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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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2
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Bioactive Oleic Derivatives of Dopamine: A Review of the Therapeutic Potential. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [PMID: 29623573 DOI: 10.1007/5584_2018_197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Lipid derivatives of dopamine are a novel class of compounds raising a research interest due to the potential of their being a vehicle for dopamine delivery to the brain. The aim of the present paper is to review the main features of the two most prominent bioactive members of this family, namely, N-oleoyl-dopamine (OLDA) and 3'-O-methyl-N-oleoyl-dopamine (OMe-OLDA), with emphasis on the possible therapeutic properties.
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3
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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4
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Matsumoto Y, Ito A, Uesugi M, Kittaka A. Efficient N-Acyldopamine Synthesis. Chem Pharm Bull (Tokyo) 2016; 64:935-40. [DOI: 10.1248/cpb.c16-00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Akihiro Ito
- Chemical Genetics Laboratory, RIKEN
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
- Institute for Chemical Research, Kyoto University
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5
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Ambrose EA. Botulinum Neurotoxin, Tetanus Toxin, and Anthrax Lethal Factor Countermeasures. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Zhang X, Amin EA. Highly predictive support vector machine (SVM) models for anthrax toxin lethal factor (LF) inhibitors. J Mol Graph Model 2016; 63:22-8. [PMID: 26615468 PMCID: PMC4713341 DOI: 10.1016/j.jmgm.2015.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/07/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Anthrax is a highly lethal, acute infectious disease caused by the rod-shaped, Gram-positive bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), a zinc metalloprotease secreted by the bacilli, plays a key role in anthrax pathogenesis and is chiefly responsible for anthrax-related toxemia and host death, partly via inactivation of mitogen-activated protein kinase kinase (MAPKK) enzymes and consequent disruption of key cellular signaling pathways. Antibiotics such as fluoroquinolones are capable of clearing the bacilli but have no effect on LF-mediated toxemia; LF itself therefore remains the preferred target for toxin inactivation. However, currently no LF inhibitor is available on the market as a therapeutic, partly due to the insufficiency of existing LF inhibitor scaffolds in terms of efficacy, selectivity, and toxicity. In the current work, we present novel support vector machine (SVM) models with high prediction accuracy that are designed to rapidly identify potential novel, structurally diverse LF inhibitor chemical matter from compound libraries. These SVM models were trained and validated using 508 compounds with published LF biological activity data and 847 inactive compounds deposited in the Pub Chem BioAssay database. One model, M1, demonstrated particularly favorable selectivity toward highly active compounds by correctly predicting 39 (95.12%) out of 41 nanomolar-level LF inhibitors, 46 (93.88%) out of 49 inactives, and 844 (99.65%) out of 847 Pub Chem inactives in external, unbiased test sets. These models are expected to facilitate the prediction of LF inhibitory activity for existing molecules, as well as identification of novel potential LF inhibitors from large datasets.
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Affiliation(s)
- Xia Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414-2959, United States
| | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414-2959, United States; Minnesota Supercomputing Institute for Advanced Computational Research, 117 Pleasant St SE, Minneapolis, MN, United States.
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7
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Kurbanov EK, Chiu TL, Solberg J, Francis S, Maize KM, Fernandez J, Johnson RL, Hawkinson JE, Walters MA, Finzel BC, Amin EA. Probing the S2′ Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates. J Med Chem 2015; 58:8723-33. [DOI: 10.1021/acs.jmedchem.5b01446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elbek K. Kurbanov
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Ting-Lan Chiu
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jonathan Solberg
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Subhashree Francis
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Kimberly M. Maize
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jenna Fernandez
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rodney L. Johnson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jon E. Hawkinson
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A. Walters
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Barry C. Finzel
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Elizabeth Ambrose Amin
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
- Minnesota
Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455, United States
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8
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Maize KM, Zhang X, Amin EA. Statistical analysis, optimization, and prioritization of virtual screening parameters for zinc enzymes including the anthrax toxin lethal factor. Curr Top Med Chem 2014; 14:2105-14. [PMID: 25373478 DOI: 10.2174/1568026614666141106163011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 09/01/2014] [Accepted: 09/09/2014] [Indexed: 11/22/2022]
Abstract
The anthrax toxin lethal factor (LF) and matrix metalloproteinase-3 (MMP-3, stromelysin-1) are popular zinc metalloenzyme drug targets, with LF primarily responsible for anthrax-related toxicity and host death, while MMP-3 is involved in cancer- and rheumatic disease-related tissue remodeling. A number of in silico screening techniques, most notably docking and scoring, have proven useful for identifying new potential drug scaffolds targeting LF and MMP-3, as well as for optimizing lead compounds and investigating mechanisms of action. However, virtual screening outcomes can vary significantly depending on the specific docking parameters chosen, and systematic statistical significance analyses are needed to prioritize key parameters for screening small molecules against these zinc systems. In the current work, we present a series of chi-square statistical analyses of virtual screening outcomes for cocrystallized LF and MMP-3 inhibitors docked into their respective targets, evaluated by predicted enzyme-inhibitor dissociation constant and root-mean-square deviation (RMSD) between predicted and experimental bound configurations, and we present a series of preferred parameters for use with these systems in the industry-standard Surflex-Dock screening program, for use by researchers utilizing in silico techniques to discover and optimize new scaffolds.
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Affiliation(s)
| | | | - Elizabeth Ambrose Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St SE, Minneapolis, MN 55416 USA.
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9
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Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis. Nat Chem Biol 2013; 9:398-405. [PMID: 23603659 DOI: 10.1038/nchembio.1236] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/21/2013] [Indexed: 12/15/2022]
Abstract
Formation of the inflammasome, a scaffolding complex that activates caspase-1, is important in numerous diseases. Pyroptotic cell death induced by anthrax lethal toxin (LT) is a model for inflammasome-mediated caspase-1 activation. We discovered 7-desacetoxy-6,7-dehydrogedunin (7DG) in a phenotypic screen as a small molecule that protects macrophages from LT-induced death. Using chemical proteomics, we identified protein kinase R (PKR) as the target of 7DG and show that RNAi knockdown of PKR phenocopies treatment with 7DG. Further, we show that PKR's role in ASC assembly and caspase-1 activation induced by several different inflammasome stimuli is independent of PKR's kinase activity, demonstrating that PKR has a previously uncharacterized role in caspase-1 activation and pyroptosis that is distinct from its reported kinase-dependent roles in apoptosis and inflammasome formation in lipopolysaccharide-primed cells. Remarkably, PKR has different roles in two distinct cell death pathways and has a broad role in inflammasome function relevant in other diseases.
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10
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Calugi C, Trabocchi A, Lalli C, Guarna A. d-Proline-based peptidomimetic inhibitors of anthrax lethal factor. Eur J Med Chem 2012; 56:96-107. [DOI: 10.1016/j.ejmech.2012.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/27/2022]
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11
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Wein AN, Williams BN, Liu S, Ermolinsky B, Provenzano D, Abagyan R, Orry A, Leppla SH, Peredelchuk M. Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization. J Med Chem 2012; 55:7998-8006. [PMID: 22954387 DOI: 10.1021/jm300804e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protective antigen (PA), lethal factor, and edema factor, the protein toxins of Bacillus anthracis , are among its most important virulence factors and play a key role in infection. We performed a virtual ligand screen of a library of 10000 members to identify compounds predicted to bind to PA and prevent its oligomerization. Four of these compounds slowed PA association in a FRET-based oligomerization assay, and two of those protected cells from intoxication at concentrations of 1-10 μM. Exploration of the protective mechanism by Western blot showed decreased SDS-resistant PA oligomer on cells and, surprisingly, decreased amounts of activated PA. In vitro assays showed that one of the inhibitors blocked furin-mediated cleavage of PA, apparently through its binding to the PA substrate. Thus, we have identified inhibitors that can independently block both PA's cleavage by furin and its subsequent oligomerization. Lead optimization on these two backbones may yield compounds with high activity and specificity for the anthrax toxins.
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Affiliation(s)
- Alexander N Wein
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, Bethesda, Maryland 20892, USA
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12
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Chiu TL, Amin EA. Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. J Chem Inf Model 2012; 52:1886-97. [PMID: 22697455 PMCID: PMC3477282 DOI: 10.1021/ci300121p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Anthrax is an acute infectious disease caused by the spore-forming bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), an 89-kDa zinc hydrolase secreted by the bacilli, is the toxin component chiefly responsible for pathogenesis and has been a popular target for rational and structure-based drug design. Although hundreds of small-molecule compounds have been designed to target the LF active site, relatively few reported inhibitors have exhibited activity in cell-based assays, and no LF inhibitor is currently available to treat or prevent anthrax. This study presents a new pharmacophore map assembly, validated by experiment, designed to rapidly identify and prioritize promising LF inhibitor scaffolds from virtual compound libraries. The new hypothesis incorporates structural information from all five available LF enzyme-inhibitor complexes deposited in the Protein Data Bank (PDB) and is the first LF pharmacophore map reported to date that includes features representing interactions involving all three key subsites of the LF catalytic binding region. In a wide-ranging validation study on all 546 compounds for which published LF biological activity data exist, this model displayed strong selectivity toward nanomolar-level LF inhibitors, successfully identifying 72.1% of existing nanomolar-level compounds in an unbiased test set, while rejecting 100% of weakly active (>100 μM) compounds. In addition to its capabilities as a database searching tool, this comprehensive model points to a number of key design principles and previously unidentified ligand-receptor interactions that are likely to influence compound potency.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
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13
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Rubert Pérez C, López-Pérez D, Chmielewski J, Lipton M. Small molecule inhibitors of anthrax toxin-induced cytotoxicity targeted against protective antigen. Chem Biol Drug Des 2012; 79:260-9. [PMID: 22146079 DOI: 10.1111/j.1747-0285.2011.01285.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two molecular scaffolds were designed using the CAVEAT molecular design package to inhibit the oligomerization of protective antigen (PA(63) ), a key protein component of anthrax toxin. The inhibitors were designed to prevent heptamerization of PA(63) by mimicking key residues of PA(63) needed for the intermolecular interactions that stabilize the heptamer. Using the scaffolds identified by CAVEAT, seven candidate inhibitors were synthesized and tested for their ability to inhibit anthrax toxin-induced cytotoxicity, with three of the agents demonstrating modest inhibition in murine J774A.1 macrophage cells.
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14
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Kim J, Park HC, Gedi V, Park HY, Roberts AG, Atkins WM, Yoon MY. Yeast-hybrid based high-throughput assay for identification of anthrax lethal factor inhibitors. Biochem Biophys Res Commun 2010; 404:517-22. [PMID: 21144836 DOI: 10.1016/j.bbrc.2010.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
Abstract
Inhibitors of anthrax lethal factor (LF) are currently being sought as effective therapeutics for the treatment of anthrax. Here we report a novel screening approach for inhibitors of LF, a yeast-hybrid-based assay system in which the expression of reporter genes from a Gal4 promoter is repressed by LF proteolytic activity. Yeast cells were co-transformed with LF and a chimeric transcription factor that contains an LF substrate sequence inserted between the DNA-binding and activation domains of Gal4. In the resulting yeast cells, LF cleaves the substrate, thus inactivating the chimeric Gal4 and resulting in lack of expression of reporter genes. Compounds that inhibit LF cleavage of its substrate are identified by changes in reporter gene activity. Relative to in vitro screens for inhibitors of LF proteolytic activity, this screen has the advantage of excluding compounds that are toxic or non-permeable to eukaryotic cells. Additionally, the screen has the advantage of being fast, easy and cheap because exogenous LF and substrate are not needed. An initial chemical library screen with this system has identified four candidate inhibitors which were confirmed to inhibit LF protease activity in an in vitro assay. Furthermore, FBS-00831, one of the compounds identified, protects Raw 264.7 macrophages from anthrax lethal toxin and the possible binding site on LF was also evaluated by molecular docking.
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Affiliation(s)
- Joungmok Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-761, South Korea
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15
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Bouzianas DG. Current and future medical approaches to combat the anthrax threat. J Med Chem 2010; 53:4305-31. [PMID: 20102155 DOI: 10.1021/jm901024b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dimitrios G Bouzianas
- Laboratory of Molecular Endocrinology, Division of Endocrinology and Metabolism, AHEPA University Hospital, 1 S. Kyriakidi Street, P.C. 54636, Thessaloniki, Macedonia, Greece.
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16
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Chiu TL, Solberg J, Patil S, Geders TW, Zhang X, Rangarajan S, Francis R, Finzel BC, Walters MA, Hook DJ, Amin EA. Identification of novel non-hydroxamate anthrax toxin lethal factor inhibitors by topomeric searching, docking and scoring, and in vitro screening. J Chem Inf Model 2009; 49:2726-34. [PMID: 19928768 PMCID: PMC2805240 DOI: 10.1021/ci900186w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anthrax is an infectious disease caused by Bacillus anthracis, a Gram-positive, rod-shaped, anaerobic bacterium. The lethal factor (LF) enzyme is secreted by B. anthracis as part of a tripartite exotoxin and is chiefly responsible for anthrax-related cytotoxicity. As LF can remain in the system long after antibiotics have eradicated B. anthracis from the body, the preferred therapeutic modality would be the administration of antibiotics together with an effective LF inhibitor. Although LF has garnered a great deal of attention as an attractive target for rational drug design, relatively few published inhibitors have demonstrated activity in cell-based assays and, to date, no LF inhibitor is available as a therapeutic or preventive agent. Here we present a novel in silico high-throughput virtual screening protocol that successfully identified 5 non-hydroxamic acid small molecules as new, preliminary LF inhibitor scaffolds with low micromolar inhibition against that target, resulting in a 12.8% experimental hit rate. This protocol screened approximately 35 million nonredundant compounds for potential activity against LF and comprised topomeric searching, docking and scoring, and drug-like filtering. Among these 5 hit compounds, none of which has previously been identified as a LF inhibitor, three exhibited experimental IC(50) values less than 100 microM. These three preliminary hits may potentially serve as scaffolds for lead optimization as well as templates for probe compounds to be used in mechanistic studies. Notably, our docking simulations predicted that these novel hits are likely to engage in critical ligand-receptor interactions with nearby residues in at least two of the three (S1', S1-S2, and S2') subsites in the LF substrate binding area. Further experimental characterization of these compounds is in process. We found that micromolar-level LF inhibition can be attained by compounds with non-hydroxamate zinc-binding groups that exhibit monodentate zinc chelation as long as key hydrophobic interactions with at least two LF subsites are retained.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Jonathan Solberg
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Satish Patil
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431
| | - Todd W. Geders
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Xia Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Subhashree Rangarajan
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Rawle Francis
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Barry C. Finzel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Michael A. Walters
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Derek J. Hook
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
- Minnesota Supercomputing Institute for Advanced Computational Research, 117 Pleasant St. SE, Minneapolis, MN 55455
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17
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Agrawal A, de Oliveira CAF, Cheng Y, Jacobsen JA, McCammon JA, Cohen SM. Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor. J Med Chem 2009; 52:1063-74. [PMID: 19170530 PMCID: PMC2698031 DOI: 10.1021/jm8013212] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Anthrax lethal factor (LF) is a critical virulence factor in the pathogenesis of anthrax. A structure-activity relationship (SAR) of potential lethal factor inhibitors (LFi) is presented in which the zinc-binding group (ZBG), linker, and backbone moieties for a series of hydroxypyrone-based compounds were systematically varied. It was found that hydroxypyrothione ZBGs generate more potent inhibitors than hydroxypyrone ZBGs. Furthermore, coupling the hydroxypyrothione to a backbone group via a thioamide bond improves potency when compared to an amide linker. QM/MM studies show that the thioamide bond in these inhibitors allows for the formation of two additional hydrogen bonds with the protein active site. In both types of hydroxypyrothione compounds, ligand efficiencies of 0.29-0.54 kcal mol(-1) per heavy atom were achieved. The results highlight the need for a better understanding to optimize the interplay between the ZBG, linker, and backbone to get improved LFi.
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Affiliation(s)
- Arpita Agrawal
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - César Augusto F. de Oliveira
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Yuhui Cheng
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Jennifer A. Jacobsen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
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18
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Verma RP, Hansch C. Combating the Threat of Anthrax: A Quantitative Structure−Activity Relationship Approach. Mol Pharm 2008; 5:745-59. [DOI: 10.1021/mp8000149] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rajeshwar P. Verma
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711
| | - Corwin Hansch
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711
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19
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Gaddis BD, Rubert Pérez CM, Chmielewski J. Inhibitors of anthrax lethal factor based upon N-oleoyldopamine. Bioorg Med Chem Lett 2008; 18:2467-70. [DOI: 10.1016/j.bmcl.2008.02.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/12/2008] [Accepted: 02/14/2008] [Indexed: 11/30/2022]
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20
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Cao S, Liu Z, Guo A, Li Y, Zhang C, Gaobing W, Chunfang F, Tan Y, Chen H. Efficient production and characterization of Bacillus anthracis lethal factor and a novel inactive mutant rLFm-Y236F. Protein Expr Purif 2008; 59:25-30. [PMID: 18276157 DOI: 10.1016/j.pep.2007.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2007] [Revised: 12/24/2007] [Accepted: 12/31/2007] [Indexed: 11/17/2022]
Abstract
Lethal factor (LF) is a 90kDa zinc metalloprotease that plays an important role in the virulence of anthrax. Recombinant LF (rLF) is an effective tool to study anthrax pathogenesis and treatment. In this study, the LF gene was cloned into the Escherichia coli expression vector pGEX-6P-1 and expressed as a GST fusion protein (GST-rLF) in E. coli BL21-codonPlus (DE3)-RIL cells with 0.2mM IPTG induction at 28 degrees C. The GST-rLF protein was purified and the GST-tag was then cleaved in a single step by combining both GST-affinity column and treatment with 3C protease. This procedure yielded 5mg of rLF protein per liter of culture. The purified rLF was functional as confirmed by cytotoxicity assay in RAW264.7 cells and Western blot assay. Furthermore, the rLF could induce strong immune response in BALB/c mice and the presence of a specific antiserum could neutralize the cytotoxicity of rLF in vitro. In addition, a novel inactive mutant (rLFm-Y236F) was obtained. Compared to the wild-type rLF, an increase by 3700 folds of the purified rLFm-Y236F was needed to achieve a similar level of cytotoxicity of the wild-type rLF. This mutant might be of significance in the study of anthrax pathogenesis and treatment.
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Affiliation(s)
- Sha Cao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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