101
|
Fullagar JL, Garner AL, Struss AK, Day JA, Martin DP, Yu J, Cai X, Janda KD, Cohen SM. Antagonism of a zinc metalloprotease using a unique metal-chelating scaffold: tropolones as inhibitors of P. aeruginosa elastase. Chem Commun (Camb) 2013; 49:3197-9. [PMID: 23482955 PMCID: PMC3618488 DOI: 10.1039/c3cc41191e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tropolone emerged from the screening of a chelator fragment library (CFL) as an inhibitor of the Zn(2+)-dependent virulence factor, Pseudomonas aeruginosa elastase (LasB). Based on this initial hit, a series of substituted tropolone-based LasB inhibitors was prepared, and a compound displaying potent activity in vitro and in a bacterial swarming assay was identified. Importantly, this inhibitor was found to be specific for LasB over other metalloenzymes, validating the usage of tropolone as a viable scaffold for identifying first-in-class LasB inhibitors.
Collapse
Affiliation(s)
- Jessica L. Fullagar
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Amanda L. Garner
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Anjali K. Struss
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Joshua A. Day
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - David P. Martin
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Jing Yu
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Xiaoqing Cai
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Kim D. Janda
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| | - Seth M. Cohen
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA 92093
| |
Collapse
|
102
|
Franz KJ. Clawing back: broadening the notion of metal chelators in medicine. Curr Opin Chem Biol 2013; 17:143-9. [PMID: 23332666 DOI: 10.1016/j.cbpa.2012.12.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/20/2012] [Accepted: 12/26/2012] [Indexed: 02/04/2023]
Abstract
The traditional notion of chelation therapy is the administration of a chemical agent to remove metals from the body. But formation of a metal-chelate can have biological ramifications that are much broader than metal elimination. Exploring these other possibilities could lead to pharmacological interventions that alter the concentration, distribution, or reactivity of metals in targeted ways for therapeutic benefit. This review highlights recent examples that showcase four general strategies of using principles of metal chelation in medicinal contexts beyond the traditional notion of chelation therapy. These strategies include altering metal biodistribution, inhibiting specific metalloenzymes associated with disease, enhancing the reactivity of a metal complex to promote cytotoxicity, and conversely, passivating the reactivity of metals by site-activated chelation to prevent cytotoxicity.
Collapse
Affiliation(s)
- Katherine J Franz
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA.
| |
Collapse
|
103
|
Bisignano P, Lambruschini C, Bicego M, Murino V, Favia AD, Cavalli A. In silico deconstruction of ATP-competitive inhibitors of glycogen synthase kinase-3β. J Chem Inf Model 2012. [PMID: 23198830 DOI: 10.1021/ci300355p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based methods have emerged in the last two decades as alternatives to traditional high throughput screenings for the identification of chemical starting points in drug discovery. One arguable yet popular assumption about fragment-based design is that the fragment binding mode remains conserved upon chemical expansion. For instance, the question of the binding conservation upon fragmentation of a molecule is still unclear. A number of papers have challenged this hypothesis by means of experimental techniques, with controversial results, "underlining" the idea that a simple generalization, maybe, is not possible. From a computational standpoint, the issue has been rarely addressed and mostly to test novel protocols on limited data sets. To fill this gap, we here report on a computational retrospective study concerned with the in silico deconstruction of leadlike compounds, active on the pharmaceutically relevant enzyme glycogen synthase kinase-3β.
Collapse
Affiliation(s)
- Paola Bisignano
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy
| | | | | | | | | | | |
Collapse
|
104
|
|
105
|
Garner AL, Struss AK, Fullagar JL, Agrawal A, Moreno AY, Cohen SM, Janda KD. 3-Hydroxy-1-alkyl-2-methylpyridine-4(1H)-thiones: Inhibition of the Pseudomonas aeruginosa Virulence Factor LasB. ACS Med Chem Lett 2012. [PMID: 23181168 DOI: 10.1021/ml300128f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Bacterial resistance coupled to our current arsenal of antibiotics presents us with a growing threat to public health, thus warranting the exploration of alternative antibacterial strategies. In particular, the targeting of virulence factors has been regarded as a "second generation" antibiotic approach. In Pseudomonas aeruginosa, a Zn(2+) metalloprotease virulence factor, LasB or P. aeruginosa elastase, has been implicated in the development of P. aeruginosa-related keratitis, pneumonia and burn infection. Moreover, the enzyme also plays a critical role in swarming and biofilm formation, both of which are processes that have been linked to antibiotic resistance. To further validate the importance of LasB in P. aeruginosa infection, we describe our efforts toward the discovery of non-peptidic small molecule inhibitors of LasB. Using identified compounds, we have confirmed the role that LasB plays in P. aeruginosa swarming and demonstrate the potential for LasB-targeted small molecules in studying antimicrobial resistant P. aeruginosa phenotypes.
Collapse
Affiliation(s)
- Amanda L. Garner
- Departments of Chemistry and
Immunology and Microbial Science, The Skaggs Institute for Chemical
Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California, United States
| | - Anjali K. Struss
- Departments of Chemistry and
Immunology and Microbial Science, The Skaggs Institute for Chemical
Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California, United States
| | - Jessica L. Fullagar
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, United States
| | - Arpita Agrawal
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, United States
| | - Amira Y. Moreno
- Departments of Chemistry and
Immunology and Microbial Science, The Skaggs Institute for Chemical
Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California, United States
| | - Seth M. Cohen
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California, United States
| | - Kim D. Janda
- Departments of Chemistry and
Immunology and Microbial Science, The Skaggs Institute for Chemical
Biology, The Worm Institute for Research and Medicine, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, California, United States
| |
Collapse
|
106
|
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.
Collapse
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
| |
Collapse
|
107
|
Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| |
Collapse
|
108
|
Martin DP, Cohen SM. Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors. Chem Commun (Camb) 2012; 48:5259-61. [PMID: 22531842 DOI: 10.1039/c2cc32013d] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of hydroxybenzoic acid derivatives have shown inhibitory activity against carbonic anhydrase (CA). X-ray crystallography shows that these molecules inhibit not by binding the active site metal ion but by strong hydrogen bonding to the metal-bound water nucleophile. The binding mode observed for these molecules is distinct when compared to other non-metal-binding CA inhibitors.
Collapse
Affiliation(s)
- David P Martin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
| | | |
Collapse
|
109
|
Flagg SC, Martin CB, Taabazuing CY, Holmes BE, Knapp MJ. Screening chelating inhibitors of HIF-prolyl hydroxylase domain 2 (PHD2) and factor inhibiting HIF (FIH). J Inorg Biochem 2012; 113:25-30. [PMID: 22687491 DOI: 10.1016/j.jinorgbio.2012.03.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 02/04/2012] [Accepted: 03/09/2012] [Indexed: 12/12/2022]
Abstract
Two primary O(2)-sensors for humans are the HIF-hydroxylases, enzymes that hydroxylate specific residues of the hypoxia inducible factor-α (HIF). These enzymes are factor inhibiting HIF (FIH) and prolyl hydroxylase-2 (PHD2), each an α-ketoglutarate (αKG) dependent, non-heme Fe(II) dioxygenase. Although the two enzymes have similar active sites, FIH hydroxylates Asn(803) of HIF-1α while PHD2 hydroxylates Pro(402) and/or Pro(564) of HIF-1α. The similar structures but unique functions of FIH and PHD2 make them prime targets for selective inhibition leading to regulatory control of diseases such as cancer and stroke. Three classes of iron chelators were tested as inhibitors for FIH and PHD2: pyridines, hydroxypyrones/hydroxypyridinones and catechols. An initial screen of the ten small molecule inhibitors at varied [αKG] revealed a non-overlapping set of inhibitors for PHD2 and FIH. Dose response curves at moderate [αKG] ([αKG]~K(M)) showed that the hydroxypyrones/hydroxypyridinones were selective inhibitors, with IC(50) in the μM range, and that the catechols were generally strong inhibitors of both FIH and PHD2, with IC(50) in the low μM range. As support for binding at the active site of each enzyme as the mode of inhibition, electron paramagnetic resonance (EPR) spectroscopy were used to demonstrate inhibitor binding to the metal center of each enzyme. This work shows some selective inhibition between FIH and PHD2, primarily through the use of simple aromatic or pseudo-aromatic chelators, and suggests that hydroxypyrones and hydroxypyridones may be promising chelates for FIH or PHD2 inhibition.
Collapse
Affiliation(s)
- Shannon C Flagg
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | | | | | | |
Collapse
|
110
|
Hanaya K, Suetsugu M, Saijo S, Yamato I, Aoki S. Potent inhibition of dinuclear zinc(II) peptidase, an aminopeptidase from Aeromonas proteolytica, by 8-quinolinol derivatives: inhibitor design based on Zn2+ fluorophores, kinetic, and X-ray crystallographic study. J Biol Inorg Chem 2012; 17:517-29. [DOI: 10.1007/s00775-012-0873-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 12/28/2011] [Indexed: 11/25/2022]
|
111
|
Johnson S, Barile E, Farina B, Purves A, Wei J, Chen LH, Shiryaev S, Zhang Z, Rodionova I, Agrawal A, Cohen SM, Osterman A, Strongin A, Pellecchia M. Targeting metalloproteins by fragment-based lead discovery. Chem Biol Drug Des 2011; 78:211-23. [PMID: 21564556 DOI: 10.1111/j.1747-0285.2011.01136.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
It has been estimated that nearly one-third of functional proteins contain a metal ion. These constitute a wide variety of possible drug targets including metalloproteinases, dehydrogenases, oxidoreductases, hydrolases, deacetylases, or many others in which the metal ion is either of catalytic or of structural nature. Despite the predominant role of a metal ion in so many classes of drug targets, current high-throughput screening techniques do not usually produce viable hits against these proteins, likely due to the lack of proper metal-binding pharmacophores in the current screening libraries. Herein, we describe a novel fragment-based drug discovery approach using a metal-targeting fragment library that is based on a variety of distinct classes of metal-binding groups designed to reliably anchor the fragments at the target's metal ions. We show that the approach can effectively identify novel, potent and selective agents that can be readily developed into metalloprotein-targeted therapeutics.
Collapse
Affiliation(s)
- Sherida Johnson
- Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
112
|
Abstract
Numerous metalloproteins are important therapeutic targets that are gaining increased attention in the medicinal and bioinorganic chemistry communities. This Perspective article describes some emerging trends and recent findings in the area of metalloprotein inhibitor discovery and development. In particular, increasing recognition of the importance of the metal-ligand interactions in these systems calls for more input and consideration from the bioinorganic community to address questions traditionally confined to the medicinal chemistry community.
Collapse
Affiliation(s)
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, U.S.A. Fax: 858-822-5598; Tel: 858-822-5596
| |
Collapse
|