1
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Gannam ZTK, Min K, Shillingford SR, Zhang L, Herrington J, Abriola L, Gareiss PC, Pantouris G, Tzouvelekis A, Kaminski N, Zhang X, Yu J, Jamali H, Ellman JA, Lolis E, Anderson KS, Bennett AM. An allosteric site on MKP5 reveals a strategy for small-molecule inhibition. Sci Signal 2020; 13:eaba3043. [PMID: 32843541 PMCID: PMC7569488 DOI: 10.1126/scisignal.aba3043] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mitogen-activated protein kinase (MAPK) phosphatases (MKPs) have been considered "undruggable," but their position as regulators of the MAPKs makes them promising therapeutic targets. MKP5 has been suggested as a potential target for the treatment of dystrophic muscle disease. Here, we identified an inhibitor of MKP5 using a p38α MAPK-derived, phosphopeptide-based small-molecule screen. We solved the structure of MKP5 in complex with this inhibitor, which revealed a previously undescribed allosteric binding pocket. Binding of the inhibitor to this pocket collapsed the MKP5 active site and was predicted to limit MAPK binding. Treatment with the inhibitor recapitulated the phenotype of MKP5 deficiency, resulting in activation of p38 MAPK and JNK. We demonstrated that MKP5 was required for TGF-β1 signaling in muscle and that the inhibitor blocked TGF-β1-mediated Smad2 phosphorylation. TGF-β1 pathway antagonism has been proposed for the treatment of dystrophic muscle disease. Thus, allosteric inhibition of MKP5 represents a therapeutic strategy against dystrophic muscle disease.
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Affiliation(s)
- Zira T K Gannam
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kisuk Min
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shanelle R Shillingford
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Lei Zhang
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - James Herrington
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Peter C Gareiss
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Georgios Pantouris
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xinbo Zhang
- Department of Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Jun Yu
- Center for Metabolic Disease Research and Department of Physiology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Haya Jamali
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | | | - Elias Lolis
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
- Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA
| | - Anton M Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
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2
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Patridge EV, Gareiss PC, Kinch MS, Hoyer DW. An analysis of original research contributions toward FDA-approved drugs. Drug Discov Today 2015; 20:1182-7. [DOI: 10.1016/j.drudis.2015.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/12/2022]
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3
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Noblin DJ, Page CM, Tae HS, Gareiss PC, Schneekloth JS, Crews CM. A HaloTag-based small molecule microarray screening methodology with increased sensitivity and multiplex capabilities. ACS Chem Biol 2012; 7:2055-63. [PMID: 23013033 DOI: 10.1021/cb300453k] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Small Molecule Microarrays (SMMs) represent a general platform for screening small molecule-protein interactions independent of functional inhibition of target proteins. In an effort to increase the scope and utility of SMMs, we have modified the SMM screening methodology to increase assay sensitivity and facilitate multiplex screening. Fusing target proteins to the HaloTag protein allows us to covalently prelabel fusion proteins with fluorophores, leading to increased assay sensitivity and an ability to conduct multiplex screens. We use the interaction between FKBP12 and two ligands, rapamycin and ARIAD's "bump" ligand, to show that the HaloTag-based SMM screening methodology significantly increases assay sensitivity. Additionally, using wild type FKBP12 and the FKBP12 F36V mutant, we show that prelabeling various protein isoforms with different fluorophores allows us to conduct multiplex screens and identify ligands to a specific isoform. Finally, we show this multiplex screening technique is capable of identifying ligands selective for a specific PTP1B isoform using a 20,000 compound screening deck.
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Affiliation(s)
| | | | | | - Peter C. Gareiss
- Yale Center for Molecular Discovery, 100 West Campus Drive, Orange,
Connecticut 06477, United States
| | - John S. Schneekloth
- Yale Center for Molecular Discovery, 100 West Campus Drive, Orange,
Connecticut 06477, United States
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4
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Buckley DL, Gustafson JL, Van Molle I, Roth AG, Tae HS, Gareiss PC, Jorgensen WL, Ciulli A, Crews CM. Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1α. Angew Chem Int Ed Engl 2012; 51:11463-7. [PMID: 23065727 PMCID: PMC3519281 DOI: 10.1002/anie.201206231] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [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: 08/03/2012] [Indexed: 01/03/2023]
Abstract
E3 ubiquitin ligases, such as the therapeutically relevant VHL, are challenging targets for traditional medicinal chemistry, as their modulation requires targeting protein-protein interactions. We report novel small-molecule inhibitors of the interaction between VHL and its molecular target HIF1α, a transcription factor involved in oxygen sensing.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Jeffrey L. Gustafson
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Inge Van Molle
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Anke G. Roth
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Hyun Seop Tae
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Peter C. Gareiss
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - William L. Jorgensen
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Craig M. Crews
- Departments of Chemistry, Molecular, Cellular & Developmental Biology and Pharmacology, and Center for Molecular Discovery, Yale University, New Haven, Connecticut 06511, United States
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5
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Buckley DL, Gustafson JL, Van Molle I, Roth AG, Tae HS, Gareiss PC, Jorgensen WL, Ciulli A, Crews CM. Niedermolekulare Inhibitoren der Wechselwirkung zwischen der E3-Ligase VHL und HIF1α. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction. J Am Chem Soc 2012; 134:4465-8. [PMID: 22369643 PMCID: PMC3448299 DOI: 10.1021/ja209924v] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [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: 12/23/2022]
Abstract
![]()
E3 ubiquitin ligases, which bind protein targets, leading
to their
ubiquitination and subsequent degradation, are attractive drug targets
due to their exquisite substrate specificity. However, the development
of small-molecule inhibitors has proven extraordinarily challenging
as modulation of E3 ligase activities requires the targeting of protein–protein
interactions. Using rational design, we have generated the first small
molecule targeting the von Hippel–Lindau protein (VHL), the
substrate recognition subunit of an E3 ligase, and an important target
in cancer, chronic anemia, and ischemia. We have also obtained the
crystal structure of VHL bound to our most potent inhibitor, confirming
that the compound mimics the binding mode of the transcription factor
HIF-1α, a substrate of VHL. These results have the potential
to guide future development of improved lead compounds as therapeutics
for the treatment of chronic anemia and ischemia.
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Affiliation(s)
- Dennis L Buckley
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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7
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Palde PB, Ofori LO, Gareiss PC, Lerea J, Miller BL. Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence. J Med Chem 2010; 53:6018-27. [PMID: 20672840 DOI: 10.1021/jm100231t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Production of the Gag-Pol polyprotein in human immunodeficiency virus (HIV) requires a -1 ribosomal frameshift, which is directed by a highly conserved RNA stem-loop. Building on our discovery of a set of disulfide-containing peptides that bind this RNA, we describe medicinal chemistry efforts designed to begin to understand the structure-activity relationships and RNA sequence-selectivity relationships associated with these compounds. Additionally, we have prepared analogues incorporating an olefin or saturated hydrocarbon bioisostere of the disulfide moiety, as a first step toward enhancing biostability. The olefin-containing compounds exhibit affinity comparable to the lead disulfide and, importantly, have no discernible toxicity when incubated with human fibroblasts at concentrations up to 1 mM.
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Affiliation(s)
- Prakash B Palde
- Department of Dermatology, University of Rochester, Rochester, NY 14642, USA
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8
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Abstract
The development of new ligands for the oncoprotein Ras can provide tools for the study of this important signaling component or potentially serve as therapeutic agents for the treatment of Ras-associated diseases. Herein, we report a peptidic Ras ligand identified through naïve phage display. Panning a phage library with a diversity of 10(9) transormants successfully identified a peptide dodecamer that contains two internal consensus motifs and binds Ras in both the active GTP- and inactive GDP-bound conformations with low micromolar dissociation constants. The dodecamer does not alter the intrinsic GTPase activity of Ras, does not compete for Ras binding to the Ras binding domain of Raf, and does not alter cell viability. This novel Ras ligand has the potential to serve in the development of higher-affinity ligands and chemical tools targeting Ras.
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Affiliation(s)
- Peter C Gareiss
- Department of Molecular, Cellular & Developmental Biology, Yale University, P. O. Box 208103, New Haven, CT 06520-8103, USA
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9
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McNaughton BR, Gareiss PC, Jacobs SE, Fricke AF, Scott GA, Miller BL. A potent activator of melanogenesis identified from small-molecule screening. ChemMedChem 2009; 4:1583-9. [PMID: 19670207 DOI: 10.1002/cmdc.200900194] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Brian R McNaughton
- Department of Chemistry, University of Rochester, Rochester, NY 14627 (USA)
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10
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Rowlett RS, Tu C, Lee J, Herman AG, Chapnick DA, Shah SH, Gareiss PC. Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase. Biochemistry 2009; 48:6146-56. [PMID: 19459702 DOI: 10.1021/bi900663h] [Citation(s) in RCA: 22] [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: 11/28/2022]
Abstract
Haemophilus influenzae beta-carbonic anhydrase (HICA) is hypothesized to be an allosteric protein that is regulated by the binding of bicarbonate ion to a non-catalytic (inhibitory) site that controls the ligation of Asp44 to the catalytically essential zinc ion. We report here the X-ray crystallographic structures of two variants (W39F and Y181F) involved in the binding of bicarbonate ion in the non-catalytic site and an active-site variant (D44N) that is incapable of forming a strong zinc ligand. The alteration of Trp39 to Phe increases the apparent K(i) for bicarbonate inhibition by 4.8-fold. While the structures of W39F and Y181F are very similar to the wild-type enzyme, the X-ray crystal structure of the D44N variant reveals that it has adopted an active-site conformation nearly identical to that of non-allosteric beta-carbonic anhydrases. We propose that the structure of the D44N variant is likely to be representative of the active conformation of the enzyme. These results lend additional support to the hypothesis that HICA is an allosteric enzyme that can adopt active and inactive conformations, the latter of which is stabilized by bicarbonate ion binding to a non-catalytic site.
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Affiliation(s)
- Roger S Rowlett
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York 13346, USA.
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11
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Gareiss PC, Miller BL. Ribosomal frameshifting: an emerging drug target for HIV. Curr Opin Investig Drugs 2009; 10:121-128. [PMID: 19197789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Combating HIV currently remains one of the key public health challenges. While immense effort has been invested in the development of HIV-targeted therapeutic agents, interfering with protein synthesis is a relatively unexplored area. HIV has an absolute requirement for a -1 ribosomal frameshift event during translation that constitutes a potentially attractive target for interfering with the viral life cycle. Research suggests that while a considerable amount of investigation is still required, targeting frameshifting in HIV with small molecules, peptides and oligonucleotides is feasible.
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Affiliation(s)
- Peter C Gareiss
- University of Rochester, Department of Dermatology, Rochester, New York, NY 14642, USA
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12
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Gareiss PC, Sobczak K, McNaughton BR, Palde PB, Thornton CA, Miller BL. Dynamic combinatorial selection of molecules capable of inhibiting the (CUG) repeat RNA-MBNL1 interaction in vitro: discovery of lead compounds targeting myotonic dystrophy (DM1). J Am Chem Soc 2008; 130:16254-61. [PMID: 18998634 PMCID: PMC2645920 DOI: 10.1021/ja804398y] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [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] [Indexed: 12/21/2022]
Abstract
Myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults, is an RNA-mediated disease. Dramatically expanded (CUG) repeats accumulate in nuclei and sequester RNA-binding proteins such as the splicing regulator MBNL1. We have employed resin-bound dynamic combinatorial chemistry (RBDCC) to identify the first examples of compounds able to inhibit MBNL1 binding to (CUG) repeat RNA. Screening an RBDCL with a theoretical diversity of 11 325 members yielded several molecules with significant selectivity for binding to (CUG) repeat RNA over other sequences. These compounds were also able to inhibit the interaction of GGG-(CUG)(109)-GGG RNA with MBNL1 in vitro, with K(i) values in the low micromolar range.
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Affiliation(s)
- Peter C. Gareiss
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
| | - Krzysztof Sobczak
- Department of Neurology, University of Rochester, Rochester, New York 14642
| | - Brian R. McNaughton
- Department of Chemistry, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
| | - Prakash B. Palde
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
| | | | - Benjamin L Miller
- Department of Dermatology, University of Rochester, Rochester, New York 14642
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
- The Center for Future Health, University of Rochester, Rochester, New York 14642
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13
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Affiliation(s)
- Prakash B. Palde
- Department of Biochemistry and Biophysics and Department of Dermatology, University of Rochester, Rochester, New York 14642
| | - Peter C. Gareiss
- Department of Biochemistry and Biophysics and Department of Dermatology, University of Rochester, Rochester, New York 14642
| | - Benjamin L. Miller
- Department of Biochemistry and Biophysics and Department of Dermatology, University of Rochester, Rochester, New York 14642
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14
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McNaughton BR, Gareiss PC, Miller BL. Identification of a selective small-molecule ligand for HIV-1 frameshift-inducing stem-loop RNA from an 11,325 member resin bound dynamic combinatorial library. J Am Chem Soc 2007; 129:11306-7. [PMID: 17722919 DOI: 10.1021/ja072114h] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian R McNaughton
- Department of Dermatology, University of Rochester, Rochester, New York 14642, USA
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15
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Gareiss PC, Palde PB, Hubbard RD, Miller BL. Conformational and Structural Analysis of ater-Cyclopentane Scaffold for Molecular Recognition. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
The first example of a designed receptor containing a cis-1,3-disubstituted cyclobutane ring has been synthesized. This molecule binds diphosphoryl lipid A (a conserved portion of the Gram-(-) bacterial cell membrane, and the causative agent of septic shock) with an affinity comparable to previously described ter-cycloalkane based lipid A-binding compounds.
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Affiliation(s)
- Kevin M Bucholtz
- Department of Chemistry, University of Rochester, Rochester, New York, USA
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17
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Cronk JD, Rowlett RS, Zhang KYJ, Tu C, Endrizzi JA, Lee J, Gareiss PC, Preiss JR. Identification of a Novel Noncatalytic Bicarbonate Binding Site in Eubacterial β-Carbonic Anhydrase. Biochemistry 2006; 45:4351-61. [PMID: 16584170 DOI: 10.1021/bi052272q] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structures of beta class carbonic anhydrases (beta-CAs) determined so far fall into two distinct subclasses based on the observed coordination of the catalytic zinc (Zn2+) ion. The subclass of beta-CAs that coordinate Zn2+ tetrahedrally with four protein-derived ligands is represented by the structures of orthologues from Porphyridium purpureum, Escherichia coli, and Mycobacterium tuberculosis. Here we present the structure of an additional member of that subclass, that from Haemophilus influenzae, as well as detailed kinetic analysis, revealing the correspondence between structural classification and kinetic profile for this subclass. In addition, we identify a unique, noncatalytic binding mode for the substrate bicarbonate that occurs in both the H. influenzae and E. coli enzymes. The kinetic and structural analysis indicates that binding of bicarbonate in this site of the enzyme may modulate its activity by influencing a pH-dependent, cooperative transition between active and inactive forms. We hypothesize that the two structural subclasses of beta-CAs may provide models for the proposed active and inactive forms of the H. influenzae and E. coli enzymes.
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Affiliation(s)
- Jeff D Cronk
- Department of Chemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258, USA.
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