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Crespo R, Dang Q, Zhou NE, Guthrie LM, Snavely TC, Dong W, Loesch KA, Suzuki T, You L, Wang W, O’Malley T, Parish T, Olsen DB, Sacchettini JC. Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase. J Med Chem 2019; 62:4483-4499. [PMID: 31002508 PMCID: PMC6511943 DOI: 10.1021/acs.jmedchem.9b00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis adenosine kinase (MtbAdoK) is an essential enzyme of Mtb and forms part of the purine salvage pathway within mycobacteria. Evidence suggests that the purine salvage pathway might play a crucial role in Mtb survival and persistence during its latent phase of infection. In these studies, we adopted a structural approach to the discovery, structure-guided design, and synthesis of a series of adenosine analogues that displayed inhibition constants ranging from 5 to 120 nM against the enzyme. Two of these compounds exhibited low micromolar activity against Mtb with half maximal effective inhibitory concentrations of 1.7 and 4.0 μM. Our selectivity and preliminary pharmacokinetic studies showed that the compounds possess a higher degree of specificity against MtbAdoK when compared with the human counterpart and are well tolerated in rodents, respectively. Finally, crystallographic studies showed the molecular basis of inhibition, potency, and selectivity and revealed the presence of a potentially therapeutically relevant cavity unique to the MtbAdoK homodimer.
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Affiliation(s)
- Roberto
A. Crespo
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Qun Dang
- Merck
Sharp Dohme Corporation, West Point Pennsylvania 19486, United States
| | - Nian E. Zhou
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Liam M. Guthrie
- College
of Medicine, Texas A&M University Health
Science Center, Bryan, Texas 77807, United
States
| | - Thomas C. Snavely
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Wen Dong
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kimberly A. Loesch
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Takao Suzuki
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Lanying You
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Wei Wang
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Theresa O’Malley
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue E, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue E, Seattle, Washington 98102, United States
| | - David B. Olsen
- Merck
Sharp Dohme Corporation, West Point Pennsylvania 19486, United States,E-mail: . Phone: 215-652-5250 (D.B.O.)
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States,E-mail: . Phone: (979) 845-8548 (J.C.S.)
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Shi J, Milo J, Brady K, Bentow C, Conklin J, O’Malley T, Poling D, Ibarra C, Mahler M, Dervieux T. Diagnostic performance of a new anti-carbamylated protein assay in rheumatic diseases. Scand J Rheumatol 2018; 48:249-250. [DOI: 10.1080/03009742.2018.1530372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- J Shi
- Exagen Diagnostics, Vista, CA, USA
| | - J Milo
- Inova Diagnostics, Inc., San Diego, CA, USA
| | - K Brady
- Exagen Diagnostics, Vista, CA, USA
| | - C Bentow
- Inova Diagnostics, Inc., San Diego, CA, USA
| | | | | | - D Poling
- Exagen Diagnostics, Vista, CA, USA
| | - C Ibarra
- Exagen Diagnostics, Vista, CA, USA
| | - M Mahler
- Inova Diagnostics, Inc., San Diego, CA, USA
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Chandrasekera NS, Berube BJ, Shetye G, Chettiar S, O’Malley T, Manning A, Flint L, Awasthi D, Ioerger TR, Sacchettini J, Masquelin T, Hipskind PA, Odingo J, Parish T. Improved Phenoxyalkylbenzimidazoles with Activity against Mycobacterium tuberculosis Appear to Target QcrB. ACS Infect Dis 2017; 3:898-916. [PMID: 29035551 PMCID: PMC5727484 DOI: 10.1021/acsinfecdis.7b00112] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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] [Indexed: 12/24/2022]
Abstract
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The phenoxy alkyl benzimidazoles
(PABs) have good antitubercular activity. We expanded our structure–activity
relationship studies to determine the core components of PABs required
for activity. The most potent compounds had minimum inhibitory concentrations
against Mycobacterium tuberculosis in the low nanomolar
range with very little cytotoxicity against eukaryotic cells as well
as activity against intracellular bacteria. We isolated resistant
mutants against PAB compounds, which had mutations in either Rv1339,
of unknown function, or qcrB, a component of the
cytochrome bc1 oxidase of the electron
transport chain. QcrB mutant strains were resistant to all PAB compounds,
whereas Rv1339 mutant strains were only resistant to a subset, suggesting
that QcrB is the target. The discovery of the target for PAB compounds
will allow for the improved design of novel compounds to target intracellular M. tuberculosis.
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Affiliation(s)
- N. Susantha Chandrasekera
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Bryan J. Berube
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Gauri Shetye
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Somsundaram Chettiar
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Theresa O’Malley
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Alyssa Manning
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Divya Awasthi
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | | | | | - Thierry Masquelin
- Lilly Research Laboratories, 307 East Merrill Street, Indianapolis, Indiana 46285, United States
| | - Philip A. Hipskind
- Lilly Research Laboratories, 307 East Merrill Street, Indianapolis, Indiana 46285, United States
| | - Joshua Odingo
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
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Bonnett SA, Ollinger J, Chandrasekera S, Florio S, O’Malley T, Files M, Jee JA, Ahn J, Casey A, Ovechkina Y, Roberts D, Korkegian A, Parish T. A Target-Based Whole Cell Screen Approach To Identify Potential Inhibitors of Mycobacterium tuberculosis Signal Peptidase. ACS Infect Dis 2016; 2:893-902. [PMID: 27642770 PMCID: PMC5215716 DOI: 10.1021/acsinfecdis.6b00075] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Indexed: 12/31/2022]
Abstract
The general secretion (Sec) pathway is a conserved essential pathway in bacteria and is the primary route of protein export across the cytoplasmic membrane. During protein export, the signal peptidase LepB catalyzes the cleavage of the signal peptide and subsequent release of mature proteins into the extracellular space. We developed a target-based whole cell assay to screen for potential inhibitors of LepB, the sole signal peptidase in Mycobacterium tuberculosis, using a strain engineered to underexpress LepB (LepB-UE). We screened 72,000 compounds against both the Lep-UE and wild-type (wt) strains. We identified the phenylhydrazone (PHY) series as having higher activity against the LepB-UE strain. We conducted a limited structure-activity relationship determination around a representative PHY compound with differential activity (MICs of 3.0 μM against the LepB-UE strain and 18 μM against the wt); several analogues were less potent against the LepB overexpressing strain. A number of chemical modifications around the hydrazone moiety resulted in improved potency. Inhibition of LepB activity was observed for a number of compounds in a biochemical assay using cell membrane fraction derived from M. tuberculosis. Compounds did not increase cell permeability, dissipate membrane potential, or inhibit an unrelated mycobacterial enzyme, suggesting a specific mode of action related to the LepB secretory mechanism.
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Affiliation(s)
- Shilah A. Bonnett
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Juliane Ollinger
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Susantha Chandrasekera
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Stephanie Florio
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Theresa O’Malley
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Megan Files
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Jo-Ann Jee
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - James Ahn
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Allen Casey
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Yulia Ovechkina
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - David Roberts
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
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5
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Ioerger TR, O’Malley T, Liao R, Guinn KM, Hickey MJ, Mohaideen N, Murphy KC, Boshoff HIM, Mizrahi V, Rubin EJ, Sassetti CM, Barry CE, Sherman DR, Parish T, Sacchettini JC. Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One 2013; 8:e75245. [PMID: 24086479 PMCID: PMC3781026 DOI: 10.1371/journal.pone.0075245] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [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: 04/02/2013] [Accepted: 08/12/2013] [Indexed: 11/18/2022] Open
Abstract
Identification of new drug targets is vital for the advancement of drug discovery against Mycobacterium tuberculosis, especially given the increase of resistance worldwide to first- and second-line drugs. Because traditional target-based screening has largely proven unsuccessful for antibiotic discovery, we have developed a scalable platform for target identification in M. tuberculosis that is based on whole-cell screening, coupled with whole-genome sequencing of resistant mutants and recombineering to confirm. The method yields targets paired with whole-cell active compounds, which can serve as novel scaffolds for drug development, molecular tools for validation, and/or as ligands for co-crystallization. It may also reveal other information about mechanisms of action, such as activation or efflux. Using this method, we identified resistance-linked genes for eight compounds with anti-tubercular activity. Four of the genes have previously been shown to be essential: AspS, aspartyl-tRNA synthetase, Pks13, a polyketide synthase involved in mycolic acid biosynthesis, MmpL3, a membrane transporter, and EccB3, a component of the ESX-3 type VII secretion system. AspS and Pks13 represent novel targets in protein translation and cell-wall biosynthesis. Both MmpL3 and EccB3 are involved in membrane transport. Pks13, AspS, and EccB3 represent novel candidates not targeted by existing TB drugs, and the availability of whole-cell active inhibitors greatly increases their potential for drug discovery.
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Affiliation(s)
- Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Theresa O’Malley
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Reiling Liao
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Kristine M. Guinn
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mark J. Hickey
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Nilofar Mohaideen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Kenan C. Murphy
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Valerie Mizrahi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher M. Sassetti
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - David R. Sherman
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Tanya Parish
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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