1
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Pavel FBA, Palmer GE, Hevener KE. Biophysical library screening using a Thermo-FMN assay to identify and characterize Clostridioides difficile FabK inhibitors. Biochem Biophys Res Commun 2024; 705:149740. [PMID: 38458032 DOI: 10.1016/j.bbrc.2024.149740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
Clostridioides difficile, a gram-positive anaerobic bacterium, is one of the most frequent causes of nosocomial infections. C. difficile infection (CDI) results in almost a half a million infections and approximately 30,000 deaths in the U.S. each year. Broad-spectrum antibacterial use is a strong risk factor for development of recurring CDI. There is a critical need for narrow-spectrum antibacterials with activity limited to C. difficile. The C. difficile enoyl-acyl carrier protein (ACP) reductase II enzyme (CdFabK), an essential and rate-limiting enzyme in the organism's fatty acid biosynthesis pathway (FAS-2), is an attractive target for narrow-spectrum CDI therapeutics as it is not present in many of the non-pathogenic gut organisms. We have previously characterized inhibitors of the CdFabK enzyme with narrow-spectrum anti-difficile activity and favorable in vivo efficacy, ADME, and low dysbiosis. To expand our knowledge of the structural requirements for CdFabK inhibition, we seek to identify new inhibitors with novel chemical scaffolds. Herein we present the optimization of a thermo-FMN biophysical assay based on the principles of differential scanning fluorimetry, or thermal shift, which leverages the fluorescence signal of the FabK enzyme's FMN prosthetic group. The optimized assay was validated by pilot testing a 10K diversity-based chemical library and novel scaffold hit compounds were identified and biochemically characterized. Additionally, we show that the thermo-FMN assay can be used to determine the thermodynamic dissociation constant, Kd, of CdFabK inhibitors.
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Affiliation(s)
- Fahad Bin Aziz Pavel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Glen E Palmer
- Department of Clinical Pharmacy and Translational Sciences, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA.
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2
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Rutherford JT, Avad K, Dureja C, Norseeda K, Gc B, Wu C, Sun D, Hevener KE, Hurdle JG. Evaluation of Fusobacterium nucleatum Enoyl-ACP Reductase (FabK) as a Narrow-Spectrum Drug Target. ACS Infect Dis 2024. [PMID: 38597503 DOI: 10.1021/acsinfecdis.3c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Fusobacterium nucleatum, a pathobiont inhabiting the oral cavity, contributes to opportunistic diseases, such as periodontal diseases and gastrointestinal cancers, which involve microbiota imbalance. Broad-spectrum antimicrobial agents, while effective against F. nucleatum infections, can exacerbate dysbiosis. This necessitates the discovery of more targeted narrow-spectrum antimicrobial agents. We therefore investigated the potential for the fusobacterial enoyl-ACP reductase II (ENR II) isoenzyme FnFabK (C4N14_ 04250) as a narrow-spectrum drug target. ENRs catalyze the rate-limiting step in the bacterial fatty acid synthesis pathway. Bioinformatics revealed that of the four distinct bacterial ENR isoforms, F. nucleatum specifically encodes FnFabK. Genetic studies revealed that fabK was indispensable for F. nucleatum growth, as the gene could not be deleted, and silencing of its mRNA inhibited growth under the test conditions. Remarkably, exogenous fatty acids failed to rescue growth inhibition caused by the silencing of fabK. Screening of synthetic phenylimidazole analogues of a known FabK inhibitor identified an inhibitor (i.e., 681) of FnFabK enzymatic activity and F. nucleatum growth, with an IC50 of 2.1 μM (1.0 μg/mL) and a MIC of 0.4 μg/mL, respectively. Exogenous fatty acids did not attenuate the activity of 681 against F. nucleatum. Furthermore, FnFabK was confirmed as the intracellular target of 681 based on the overexpression of FnFabK shifting MICs and 681-resistant mutants having amino acid substitutions in FnFabK or mutations in other genetic loci affecting fatty acid biosynthesis. 681 had minimal activity against a range of commensal flora, and it was less active against streptococci in physiologic fatty acids. Taken together, FnFabK is an essential enzyme that is amenable to drug targeting for the discovery and development of narrow-spectrum antimicrobial agents.
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Affiliation(s)
- Jacob T Rutherford
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Kristiana Avad
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Krissada Norseeda
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Bibek Gc
- Department of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
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3
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Dureja C, Rutherford JT, Pavel FB, Norseeda K, Prah I, Sun D, Hevener KE, Hurdle JG. In vivo evaluation of Clostridioides difficile enoyl-ACP reductase II (FabK) inhibition by phenylimidazole unveils a promising narrow-spectrum antimicrobial strategy. Antimicrob Agents Chemother 2024; 68:e0122223. [PMID: 38265216 PMCID: PMC10916379 DOI: 10.1128/aac.01222-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Clostridioides difficile infection (CDI) is a leading cause of hospital-acquired diarrhea, which often stems from disruption of the gut microbiota by broad-spectrum antibiotics. The increasing prevalence of antibiotic-resistant C. difficile strains, combined with disappointing clinical trial results for recent antibiotic candidates, underscores the urgent need for novel CDI antibiotics. To this end, we investigated C. difficile enoyl ACP reductase (CdFabK), a crucial enzyme in de novo fatty acid synthesis, as a drug target for microbiome-sparing antibiotics. To test this concept, we evaluated the efficacy and in vivo spectrum of activity of the phenylimidazole analog 296, which is validated to inhibit intracellular CdFabK. Against major CDI-associated ribotypes 296 had an Minimum inhibitory concentration (MIC90) of 2 µg/mL, which was comparable to vancomycin (1 µg/mL), a standard of care antibiotic. In addition, 296 achieved high colonic concentrations and displayed dosed-dependent efficacy in mice with colitis CDI. Mice that were given 296 retained colonization resistance to C. difficile and had microbiomes that resembled the untreated mice. Conversely, both vancomycin and fidaxomicin induced significant changes to mice microbiomes, in a manner consistent with prior reports. CdFabK, therefore, represents a potential target for microbiome-sparing CDI antibiotics, with phenylimidazoles providing a good chemical starting point for designing such agents.
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Affiliation(s)
- Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Jacob T. Rutherford
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Fahad B.A. Pavel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Krissada Norseeda
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii, USA
| | - Isaac Prah
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii, USA
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Julian G. Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
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4
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Dureja C, Rutherford JT, Pavel FBA, Norseeda K, Prah I, Sun D, Hevener KE, Hurdle JG. In vivo evaluation of Clostridioides difficile enoyl-ACP reductase II (FabK) Inhibition by phenylimidazole unveils a promising narrow-spectrum antimicrobial strategy. bioRxiv 2023:2023.09.22.559005. [PMID: 37790427 PMCID: PMC10543012 DOI: 10.1101/2023.09.22.559005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Clostridioides difficile infection (CDI) is a leading cause of hospital-acquired diarrhea, which often stem from disruption of the gut microbiota by broad-spectrum antibiotics. The increasing prevalence of antibiotic-resistant C. difficile strains, combined with disappointing clinical trials results for recent antibiotic candidates, underscore the urgent need for novel CDI antibiotics. To this end, we investigated C. difficile enoyl ACP reductase (CdFabK), a crucial enzyme in de novo fatty acid synthesis, as a drug target for microbiome-sparing antibiotics. To test this concept, we evaluated the efficacy and in vivo spectrum of activity of the phenylimidazole analog 296, which is validated to inhibit intracellular CdFabK. Against major CDI-associated ribotypes 296 had an MIC90 of 2 μg/ml, which was comparable to vancomycin (1 μg/ml), a standard of care antibiotic. In addition, 296 achieved high colonic concentrations and displayed dosed-dependent efficacy in mice with colitis CDI. Mice that were given 296 retained colonization resistance to C. difficile and had microbiomes that resembled the untreated mice. Conversely, both vancomycin and fidaxomicin induced significant changes to mice microbiomes, in a manner consistent with prior reports. CdFabK therefore represents a potential target for microbiome-sparing CDI antibiotics, with phenylimidazoles providing a good chemical starting point for designing such agents.
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Affiliation(s)
- Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Blvd., Houston, Texas 77030, USA
| | - Jacob T. Rutherford
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Blvd., Houston, Texas 77030, USA
| | - Fahad B. A. Pavel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38105, USA
| | - Krissada Norseeda
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 200 W. Kawili Street, Hilo, Hawaii 96720, USA
| | - Isaac Prah
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Blvd., Houston, Texas 77030, USA
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 200 W. Kawili Street, Hilo, Hawaii 96720, USA
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38105, USA
| | - Julian G. Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Blvd., Houston, Texas 77030, USA
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5
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Olaitan AO, Dureja C, Youngblom MA, Topf MA, Shen WJ, Gonzales-Luna AJ, Deshpande A, Hevener KE, Freeman J, Wilcox MH, Palmer KL, Garey KW, Pepperell CS, Hurdle JG. Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile. Nat Commun 2023; 14:4130. [PMID: 37438331 DOI: 10.1038/s41467-023-39429-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/13/2023] [Indexed: 07/14/2023] Open
Abstract
Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests using molecularly intact heme. Here, we describe the mechanism underlying this trait. We find that most metronidazole-resistant C. difficile strains carry a T-to-G mutation (which we term PnimBG) in the promoter of gene nimB, resulting in constitutive transcription. Silencing or deleting nimB eliminates metronidazole resistance. NimB is related to Nim proteins that are known to confer resistance to nitroimidazoles. We show that NimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. Furthermore, occurrence of the PnimBG mutation is associated with a Thr82Ile substitution in DNA gyrase that confers fluoroquinolone resistance in epidemic strains. Our findings suggest that the pandemic of fluoroquinolone-resistant C. difficile occurring over the past few decades has also been characterized by widespread resistance to metronidazole.
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Affiliation(s)
- Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Madison A Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Madeline A Topf
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA.
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA.
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6
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Norseeda K, Bin Aziz Pavel F, Rutherford JT, Meer HN, Dureja C, Hurdle JG, Hevener KE, Sun D. Synthesis and evaluation of phenylimidazole FabK inhibitors as new Anti-C. Difficile agents. Bioorg Med Chem 2023; 88-89:117330. [PMID: 37224699 PMCID: PMC10834300 DOI: 10.1016/j.bmc.2023.117330] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
Previously, 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(5-(pyridin-2-ylthio)thiazol-2-yl)urea bearing a p-bromine substitution was shown to possess selective inhibitory activity against the Clostridioides difficile enoyl-acyl carrier protein (ACP) reductase II enzyme, FabK. Inhibition of CdFabK by this compound translated to promising antibacterial activity in the low micromolar range. In these studies, we sought to expand our knowledge of the SAR of the phenylimidazole CdFabK inhibitor series while improving the potency of the compounds. Three main series of compounds were synthesized and evaluated based on: 1) pyridine head group modifications including the replacement with a benzothiazole moiety, 2) linker explorations, and 3) phenylimidazole tail group modifications. Overall, improvement in the CdFabK inhibition was achieved, while maintaining the whole cell antibacterial activity. Specifically, compounds 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(5-((3-(trifluoromethyl)pyridin-2-yl)thio)thiazol-2-yl)urea, 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(6-(trifluoromethyl)benzo[d]thiazol-2-yl)urea, and 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(6-chlorobenzo[d]thiazol-2-yl)urea showed CdFabK inhibition (IC50 = 0.10 to 0.24 μM), a 5 to 10-fold improvement in biochemical activity relative to 1-((4-(4-bromophenyl)-1H-imidazol-2-yl)methyl)-3-(5-(pyridin-2-ylthio)thiazol-2-yl)urea, with anti-C. difficile activity ranging from 1.56 to 6.25 μg/mL. Detailed analysis of the expanded SAR, supported by computational analysis, is presented.
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Affiliation(s)
- Krissada Norseeda
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, United States
| | - Fahad Bin Aziz Pavel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Jacob T Rutherford
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
| | - Humna N Meer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States.
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI 96720, United States.
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7
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Mitachi K, Mingle D, Effah W, Sánchez‐Ruiz A, Hevener KE, Narayanan R, Clemons WM, Sarabia F, Kurosu M. Concise Synthesis of Tunicamycin V and Discovery of a Cytostatic DPAGT1 Inhibitor. Angew Chem Int Ed Engl 2022; 61:e202203225. [PMID: 35594368 PMCID: PMC9329268 DOI: 10.1002/anie.202203225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/11/2022]
Abstract
A short total synthesis of tunicamycin V (1), a non-selective phosphotransferase inhibitor, is achieved via a Büchner-Curtius-Schlotterbeck type reaction. Tunicamycin V can be synthesized in 15 chemical steps from D-galactal with 21 % overall yield. The established synthetic scheme is operationally very simple and flexible to introduce building blocks of interest. The inhibitory activity of one of the designed analogues 28 against human dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 (DPAGT1) is 12.5 times greater than 1. While tunicamycins are cytotoxic molecules with a low selectivity, the novel analogue 28 displays selective cytostatic activity against breast cancer cell lines including a triple-negative breast cancer.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
| | - David Mingle
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
| | - Wendy Effah
- Department of Medicine University of Tennessee Health Science Center 19 S. Manassas, Room 120 Memphis TN 38103 USA
| | - Antonio Sánchez‐Ruiz
- Faculty of Pharmacy Campus de Albacete Universidad de Castilla-La Mancha Avda. Dr. José María Sánchez Ibáñez S/N 02008 Albacete Spain
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
| | - Ramesh Narayanan
- Department of Medicine University of Tennessee Health Science Center 19 S. Manassas, Room 120 Memphis TN 38103 USA
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Francisco Sarabia
- Department of Organic Chemistry Faculty of Sciences Universidad de Málaga, Campus de Teatinos 29071 Málaga Spain
| | - Michio Kurosu
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
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8
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Mitachi K, Mingle D, Effah W, Sánchez-Ruiz A, Hevener KE, Narayanan R, Clemons WM, Sarabia F, Kurosu M. Concise Synthesis of Tunicamycin V and Discovery of a Cytostatic DPAGT1 Inhibitor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katsuhiko Mitachi
- The University of Tennessee Health Science Center College of Pharmacy Pharmacy 881 Madison AvenueROOM 557 38163 MEMPHS UNITED STATES
| | - David Mingle
- The University of Tennessee Health Science Center College of Pharmacy Pharmacy 881 MADISON AVE 38163 MEMPHS UNITED STATES
| | - Wendy Effah
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Medicine UNITED STATES
| | | | - Kirk E. Hevener
- UTHSC College of Pharmacy Memphis: The University of Tennessee Health Science Center College of Pharmacy Pharmacy UNITED STATES
| | - Ramesh Narayanan
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Medicine 19, S. Manassas 38013 Memphis UNITED STATES
| | - William M. Clemons
- Caltech: California Institute of Technology Chemistry and Chemical Engineering UNITED STATES
| | - Francisco Sarabia
- University of Malaga: Universidad de Malaga Organic Chemistry UNITED STATES
| | - Michio Kurosu
- UTHSC College of Pharmacy Memphis: The University of Tennessee Health Science Center College of Pharmacy Department of Pharmaceutical Sciences, College of Pharmacy 881 MADISON AVEROOM 557 38163 Memphis UNITED STATES
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9
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Lowes DJ, Miao J, Al-waqfi RA, Avad KA, Hevener KE, Peters BM. Identification of Dual-Target Compounds with Antifungal and Anti-NLRP3 Inflammasome Activity. ACS Infect Dis 2021; 7:2522-2535. [PMID: 34260210 DOI: 10.1021/acsinfecdis.1c00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Invasive and superficial infections caused by the Candida species result in significant global morbidity and mortality. As the pathogenicity of these organisms is intimately intertwined with host immune response, therapies to target both the fungus and host inflammation may be warranted. Structural similarities exist between established inhibitors of the NLRP3 inflammasome and those of fungal acetohydroxyacid synthase (AHAS). Therefore, we leveraged this information to conduct an in silico molecular docking screen to find novel polypharmacologic inhibitors of these targets that resulted in the identification of 12 candidate molecules. Of these, compound 10 significantly attenuated activation of the NLPR3 inflammasome by LPS + ATP, while also demonstrating growth inhibitory activity against C. albicans that was alleviated in the presence of exogenous branched chain amino acids, consistent with targeting of fungal AHAS. SAR studies delineated an essential molecular scaffold required for dual activity. Ultimately, 10 and its analog 10a resulted in IC50 (IL-1β release) and MIC50 (fungal growth) values with low μM potency against several Candida species. Collectively, this work demonstrates promising potential of dual-target approaches for improved management of fungal infections.
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Affiliation(s)
- David J Lowes
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Jian Miao
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Rand A Al-waqfi
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kristiana A. Avad
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Doctor of Pharmacy Program, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Brian M Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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10
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Shen WJ, Deshpande A, Hevener KE, Endres BT, Garey KW, Palmer KL, Hurdle JG. Constitutive expression of the cryptic vanGCd operon promotes vancomycin resistance in Clostridioides difficile clinical isolates. J Antimicrob Chemother 2021; 75:859-867. [PMID: 31873741 DOI: 10.1093/jac/dkz513] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/01/2019] [Accepted: 11/09/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To describe, for the first time (to the best of our knowledge), the genetic mechanisms of vancomycin resistance in clinical isolates of Clostridioides difficile ribotype 027. METHODS Clinical isolates and laboratory mutants were analysed: genomically to identify resistance mutations; by transcriptional analysis of vanGCd, the vancomycin resistance operon encoding lipid II d-alanine-d-serine that is less bound by vancomycin than native lipid II d-alanine-d-alanine; by imaging of vancomycin binding to cell walls; and for changes in vancomycin bactericidal activity and autolysis. RESULTS Vancomycin-resistant laboratory mutants and clinical isolates acquired mutations to the vanSR two-component system that regulates vanGCd. The substitutions impaired VanSR's function, resulting in constitutive transcription of vanGCd. Resistance was reversed by silencing vanG, encoding d-alanine-d-serine ligase in the vanGCd operon. In resistant cells, vancomycin was less bound to the cell wall septum, the site where vancomycin interacts with lipid II. Vancomycin's bactericidal activity was reduced against clinical isolates and laboratory mutants (64 and ≥1024 mg/L, respectively) compared with WT strains (4 mg/L). Truncation of the potassium transporter TrkA occurred in laboratory mutants, which were refractory to autolysis, accounting for their survival in high drug concentrations. CONCLUSIONS Ribotype 027 evolved first-step resistance to vancomycin by constitutively expressing vanGCd, which is otherwise silent. Experimental evolutions and bactericidal assays show that ribotype 027 can acquire mutations to drastically enhance its tolerance to vancomycin. Thus, further epidemiological studies are warranted to examine the extent to which vancomycin resistance impacts clinical outcomes and the potential for these strains to evolve higher-level resistance, which would be devastating.
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Affiliation(s)
- Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
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11
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Mugengana AK, Vita NA, Brown Gandt A, Moran K, Agyapong G, Sharma LK, Griffith EC, Liu J, Yang L, Gavrish E, Hevener KE, LaFleur MD, Lee RE. The Discovery and Development of Thienopyrimidines as Inhibitors of Helicobacter pylori That Act through Inhibition of the Respiratory Complex I. ACS Infect Dis 2021; 7:1044-1058. [PMID: 33471519 DOI: 10.1021/acsinfecdis.0c00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The successful treatment of Helicobacter pylori infections is becoming increasingly difficult due to the rise of resistance against current broad spectrum triple therapy regimens. In the search for narrow-spectrum agents against H. pylori, a high-throughput screen identified two structurally related thienopyrimidine compounds that selectively inhibited H. pylori over commensal members of the gut microbiota. To develop the structure-activity relationship (SAR) of the thienopyrimidines against H. pylori, this study employed four series of modifications in which systematic substitution to the thienopyrimidine core was explored and ultimately side-chain elements optimized from the two original hits were merged into lead compounds. During the development of this series, the mode of action studies identified H. pylori's respiratory complex I subunit NuoD as the target for lead thienopyrimidines. As this enzyme complex is uniquely essential for ATP synthesis in H. pylori, a homology model of the H. pylori NuoB-NuoD binding interface was generated to help rationalize the SAR and guide further development of the series. From these studies, lead compounds emerged with increased potency against H. pylori, improved safety indices, and a good overall pharmacokinetic profile with the exception of high protein binding and poor solubility. Although lead compounds in the series demonstrated efficacy in an ex vivo infection model, the compounds had no efficacy in a mouse model of H. pylori infection. Additional optimization of pharmacological properties of the series to increase solubility and free-drug levels at the sequestered sites of H. pylori infection would potentially result in a gain of in vivo efficacy. The thienopyrimidine series developed in this study demonstrates that NuoB-NuoD of the respiratory complex I can be targeted for development of novel narrow spectrum agents against H. pylori and that thienopyrimines can serve as the basis for future advancement of these studies.
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Affiliation(s)
- Alex K. Mugengana
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Nicole A. Vita
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | - Kevin Moran
- Arietis Pharma, Boston, Massachusetts 02118, United States
| | | | - Lalit K. Sharma
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
| | - Elizabeth C. Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
| | - Jiuyu Liu
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
| | | | - Kirk E. Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, MS#1000, Memphis, Tennessee 38105, United States
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12
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Uz Zaman KA, Wu X, Hu Z, Yoshida W, Hou S, Saito J, Avad KA, Hevener KE, Alumasa JN, Cao S. Antibacterial kaneoheoic acids A-F from a Hawaiian fungus Fusarium sp. FM701. Phytochemistry 2021; 181:112545. [PMID: 33217722 PMCID: PMC7869588 DOI: 10.1016/j.phytochem.2020.112545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 05/10/2023]
Abstract
Alarming rate of resistance to the existing antibiotics exhibits the importance of developing new antibiotic molecules from relatively under explored sources as well as implementing alternative approaches like antibiotic adjuvants. Six previously undescribed fungal polyketides, kaneoheoic acids A-F (1-6) were isolated from a fungal strain Fusarium sp. FM701 which was collected from a muddy sample of Hawaiian beach. The structures of these six compounds were elucidated by spectroscopic interpretation, including HRESIMS and NMR, and electronic circular dichroism (ECD) analysis. All six compounds that were inactive when tested alone showed significant antibacterial activity against Staphylococcus aureus and Bacillus subtilis, in the range of 10-80 μg/mL when assayed in combination with either chloramphenicol (half of the MIC, 1 μg/mL), an FDA approved antibiotic or disulfiram (6 μg/mL), an established antibiotic adjuvant that augmented the activity of antibiotics.
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Affiliation(s)
- Kh Ahammad Uz Zaman
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, 96720, United States
| | - Xiaohua Wu
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, 96720, United States
| | - Zhenquan Hu
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, People's Republic of China; School of Chemistry and Materials Science, University of Science and Technology of China, People's Republic of China
| | - Wesley Yoshida
- Department of Chemistry, University of Hawai'i at Manoa, Hawaii, United States
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), University of Hawai'i at Manoa, Honolulu, HI, 96822, United States
| | - Jennifer Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics (ASGPB), University of Hawai'i at Manoa, Honolulu, HI, 96822, United States
| | | | - Kirk E Hevener
- College of Pharmacy, University of Tennessee Health Science Center, United States
| | - John N Alumasa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, United States
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, 96720, United States; Cancer Biology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, Hawai'i, 96813, United States.
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13
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Wahrmund RD, Avad KA, Reeve SM, Jones JA, La T, Lee RE, Hevener KE. 1233. Identification of Novel Inhibitors of Clostridioides difficile Enoyl-Reductase II (FabK) by High-Throughput Virtual and Experimental Screening. Open Forum Infect Dis 2020. [PMCID: PMC7777309 DOI: 10.1093/ofid/ofaa439.1418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Clostridioides difficile is one of only three bacteria categorized as an ‘urgent’ drug-resistant threat by the CDC. This pathogen is responsible for nearly 500,000 hospital-acquired infections and 29,000 deaths per year at a cost of nearly $4.8 billion. There is a critical need for the identification of novel, anti-difficile agents with narrow-spectrum activity that can spare the human microbiome. We previously reported the essentiality of the FAS-II enzyme, enoyl-ACP reductase (FabK) in C. difficile, and the narrow-spectrum activity of a series of phenylimidazole inhibitors. We present here experimental and virtual compound screening studies that identified novel FabK inhibitors with sub-micromolar activity and follow-up SAR and structural studies.
Methods
Using a novel luminescence assay, 20K diverse compounds from the St. Jude drug-like and lead-like libraries were screened. In parallel, a ligand-based virtual screen was performed against 2.4 million lead- and drug-like compounds from commercial libraries. Hit compounds were confirmed using an orthogonal fluorescence-intensity assay and SAR studies were performed by testing commercially available hit analogs. The most potent inhibitor was advanced into co-crystallography structural studies.
Results
The compound screening campaigns resulted in the identification of several confirmed hit compounds with low to sub-micromolar activity and novel scaffolds relative to the known phenylimidazole inhibitors. Importantly, the first confirmed nanomolar inhibitor of C. difficile FabK was identified and validated with an IC50 of 0.35 μM. SAR studies of the hits along with a high-resolution co-crystal structure have allowed new insights into the key binding determinants and structural requirements for activity as well as the structural requirements for species specificity.
Conclusion
The C. difficile FabK enzyme offers a promising narrow-spectrum drug target that can potentially spare the human microbiome. The known activity of the phenylimidazole inhibitor series supports the druggability of this target. The newly discovered inhibitor class presented here further demonstrates the potential of FabK inhibition and will facilitate the development of clinically relevant, narrow-spectrum anti-difficile agents.
Disclosures
All Authors: No reported disclosures
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Affiliation(s)
| | - Kristiana A Avad
- University of Tennessee Health Science Center, Memphis, Tennessee
| | | | - Jesse A Jones
- University of Tennessee Health Science Center, Memphis, Tennessee
| | - Thao La
- University of Tennessee Health Science Center, Memphis, Tennessee
| | - Richard E Lee
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Kirk E Hevener
- University of Tennessee Health Science Center, Memphis, Tennessee
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14
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Mitachi K, Kansal RG, Hevener KE, Gillman CD, Hussain SM, Yun HG, Miranda-Carboni GA, Glazer ES, Clemons WM, Kurosu M. DPAGT1 Inhibitors of Capuramycin Analogues and Their Antimigratory Activities of Solid Tumors. J Med Chem 2020; 63:10855-10878. [PMID: 32886511 DOI: 10.1021/acs.jmedchem.0c00545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Capuramycin displays a narrow spectrum of antibacterial activity by targeting bacterial translocase I (MraY). In our program of development of new N-acetylglucosaminephosphotransferase1 (DPAGT1) inhibitors, we have identified that a capuramycin phenoxypiperidinylbenzylamide analogue (CPPB) inhibits DPAGT1 enzyme with an IC50 value of 200 nM. Despite a strong DPAGT1 inhibitory activity, CPPB does not show cytotoxicity against normal cells and a series of cancer cell lines. However, CPPB inhibits migrations of several solid cancers including pancreatic cancers that require high DPAGT1 expression in order for tumor progression. DPAGT1 inhibition by CPPB leads to a reduced expression level of Snail but does not reduce E-cadherin expression level at the IC50 (DPAGT1) concentration. CPPB displays a strong synergistic effect with paclitaxel against growth-inhibitory action of a patient-derived pancreatic adenocarcinoma, PD002: paclitaxel (IC50: 1.25 μM) inhibits growth of PD002 at 0.0024-0.16 μM in combination with 0.10-2.0 μM CPPB (IC50: 35 μM).
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Rita G Kansal
- Department of Surgery and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, 910 Madison St., Suite 300, Memphis, Tennessee 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Cody D Gillman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Syed M Hussain
- Department of Surgery and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, 910 Madison St., Suite 300, Memphis, Tennessee 38163, United States
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Gustavo A Miranda-Carboni
- Department of Medicine, Division of Hematology-Oncology, University of Tennessee Health Science Center, 19 S. Manassas Avenue, Memphis, Tennessee 38163, United States
| | - Evan S Glazer
- Department of Surgery and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, 910 Madison St., Suite 300, Memphis, Tennessee 38163, United States
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
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15
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Jones JA, Prior AM, Marreddy RKR, Wahrmund RD, Hurdle JG, Sun D, Hevener KE. Small-Molecule Inhibition of the C. difficile FAS-II Enzyme, FabK, Results in Selective Activity. ACS Chem Biol 2019; 14:1528-1535. [PMID: 31184849 DOI: 10.1021/acschembio.9b00293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile infection (CDI) is a leading cause of significant morbidity, mortality, and healthcare-related costs in the United States. After standard therapy, recurrence rates remain high, and multiple recurrences are not uncommon. Causes include treatments employing broad-spectrum agents that disrupt the normal host microbiota, as well as treatment-resistant spore formation by C. difficile. Thus, novel druggable anti-C. difficile targets that promote narrow-spectrum eradication and inhibition of sporulation are desired. As a critical rate-limiting step within the FAS-II bacterial fatty acid synthesis pathway, which supplies precursory component phospholipids found in bacterial cytoplasmic and spore-mediated membranes, enoyl-acyl carrier protein (ACP) reductase II (FabK) represents such a target. FabK is essential in C. difficile (CdFabK) and is structurally and mechanistically distinct from other isozymes found in gut microbiota species, making CdFabK an attractive narrow-spectrum target. We report here the kinetic evaluation of CdFabK, the biochemical activity of a series of phenylimidazole analogues, and microbiological data suggesting these compounds' selective antibacterial activity against C. difficile versus several other prominent gut organisms. The compounds display promising, selective, low micromolar CdFabK inhibitory activity without significantly affecting the growth of other gut organisms, and the series prototype (1b) is shown to be competitive for the CdFabK cofactor and uncompetitive for the substrate. A series analogue (1g) shows maintained inhibitory activity while also possessing increased solubility. These findings represent the basis for future drug discovery efforts by characterizing the CdFabK enzyme while demonstrating its druggability and potential role as a narrow-spectrum antidifficile target.
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Affiliation(s)
- Jesse A. Jones
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Allan M. Prior
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii, 96720, United States
| | - Ravi K. R. Marreddy
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Rebecca D. Wahrmund
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Julian G. Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii, 96720, United States
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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16
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Jones JA, Hevener KE. Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. Biochem Biophys Res Commun 2019; 516:333-338. [PMID: 31204053 DOI: 10.1016/j.bbrc.2019.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/06/2023]
Abstract
Herein we report the first structure of topoisomerase I determined from the gram-positive bacterium, S. mutans. Bacterial topoisomerase I is an ATP-independent type 1A topoisomerase that uses the inherent torsional strain within hyper-negatively supercoiled DNA as an energy source for its critical function of DNA relaxation. Interest in the enzyme has gained momentum as it has proven to be essential in various bacterial organisms. In order to aid in further biochemical characterization, the apo 65-kDa amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans was crystalized and a three-dimensional structure was determined to 2.06 Å resolution via x-ray crystallography. The overall structure illustrates the four classic major domains that create the traditional topoisomerase I "lock" formation comprised of a sizable toroidal aperture atop what is considered to be a highly dynamic body. A catalytic tyrosine residue resides at the interface between two domains and is known to form a 5' phosphotyrosine DNA-enzyme intermediate during transient single-stranded cleavage required for enzymatic relaxation of hyper negative DNA supercoils. Surrounding the catalytic tyrosine residue is the remainder of the highly conserved active site. Within 5 Å from the catalytic center, only one dissimilar residue is observed between topoisomerase I from S. mutans and the gram-negative model organism E. coli. Immediately adjacent to the conserved active site, however, S. mutans topoisomerase I displays a somewhat unique nine residue loop extension not present in any bacterial topoisomerase I structures previously determined other than that of an extremophile.
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Affiliation(s)
- Jesse A Jones
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.
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17
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Marreddy RKR, Wu X, Sapkota M, Prior AM, Jones JA, Sun D, Hevener KE, Hurdle JG. The Fatty Acid Synthesis Protein Enoyl-ACP Reductase II (FabK) is a Target for Narrow-Spectrum Antibacterials for Clostridium difficile Infection. ACS Infect Dis 2019; 5:208-217. [PMID: 30501172 DOI: 10.1021/acsinfecdis.8b00205] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clostridium difficile infection (CDI) is an antibiotic-induced microbiota shift disease of the large bowel. While there is a need for narrow-spectrum CDI antibiotics, it is unclear which cellular proteins are appropriate drug targets to specifically inhibit C. difficile. We evaluated the enoyl-acyl carrier protein (ACP) reductase II (FabK), which catalyzes the final step of bacterial fatty acid biosynthesis. Bioinformatics showed that C. difficile uses FabK as its sole enoyl-ACP reductase, unlike several major microbiota species. The essentiality of fabK for C. difficile growth was confirmed by failure to delete this gene using ClosTron mutagenesis and by growth inhibition upon gene silencing with CRISPR interference antisense to fabK transcription or by blocking protein translation. Inhibition of C. difficile's FASII pathway could not be circumvented by supply of exogenous fatty acids, either during fabK's gene silencing or upon inhibition of the enzyme with a phenylimidazole-derived inhibitor (1). The inability of fatty acids to bypass FASII inhibition is likely due to the function of the transcriptional repressor FapR. Inhibition of FabK also inhibited spore formation, reflecting the enzyme's role in de novo fatty acid biosynthesis for the formation of spore membrane lipids. Compound 1 did not inhibit growth of key microbiota species. These findings suggest that C. difficile FabK is a druggable target for discovering narrow-spectrum anti- C. difficile drugs that treat CDI but avoid collateral damage to the gut microbiota.
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Affiliation(s)
- Ravi K. R. Marreddy
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Boulevard, Houston, Texas 77030, United States
| | - Xiaoqian Wu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Boulevard, Houston, Texas 77030, United States
| | - Madhab Sapkota
- Department of Biology, University of Texas Arlington, 701 West Nedderman Drive, Arlington, Texas 76019, United States
| | - Allan M. Prior
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | - Jesse A. Jones
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38105, United States
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38105, United States
| | - Julian G. Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 West Holcombe Boulevard, Houston, Texas 77030, United States
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18
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Zhang M, Prior AM, Maddox MM, Shen WJ, Hevener KE, Bruhn DF, Lee RB, Singh AP, Reinicke J, Simmons CJ, Hurdle JG, Lee RE, Sun D. Pharmacophore Modeling, Synthesis, and Antibacterial Evaluation of Chalcones and Derivatives. ACS Omega 2018; 3:18343-18360. [PMID: 30613820 PMCID: PMC6312637 DOI: 10.1021/acsomega.8b03174] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
A series of novel chalcone and thiol-Michael addition analogues was synthesized and tested against Mycobacterium tuberculosis and other clinically significant bacterial pathogens. Previously reported chalcone-like antibacterials (1a-c and 2) were used as a training set to generate a pharmacophore model. The chalcone derivative hit compound 3 was subsequently identified through a pharmacophore-based virtual screen of the Specs library of >200 000 compounds. Among the newly synthesized chalcones and thiol-Michael addition analogues, chalcones 6r and 6s were active (minimum inhibitory concentrations (MICs) = 1.56-6.25 μg/mL) against Gram-positive pathogens Bacillus anthracis and Staphylococcus aureus [methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA)]. The chalcone thiol-Michael addition derivatives 7j-m showed good to excellent antibacterial activities (MICs = 0.78-6.25 μg/mL) against Enterococcus faecalis, B. anthracis, and S. aureus. Interestingly, the amine-Michael addition analogue 12a showed promising anti-MRSA activity (MIC = 1.56 μg/mL) with a selectivity index of 14 toward mammalian Vero cells. In addition, evaluation of selected compounds against biofilm and planktonic S. aureus (MSSA and MRSA) revealed that 12a exhibited bactericidal activities in these assays, which was overall superior to vancomycin. These properties may result from the compounds dissipating the proton motive force of bacterial membranes.
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Affiliation(s)
- Mingming Zhang
- Department of Pharmaceutical
Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | - Allan M. Prior
- Department of Pharmaceutical
Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | - Marcus M. Maddox
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS#1000, Memphis, Tennessee 38105, United States
| | - Wan-Jou Shen
- Center for
Infectious and Inflammatory Diseases, Texas
A&M Health Science Center, 2121 West Holcombe Boulevard, Houston, Texas 77030, United States
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences,
College of Pharmacy, University of Tennessee
Health Science Center, Memphis, Tennessee 38163, United States
| | - David F. Bruhn
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS#1000, Memphis, Tennessee 38105, United States
| | - Robin B. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS#1000, Memphis, Tennessee 38105, United States
| | - Aman P. Singh
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS#1000, Memphis, Tennessee 38105, United States
| | - Justin Reinicke
- Department of Pharmaceutical
Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 34 Rainbow Drive, Hilo, Hawaii 96720, United States
| | - Charles J. Simmons
- Department of Chemistry, University of Hawai’i at Hilo, Hilo, Hawaii 96720, United States
| | - Julian G. Hurdle
- Center for
Infectious and Inflammatory Diseases, Texas
A&M Health Science Center, 2121 West Holcombe Boulevard, Houston, Texas 77030, United States
| | - Richard E. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS#1000, Memphis, Tennessee 38105, United States
| | - Dianqing Sun
- Department of Pharmaceutical
Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 34 Rainbow Drive, Hilo, Hawaii 96720, United States
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Hevener KE, Santarsiero BD, Lee H, Jones JA, Boci T, Johnson ME, Mehboob S. Structural characterization of Porphyromonas gingivalis enoyl-ACP reductase II (FabK). Acta Crystallogr F Struct Biol Commun 2018; 74:105-112. [PMID: 29400320 PMCID: PMC5947681 DOI: 10.1107/s2053230x18000262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/04/2018] [Indexed: 01/24/2023] Open
Abstract
Enoyl-acyl carrier protein (ACP) reductase II (FabK) is a critical rate-limiting enzyme in the bacterial type II fatty-acid synthesis (FAS II) pathway. FAS II pathway enzymes are markedly disparate from their mammalian analogs in the FAS I pathway in both structure and mechanism. Enzymes involved in bacterial fatty-acid synthesis represent viable drug targets for Gram-negative pathogens, and historical precedent exists for targeting them in the treatment of diseases of the oral cavity. The Gram-negative organism Porphyromonas gingivalis represents a key causative agent of the costly and highly prevalent disease known as chronic periodontitis, and exclusively expresses FabK as its enoyl reductase enzyme in the FAS-II pathway. Together, these characteristics distinguish P. gingivalis FabK (PgFabK) as an attractive and novel narrow-spectrum antibacterial target candidate. PgFabK is a flavoenzyme that is dependent on FMN and NADPH as cofactors for the enzymatic reaction, which reduces the enoyl substrate via a ping-pong mechanism. Here, the structure of the PgFabK enzyme as determined using X-ray crystallography is reported to 1.9 Å resolution with endogenous FMN fully resolved and the NADPH cofactor partially resolved. PgFabK possesses a TIM-barrel motif, and all flexible loops are visible. The determined structure has allowed insight into the structural basis for the NADPH dependence observed in PgFabK and the role of a monovalent cation that has been observed in previous studies to be stringently required for FabK activity. The PgFabK structure and the insights gleaned from its analysis will facilitate structure-based drug-discovery efforts towards the prevention and treatment of P. gingivalis infection.
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Affiliation(s)
- Kirk E. Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Suite 571, Memphis, TN 38163-2198, USA
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Bernard D. Santarsiero
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Hyun Lee
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Jesse A. Jones
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Suite 571, Memphis, TN 38163-2198, USA
| | - Teuta Boci
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Shahila Mehboob
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
- Novalex Therapeutics, Chicago, IL 60612, USA
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20
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Abstract
The discovery of molecular toxicity in a clinical drug candidate can have a significant impact on both the cost and timeline of the drug discovery process. Early identification of potentially toxic compounds during screening library preparation or, alternatively, during the hit validation process, is critical to ensure that valuable time and resources are not spent pursuing compounds that may possess a high propensity for human toxicity. This chapter focuses on the application of computational molecular filters, applied either prescreening or postscreening, to identify and remove known reactive and/or potentially toxic compounds from consideration in drug discovery campaigns.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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Jones JA, Virga KG, Gumina G, Hevener KE. Recent Advances in the Rational Design and Optimization of Antibacterial Agents. Medchemcomm 2016; 7:1694-1715. [PMID: 27642504 DOI: 10.1039/c6md00232c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This review discusses next-generation antibacterial agents developed using rational, or targeted, drug design strategies. The focus of this review is on small-molecule compounds that have been designed to bypass developing bacterial resistance, improve the antibacterial spectrum of activity, and/or to optimize other properties, including physicochemical and pharmacokinetic properties. Agents are discussed that affect known antibacterial targets, such as the bacterial ribosome, nucleic acid binding proteins, and proteins involved in cell-wall biosynthesis; as well as some affecting novel bacterial targets which do not have currently marketed agents. The discussion of the agents focuses on the rational design strategies employed and the synthetic medicinal chemistry and structure-based design techniques utilized by the scientists involved in the discoveries, including such methods as ligand- and structure-based strategies, structure-activity relationship (SAR) expansion strategies, and novel synthetic organic chemistry methods. As such, the discussion is limited to small-molecule therapeutics that have confirmed macromolecular targets and encompasses only a fraction of all antibacterial agents recently approved or in late-stage clinical trials. The antibacterial agents selected have been recently approved for use on the U.S. or European markets or have shown promising results in phase 2 or phase 3 U.S. CLINICAL TRIALS
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991 (USA)
| | - Kristopher G Virga
- Department of Pharmaceutical Sciences, Presbyterian College School of Pharmacy, 307 North Broad Street, Clinton, SC 29325 (USA)
| | - Giuseppe Gumina
- Department of Pharmaceutical Sciences, Presbyterian College School of Pharmacy, 307 North Broad Street, Clinton, SC 29325 (USA)
| | - Kirk E Hevener
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991 (USA)
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Jones JA, Price E, Miller D, Hevener KE. A simplified protocol for high-yield expression and purification of bacterial topoisomerase I. Protein Expr Purif 2016; 124:32-40. [PMID: 27117979 DOI: 10.1016/j.pep.2016.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/15/2022]
Abstract
Type IA topoisomerases represent promising antibacterial drug targets. Data exists suggesting that the two bacterial type IA topoisomerase enzymes-topoisomerase I and topoisomerase III-share an overlapping biological role. Furthermore, topoisomerase I has been shown to be essential for the survival of certain organisms lacking topoisomerase III. With this in mind, it is plausible that topoisomerase I may represent a potential target for selective antibacterial drug development. As many reported bacterial topoisomerase I purification protocols have either suffered from relatively low yield, numerous steps, or a simple failure to report target protein yield altogether, a high-yield and high-purity bacterial topoisomerase I expression and purification protocol is highly desirable. The goal of this study was therefore to optimize the expression and purification of topoisomerase I from Streptococcus mutans, a clinically relevant organism that plays a significant role in oral and extra-oral infection, in order to quickly and easily attain the requisite quantities of pure target enzyme suitable for use in assay development, compound library screening, and carrying out further structural and biochemical characterization analyses. Herein we report the systematic implementation and analysis of various expression and purification techniques leading to the development and optimization of a rapid and straightforward protocol for the auto-induced expression and two-step, affinity tag purification of Streptococcus mutans topoisomerase I yielding >20 mg/L of enzyme at over 95% purity.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA
| | - Emily Price
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA
| | - Donovan Miller
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA
| | - Kirk E Hevener
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA.
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23
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Su PC, Tsai CC, Mehboob S, Hevener KE, Johnson ME. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI). J Comput Chem 2015; 36:1859-73. [PMID: 26216222 PMCID: PMC4688044 DOI: 10.1002/jcc.24011] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/20/2015] [Accepted: 06/22/2015] [Indexed: 01/10/2023]
Abstract
To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM-PBSA, MM-GBSA, and QM/MM-GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM-GBSA using 6 ns MD simulation trajectories together with GB(neck2) , PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r(2) = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called "multiple independent sampling"), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB(HCT) and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r(2) = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive "multiple independent sampling method" may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM-P(G)BSA were limited to inhibitors' relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program.
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Affiliation(s)
- Pin-Chih Su
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Cheng-Chieh Tsai
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Shahila Mehboob
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Kirk E. Hevener
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
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Mehboob S, Song J, Hevener KE, Su PC, Boci T, Brubaker L, Truong L, Mistry T, Deng J, Cook JL, Santarsiero BD, Ghosh AK, Johnson ME. Structural and biological evaluation of a novel series of benzimidazole inhibitors of Francisella tularensis enoyl-ACP reductase (FabI). Bioorg Med Chem Lett 2015; 25:1292-6. [PMID: 25677657 DOI: 10.1016/j.bmcl.2015.01.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 12/13/2022]
Abstract
Francisella tularensis, the causative agent of tularemia, presents a significant biological threat and is a Category A priority pathogen due to its potential for weaponization. The bacterial FASII pathway is a viable target for the development of novel antibacterial agents treating Gram-negative infections. Here we report the advancement of a promising series of benzimidazole FabI (enoyl-ACP reductase) inhibitors to a second-generation using a systematic, structure-guided lead optimization strategy, and the determination of several co-crystal structures that confirm the binding mode of designed inhibitors. These compounds display an improved low nanomolar enzymatic activity as well as promising low microgram/mL antibacterial activity against both F. tularensis and Staphylococcus aureus and its methicillin-resistant strain (MRSA). The improvements in activity accompanying structural modifications lead to a better understanding of the relationship between the chemical structure and biological activity that encompasses both enzymatic and whole-cell activity.
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Affiliation(s)
- Shahila Mehboob
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States; Novalex Therapeutics, 2242 W. Harrison, Chicago, IL 60612, United States.
| | - Jinhua Song
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Kirk E Hevener
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Pin-Chih Su
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Teuta Boci
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Libby Brubaker
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Lena Truong
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Tina Mistry
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Jiangping Deng
- Division of Infectious Diseases, Loyola University Chicago, Maywood, IL 60153, United States; Edward Hines Jr. VA Hospital, Hines, IL 60141, United States
| | - James L Cook
- Division of Infectious Diseases, Loyola University Chicago, Maywood, IL 60153, United States; Edward Hines Jr. VA Hospital, Hines, IL 60141, United States
| | - Bernard D Santarsiero
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States; Novalex Therapeutics, 2242 W. Harrison, Chicago, IL 60612, United States.
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25
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Lee H, Zhu T, Patel K, Zhang YY, Truong L, Hevener KE, Gatuz JL, Subramanya G, Jeong HY, Uprichard SL, Johnson ME. High-throughput screening (HTS) and hit validation to identify small molecule inhibitors with activity against NS3/4A proteases from multiple hepatitis C virus genotypes. PLoS One 2013; 8:e75144. [PMID: 24130685 PMCID: PMC3793977 DOI: 10.1371/journal.pone.0075144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/09/2013] [Indexed: 01/08/2023] Open
Abstract
Development of drug-resistant mutations has been a major problem with all currently developed Hepatitis C Virus (HCV) NS3/4A inhibitors, including the two FDA approved drugs, significantly reducing the efficacy of these inhibitors. The high incidence of drug-resistance mutations and the limited utility of these inhibitors against only genotype 1 highlight the need for novel, broad-spectrum HCV therapies. Here we used high-throughput screening (HTS) to identify low molecular weight inhibitors against NS3/4A from multiple genotypes. A total of 40,967 compounds from four structurally diverse molecular libraries were screened by HTS using fluorescence-based enzymatic assays, followed by an orthogonal binding analysis using surface plasmon resonance (SPR) to eliminate false positives. A novel small molecule compound was identified with an IC50 value of 2.2 µM against the NS3/4A from genotype 1b. Mode of inhibition analysis subsequently confirmed this compound to be a competitive inhibitor with respect to the substrate, indicating direct binding to the protease active site, rather than to the allosteric binding pocket that was discovered to be the binding site of a few recently discovered small molecule inhibitors. This newly discovered inhibitor also showed promising inhibitory activity against the NS3/4As from three other HCV genotypes, as well as five common drug-resistant mutants of genotype 1b NS3/4A. The inhibitor was selective for NS3 from multiple HCV genotypes over two human serine proteases, and a whole cell lysate assay confirmed inhibitory activity in the cellular environment. This compound provides a lead for further development of potentially broader spectrum inhibitors.
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Affiliation(s)
- Hyun Lee
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Tian Zhu
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yan-Yan Zhang
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Lena Truong
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kirk E. Hevener
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joseph L. Gatuz
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Gitanjali Subramanya
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Hyun-Young Jeong
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Susan L. Uprichard
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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26
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Lee H, Cao S, Hevener KE, Truong L, Gatuz JL, Patel K, Ghosh AK, Johnson ME. Synergistic inhibitor binding to the papain-like protease of human SARS coronavirus: mechanistic and inhibitor design implications. ChemMedChem 2013; 8:1361-72. [PMID: 23788528 PMCID: PMC3954986 DOI: 10.1002/cmdc.201300134] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/29/2013] [Indexed: 11/09/2022]
Abstract
We previously developed two potent chemical classes that inhibit the essential papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus. In this study, we applied a novel approach to identify small fragments that act synergistically with these inhibitors. A fragment library was screened in combination with four previously developed lead inhibitors by fluorescence-based enzymatic assays. Several fragment compounds synergistically enhanced the inhibitory activity of the lead inhibitors by approximately an order of magnitude. Surface plasmon resonance measurements showed that three fragments bind specifically to the PLpro enzyme. Mode of inhibition, computational solvent mapping, and molecular docking studies suggest that these fragments bind adjacent to the binding site of the lead inhibitors and further stabilize the inhibitor-bound state. We propose potential next-generation compounds based on a computational fragment-merging approach. This approach provides an alternative strategy for lead optimization for cases in which direct co-crystallization is difficult.
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Affiliation(s)
- Hyun Lee
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
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27
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Zhu T, Cao S, Su PC, Patel R, Shah D, Chokshi HB, Szukala R, Johnson ME, Hevener KE. Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis. J Med Chem 2013; 56:6560-72. [PMID: 23688234 DOI: 10.1021/jm301916b] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses, and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, druglike, and ADMET filters were applied to the reported hits to assess the quality of compounds reported, and a careful analysis of a subset of the studies that presented hit optimization was performed. These data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, definition of hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria.
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Affiliation(s)
- Tian Zhu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago , 900 S. Ashland Avenue, Suite 3100, Chicago, Illinois 60607-7173, United States
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28
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Zhu T, Lee H, Lei H, Jones C, Patel K, Johnson ME, Hevener KE. Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol. J Chem Inf Model 2013; 53:560-72. [PMID: 23432621 DOI: 10.1021/ci300502h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have developed a rigorous computational screening protocol to identify novel fragment-like inhibitors of N(5)-CAIR mutase (PurE), a key enzyme involved in de novo purine synthesis that represents a novel target for the design of antibacterial agents. This computational screening protocol utilizes molecular docking, graphics processing unit (GPU)-accelerated molecular dynamics, and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) free energy estimations to investigate the binding modes and energies of fragments in the active sites of PurE. PurE is a functional octamer comprised of identical subunits. The octameric structure, with its eight active sites, provided a distinct advantage in these studies because, for a given simulation length, we were able to place eight separate fragment compounds in the active sites to increase the throughput of the MM/PBSA analysis. To validate this protocol, we have screened an in-house fragment library consisting of 352 compounds. The theoretical results were then compared with the results of two experimental fragment screens, Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) binding analyses. In these validation studies, the protocol was able to effectively identify the competitive binders that had been independently identified by experimental testing, suggesting the potential utility of this method for the identification of novel fragments for future development as PurE inhibitors.
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Affiliation(s)
- Tian Zhu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago , 900 S Ashland Avenue, Suite 3100, Chicago, Illinois 60607-7173, United States
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29
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Truong L, Hevener KE, Rice AJ, Patel K, Johnson ME, Lee H. High-level expression, purification, and characterization of Staphylococcus aureus dihydroorotase (PyrC) as a cleavable His-SUMO fusion. Protein Expr Purif 2012; 88:98-106. [PMID: 23246866 DOI: 10.1016/j.pep.2012.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/21/2012] [Accepted: 11/29/2012] [Indexed: 01/29/2023]
Abstract
Staphylococcus aureus is a pathogenic bacterium that causes a variety of mild to lethal human diseases. The rapid spread of multidrug-resistant strains makes the discovery of new antimicrobial agents critical. Dihydroorotase (PyrC), the third enzyme in the bacterial pyrimidine biosynthesis pathway, is structurally and mechanistically distinct from its mammalian counterpart. It has been confirmed to be essential in S. aureus making it an attractive antibacterial drug target. No protocol to express and purify S. aureus PyrC (SaPyrC) has been reported. To obtain the SaPyrC enzyme and overcome anticipated solubility problems, the SaPyrC gene was cloned into the pET-SUMO vector. The N-terminal His-SUMO fused SaPyrC was expressed in Escherichia coli BL21 (DE3) with an HRV 3C protease recognition site inserted between the SUMO tag and SaPyrC to allow for improved cleavage by HRV protease. Purification of cleaved protein using HisTrap affinity and gel filtration columns resulted in native SaPyrC with estimated 95% purity and 40% yield. Both His-SUMO tagged and native SaPyrC form dimers, and enzyme characterization studies have shown that the His-SUMO tag affects enzyme activity slightly. Forward and reverse kinetic rate constants for both tagged and native SaPyrC were determined, and pH profiling studies revealed the optimal pH values for forward and reverse reactions.
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Affiliation(s)
- Lena Truong
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Ave., Suite 3100, Chicago, IL 60607-7173, USA
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30
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Hevener KE, Mehboob S, Boci T, Truong K, Santarsiero BD, Johnson ME. Expression, purification and characterization of enoyl-ACP reductase II, FabK, from Porphyromonas gingivalis. Protein Expr Purif 2012; 85:100-8. [PMID: 22820244 DOI: 10.1016/j.pep.2012.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/02/2012] [Accepted: 07/05/2012] [Indexed: 12/01/2022]
Abstract
The rapid rise in bacterial drug resistance coupled with the low number of novel antimicrobial compounds in the discovery pipeline has led to a critical situation requiring the expedient discovery and characterization of new antimicrobial drug targets. Enzymes in the bacterial fatty acid synthesis pathway, FAS-II, are distinct from their mammalian counterparts, FAS-I, in terms of both structure and mechanism. As such, they represent attractive targets for the design of novel antimicrobial compounds. Enoyl-acyl carrier protein reductase II, FabK, is a key, rate-limiting enzyme in the FAS-II pathway for several bacterial pathogens. The organism, Porphyromonas gingivalis, is a causative agent of chronic periodontitis that affects up to 25% of the US population and incurs a high national burden in terms of cost of treatment. P. gingivalis expresses FabK as the sole enoyl reductase enzyme in its FAS-II cycle, which makes this a particularly appealing target with potential for selective antimicrobial therapy. Herein we report the molecular cloning, expression, purification and characterization of the FabK enzyme from P. gingivalis, only the second organism from which this enzyme has been isolated. Characterization studies have shown that the enzyme is a flavoprotein, the reaction dependent upon FMN and NADPH and proceeding via a Ping-Pong Bi-Bi mechanism to reduce the enoyl substrate. A sensitive assay measuring the fluorescence decrease of NADPH as it is converted to NADP(+) during the reaction has been optimized for high-throughput screening. Finally, protein crystallization conditions have been identified which led to protein crystals that diffract x-rays to high resolution.
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Affiliation(s)
- Kirk E Hevener
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607-7173, USA.
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31
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Mehboob S, Hevener KE, Truong K, Boci T, Santarsiero BD, Johnson ME. Structural and enzymatic analyses reveal the binding mode of a novel series of Francisella tularensis enoyl reductase (FabI) inhibitors. J Med Chem 2012; 55:5933-41. [PMID: 22642319 DOI: 10.1021/jm300489v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motif of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.
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Affiliation(s)
- Shahila Mehboob
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, Illinois 60607-7173, United States.
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Hevener KE, Mehboob S, Su PC, Truong K, Boci T, Deng J, Ghassemi M, Cook JL, Johnson ME. Discovery of a novel and potent class of F. tularensis enoyl-reductase (FabI) inhibitors by molecular shape and electrostatic matching. J Med Chem 2011; 55:268-79. [PMID: 22098466 DOI: 10.1021/jm201168g] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enoyl-acyl carrier protein (ACP) reductase, FabI, is a key enzyme in the bacterial fatty acid biosynthesis pathway (FAS II). FabI is an NADH-dependent oxidoreductase that acts to reduce enoyl-ACP substrates in a final step of the pathway. The absence of this enzyme in humans makes it an attractive target for the development of new antibacterial agents. FabI is known to be unresponsive to structure-based design efforts due to a high degree of induced fit and a mobile flexible loop encompassing the active site. Here we discuss the development, validation, and careful application of a ligand-based virtual screen used for the identification of novel inhibitors of the Francisella tularensis FabI target. In this study, four known classes of FabI inhibitors were used as templates for virtual screens that involved molecular shape and electrostatic matching. The program ROCS was used to search a high-throughput screening library for compounds that matched any of the four molecular shape queries. Matching compounds were further refined using the program EON, which compares and scores compounds by matching electrostatic properties. Using these techniques, 50 compounds were selected, ordered, and tested. The tested compounds possessed novel chemical scaffolds when compared to the input query compounds. Several hits with low micromolar activity were identified and follow-up scaffold-based searches resulted in the identification of a lead series with submicromolar enzyme inhibition, high ligand efficiency, and a novel scaffold. Additionally, one of the most active compounds showed promising whole-cell antibacterial activity against several Gram-positive and Gram-negative species, including the target pathogen. The results of a preliminary structure-activity relationship analysis are presented.
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Affiliation(s)
- Kirk E Hevener
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607-7173, United States
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Hevener KE, Yun MK, Qi J, Kerr ID, Babaoglu K, Hurdle JG, Balakrishna K, White SW, Lee RE. Structural studies of pterin-based inhibitors of dihydropteroate synthase. J Med Chem 2010; 53:166-77. [PMID: 19899766 DOI: 10.1021/jm900861d] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydropteroate synthase (DHPS) is a key enzyme in bacterial folate synthesis and the target of the sulfonamide class of antibacterials. Resistance and toxicities associated with sulfonamides have led to a decrease in their clinical use. Compounds that bind to the pterin binding site of DHPS, as opposed to the p-amino benzoic acid (pABA) binding site targeted by the sulfonamide agents, are anticipated to bypass sulfonamide resistance. To identify such inhibitors and map the pterin binding pocket, we have performed virtual screening, synthetic, and structural studies using Bacillus anthracis DHPS. Several compounds with inhibitory activity have been identified, and crystal structures have been determined that show how the compounds engage the pterin site. The structural studies identify the key binding elements and have been used to generate a structure-activity based pharmacophore map that will facilitate the development of the next generation of DHPS inhibitors which specifically target the pterin site.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Avenue, Room 327 Johnson Building, Memphis, Tennessee 38163, USA
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Zhao W, Hevener KE, White SW, Lee RE, Boyett JM. A statistical framework to evaluate virtual screening. BMC Bioinformatics 2009; 10:225. [PMID: 19619306 PMCID: PMC2722655 DOI: 10.1186/1471-2105-10-225] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 07/20/2009] [Indexed: 02/08/2023] Open
Abstract
Background Receiver operating characteristic (ROC) curve is widely used to evaluate virtual screening (VS) studies. However, the method fails to address the "early recognition" problem specific to VS. Although many other metrics, such as RIE, BEDROC, and pROC that emphasize "early recognition" have been proposed, there are no rigorous statistical guidelines for determining the thresholds and performing significance tests. Also no comparisons have been made between these metrics under a statistical framework to better understand their performances. Results We have proposed a statistical framework to evaluate VS studies by which the threshold to determine whether a ranking method is better than random ranking can be derived by bootstrap simulations and 2 ranking methods can be compared by permutation test. We found that different metrics emphasize "early recognition" differently. BEDROC and RIE are 2 statistically equivalent metrics. Our newly proposed metric SLR is superior to pROC. Through extensive simulations, we observed a "seesaw effect" – overemphasizing early recognition reduces the statistical power of a metric to detect true early recognitions. Conclusion The statistical framework developed and tested by us is applicable to any other metric as well, even if their exact distribution is unknown. Under this framework, a threshold can be easily selected according to a pre-specified type I error rate and statistical comparisons between 2 ranking methods becomes possible. The theoretical null distribution of SLR metric is available so that the threshold of SLR can be exactly determined without resorting to bootstrap simulations, which makes it easy to use in practical virtual screening studies.
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Affiliation(s)
- Wei Zhao
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA.
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Hevener KE, Zhao W, Ball DM, Babaoglu K, Qi J, White SW, Lee RE. Validation of molecular docking programs for virtual screening against dihydropteroate synthase. J Chem Inf Model 2009; 49:444-60. [PMID: 19434845 DOI: 10.1021/ci800293n] [Citation(s) in RCA: 315] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydropteroate synthase (DHPS) is the target of the sulfonamide class of antibiotics and has been a validated antibacterial drug target for nearly 70 years. The sulfonamides target the p-aminobenzoic acid (pABA) binding site of DHPS and interfere with folate biosynthesis and ultimately prevent bacterial replication. However, widespread bacterial resistance to these drugs has severely limited their effectiveness. This study explores the second and more highly conserved pterin binding site of DHPS as an alternative approach to developing novel antibiotics that avoid resistance. In this study, five commonly used docking programs, FlexX, Surflex, Glide, GOLD, and DOCK, and nine scoring functions, were evaluated for their ability to rank-order potential lead compounds for an extensive virtual screening study of the pterin binding site of B. anthracis DHPS. Their performance in ligand docking and scoring was judged by their ability to reproduce a known inhibitor conformation and to efficiently detect known active compounds seeded into three separate decoy sets. Two other metrics were used to assess performance; enrichment at 1% and 2% and Receiver Operating Characteristic (ROC) curves. The effectiveness of postdocking relaxation prior to rescoring and consensus scoring were also evaluated. Finally, we have developed a straightforward statistical method of including the inhibition constants of the known active compounds when analyzing enrichment results to more accurately assess scoring performance, which we call the 'sum of the sum of log rank' or SSLR. Of the docking and scoring functions evaluated, Surflex with Surflex-Score and Glide with GlideScore were the best overall performers for use in virtual screening against the DHPS target, with neither combination showing statistically significant superiority over the other in enrichment studies or pose selection. Postdocking ligand relaxation and consensus scoring did not improve overall enrichment.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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Hevener KE, Ball DM, Buolamwini JK, Lee RE. Quantitative structure-activity relationship studies on nitrofuranyl anti-tubercular agents. Bioorg Med Chem 2008; 16:8042-53. [PMID: 18701298 DOI: 10.1016/j.bmc.2008.07.070] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 07/16/2008] [Accepted: 07/22/2008] [Indexed: 11/17/2022]
Abstract
A series of nitrofuranylamide and related aromatic compounds displaying potent activity against Mycobacterium tuberculosis have been investigated utilizing 3-dimensional quantitative structure-activity relationship (3D-QSAR) techniques. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were used to produce 3D-QSAR models that correlated the minimum inhibitory concentration (MIC) values against M. tuberculosis with the molecular structures of the active compounds. A training set of 95 active compounds was used to develop the models, which were then evaluated by a series of internal and external cross-validation techniques. A test set of 15 compounds was used for the external validation. Different alignment and ionization rules were investigated as well as the effect of global molecular descriptors including lipophilicity (cLogP, LogD), polar surface area (PSA), and steric bulk (CMR), on model predictivity. Models with greater than 70% predictive ability, as determined by external validation, and high internal validity (cross-validated r(2)>.5) have been developed. Incorporation of lipophilicity descriptors into the models had negligible effects on model predictivity. The models developed will be used to predict the activity of proposed new structures and advance the development of next generation nitrofuranyl and related nitroaromatic anti-tuberculosis agents.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Avenue, Suite 327, Memphis, TN 38163, USA
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