitors for metalloproteases (MPs) account for only a small proportion of all approved drugs, failures of which have typically been associated with lack of selectivity. In this study, the authors describe a novel and universal binding assay based on an actinonin derivative and show its binding activities for several MPs and its lack of activity toward all the non-MPs tested. This newly developed assay would allow for the rapid screening for inhibitors of a given MP and for the selectivity profiling of the resulting hits. The assay has successfully enabled for the first time simultaneous profiling of 8 well-known inhibitors against a panel of selected MPs. Previously published activities for these inhibitors were confirmed, and the authors have also discovered new molecular targets for some of them. The authors conclude that their profiling platform provides a generic assay solution for the identification of novel metalloprotease inhibitors as well as their selectivity profiling using a simple and homogeneous assay.
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Affiliation(s)
- Christophe Antczak
- High Throughput Screening Core Facility Molecular Pharmacology and Chemistry Program Memorial Sloan-Kettering Cancer Center 1275 York Avenue, New York 10065, USA
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39
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Min BR, Lee YM, Park JS, Choi WI, Kwon KY. Roles of Matrix Metalloproteinases on Intracellular Staphylococcus aureus Growth in Bronchial Epithelial Cell. Tuberc Respir Dis (Seoul) 2008. [DOI: 10.4046/trd.2008.64.1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Bo Ram Min
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Young Mi Lee
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Jae Seok Park
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Won-Il Choi
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Kun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
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40
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Paland N, Böhme L, Gurumurthy RK, Mäurer A, Szczepek AJ, Rudel T. Reduced display of tumor necrosis factor receptor I at the host cell surface supports infection with Chlamydia trachomatis. J Biol Chem 2007; 283:6438-48. [PMID: 18167350 DOI: 10.1074/jbc.m708422200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The obligate intracellular human pathogenic bacterium Chlamydia trachomatis has evolved multiple mechanisms to circumvent the host immune system. Infected cells exhibit a profound resistance to the induction of apoptosis and down-regulate the expression of major histocompatibility complex class I and class II molecules to evade the cytotoxic effect of effector immune cells. Here we demonstrate the down-regulation of tumor necrosis factor receptor 1 (TNFR1) on the surface of infected cells. Interestingly, other members of the TNFR family such as TNFR2 and CD95 (Fas/Apo-1) were not modulated during infection, suggesting a selective mechanism underlying surface reduction of TNFR1. The observed effect was not due to reduced expression since the overall amount of TNFR1 protein was increased in infected cells. TNFR1 accumulated at the chlamydial inclusion and was shed by the infected cell into the culture supernatant. Receptor shedding depended on the infection-induced activation of the MEK-ERK pathway and the metalloproteinase TACE (TNFalpha converting enzyme). Our results point to a new function of TNFR1 modulation by C. trachomatis in controlling inflammatory signals during infection.
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Affiliation(s)
- Nicole Paland
- Research Group for Molecular Infection and Tumor Biology, Max Planck Institute for Infection Biology, Charitéplatz 1, Berlin, Germany
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41
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Rottlerin inhibits chlamydial intracellular growth and blocks chlamydial acquisition of sphingolipids from host cells. Appl Environ Microbiol 2007; 74:1243-9. [PMID: 18083882 DOI: 10.1128/aem.02151-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report that rottlerin, a plant-derived compound known to inhibit various mammalian kinases, profoundly inhibited chlamydial growth in cell culture with a minimal inhibition concentration of 1 microM. The inhibition was effective even when rottlerin was added as late as the middle stage of chlamydial infection cycle, against multiple Chlamydia species, and in different host cell lines. Pretreatment of host cells with rottlerin prior to infection also blocked chlamydial growth, suggesting that rottlerin targets host factors. Moreover, rottlerin did not alter the chlamydial infection rate and did not directly target chlamydial protein synthesis and secretion. The rottlerin-mediated inhibition of chlamydial replication and inclusion expansion correlated well with the rottlerin-induced blockade of host cell sphingolipid trafficking from the Golgi apparatus into chlamydial inclusions. These studies not only allowed us to identify a novel antimicrobial activity for rottlerin but also allowed us to uncover a potential mechanism for rottlerin inhibition of chlamydial growth.
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42
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Salisbury C, Cravatt B. Click Chemistry-Led Advances in High Content Functional Proteomics. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200740090] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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43
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Balakrishnan A, Wang L, Li X, Ohman-Strickland P, Malatesta P, Fan H. Inhibition of chlamydial infection in the genital tract of female mice by topical application of a peptide deformylase inhibitor. Microbiol Res 2007; 164:338-46. [PMID: 17936604 DOI: 10.1016/j.micres.2007.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 03/28/2007] [Accepted: 05/08/2007] [Indexed: 11/15/2022]
Abstract
Chlamydia trachomatis is an obligate intracellular bacterium responsible for a number of health problems, including sexually transmitted infection in humans. We recently discovered that C. trachomatis infection in cell culture is highly susceptible to inhibitors of peptide deformylase, an enzyme that removes the N-formyl group from newly synthesized polypeptides. In this study, one of the deformylase inhibitors, GM6001, was tested for potential antichlamydial activity using a murine genital C. muridarum infection model. Topical application of GM6001 significantly reduced C. muridarum loading in BALB/c mice that were vaginally infected with the pathogen. In striking contrast, growth of the probiotic Lactobacillus plantarum is strongly resistant to the PDF inhibitor. GM6001 demonstrated no detectable toxicity against host cells. On the basis of these data and our previous observations, we conclude that further evaluation of PDF inhibitors for prevention and treatment of sexually transmitted chlamydial infection is warranted.
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Affiliation(s)
- Amit Balakrishnan
- University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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Dean CR, Narayan S, Richards J, Daigle DM, Esterow S, Leeds JA, Kamp H, Puyang X, Wiedmann B, Mueller D, Voshol H, van Oostrum J, Wall D, Koehn J, Dzink-Fox J, Ryder NS. Reduced susceptibility of Haemophilus influenzae to the peptide deformylase inhibitor LBM415 can result from target protein overexpression due to amplified chromosomal def gene copy number. Antimicrob Agents Chemother 2007; 51:1004-10. [PMID: 17220413 PMCID: PMC1803149 DOI: 10.1128/aac.01103-06] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous genetic analysis of Haemophilus influenzae revealed two mechanisms associated with decreased susceptibility to the novel peptide deformylase inhibitor LBM415: AcrAB-TolC-mediated efflux and Fmt bypass, resulting from mutations in the pump repressor gene acrR and in the fmt gene, respectively. We have isolated an additional mutant, CDS23 (LBM415 MIC, 64 microg/ml versus 4 microg/ml against the parent strain NB65044) that lacks mutations in the acrR or fmt structural genes or in the gene encoding Def, the intracellular target of LBM415. Western immunoblot analysis, two-dimensional gel electrophoresis, and tryptic digestion combined with mass spectrometric identification showed that the Def protein was highly overexpressed in the mutant strain. Consistent with this, real-time reverse transcription-PCR revealed a significant increase in def transcript titer. No mutations were found in the region upstream of def that might account for altered expression; however, pulsed-field gel electrophoresis suggested that a genetic rearrangement of the region containing def had occurred. Using a combination of PCR, sequencing, and Southern blot analyses, it was determined that the def gene had undergone copy number amplification, explaining the high level of target protein expression. Inactivation of the AcrAB-TolC efflux pump in this mutant increased susceptibility 16-fold, highlighting the role of efflux in exacerbating the overall reduced susceptibility resulting from target overexpression.
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Affiliation(s)
- Charles R Dean
- Infectious Diseases, Novartis Institutes for BioMedical Research, 500 Technology Square, Cambridge, MA 02139, USA.
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Imtiaz MT, Schripsema JH, Sigar IM, Kasimos JN, Ramsey KH. Inhibition of matrix metalloproteinases protects mice from ascending infection and chronic disease manifestations resulting from urogenital Chlamydia muridarum infection. Infect Immun 2006; 74:5513-21. [PMID: 16988226 PMCID: PMC1594914 DOI: 10.1128/iai.00730-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 06/27/2006] [Accepted: 07/20/2006] [Indexed: 01/18/2023] Open
Abstract
Matrix metalloproteinases (MMP) are a family of host-derived enzymes involved in the turnover of extracellular matrix molecules. We have previously reported enhanced expression of matrix metalloproteinases in Chlamydia muridarum urogenital tract infection of female mice. Kinetics and patterns of MMP expression as well as enhanced expression in susceptible strains of mice in the prior study implied a role for MMP in pathogenesis. To explore this further, we infected a susceptible strain of mice (C3H/HeN) with C. muridarum and treated two groups of mice with either one of two chemical inhibitors of MMP (MMPi; captopril and a chemically modified tetracycline) and reserved infected sham-treated mice as controls. Neither of the treatments affected shedding of viable chlamydiae from the lower urogenital tract, but the administration of either MMPi protected mice from the formation of hydrosalpinx-a surrogate marker of oviduct occlusion and infertility. Interestingly, the mechanism of protection for mice treated with chemically modified tetracycline 3, appeared to be related to prevention of ascending upper genital tract infection. These results imply that MMP are involved in pathogenesis of chlamydial infection in this model by mediating ascension of the infection into the upper genital tract.
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Affiliation(s)
- Muhammad T Imtiaz
- Department of Microbiology and Immunology, Chicago College of Osteopathic Medicine, Midwestern University, 555 31st St., Downers Grove, IL 60516, USA.
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