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Zhukovets AA, Chernyshov VV, Al’mukhametov AZ, Seregina TA, Revtovich SV, Kasatkina MA, Isakova YE, Kulikova VV, Morozova EA, Cherkasova AI, Mannanov TA, Anashkina AA, Solyev PN, Mitkevich VA, Ivanov RA. Novel Hydroxamic Acids Containing Aryl-Substituted 1,2,4- or 1,3,4-Oxadiazole Backbones and an Investigation of Their Antibiotic Potentiation Activity. Int J Mol Sci 2023; 25:96. [PMID: 38203266 PMCID: PMC10779255 DOI: 10.3390/ijms25010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a zinc amidase that catalyzes the second step of the biosynthesis of lipid A, which is an outer membrane essential structural component of Gram-negative bacteria. Inhibitors of this enzyme can be attributed to two main categories, non-hydroxamate and hydroxamate inhibitors, with the latter being the most effective given the chelation of Zn2+ in the active site. Compounds containing diacetylene or acetylene tails and the sulfonic head, as well as oxazoline derivatives of hydroxamic acids, are among the LpxC inhibitors with the most profound antibacterial activity. The present article describes the synthesis of novel functional derivatives of hydroxamic acids-bioisosteric to oxazoline inhibitors-containing 1,2,4- and 1,3,4-oxadiazole cores and studies of their cytotoxicity, antibacterial activity, and antibiotic potentiation. Some of the hydroxamic acids we obtained (9c, 9d, 23a, 23c, 30b, 36) showed significant potentiation in nalidixic acid, rifampicin, and kanamycin against the growth of laboratory-strain Escherichia coli MG1655. Two lead compounds (9c, 9d) significantly reduced Pseudomonas aeruginosa ATCC 27853 growth in the presence of nalidixic acid and rifampicin.
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Affiliation(s)
- Anastasia A. Zhukovets
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Vladimir V. Chernyshov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Aidar Z. Al’mukhametov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Tatiana A. Seregina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Svetlana V. Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Mariia A. Kasatkina
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Yulia E. Isakova
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Vitalia V. Kulikova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Elena A. Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Anastasia I. Cherkasova
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Timur A. Mannanov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
| | - Anastasia A. Anashkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Pavel N. Solyev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia; (T.A.S.); (S.V.R.); (V.V.K.); (E.A.M.); (A.A.A.); (P.N.S.); (V.A.M.)
| | - Roman A. Ivanov
- Translational Medicine Research Center, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (A.A.Z.); (A.Z.A.); (M.A.K.); (Y.E.I.); (A.I.C.); (T.A.M.); (R.A.I.)
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2
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Nargund R, Wyvratt M, Lin S, Sebhat I, Greenlee W. Annotated Bibliography of Dr. Arthur A. Patchett. J Med Chem 2023; 66:15567-15575. [PMID: 38032081 DOI: 10.1021/acs.jmedchem.3c02131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
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3
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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4
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Evenson GE, Powell WC, Hinds AB, Walczak MA. Catalytic Amide Activation with Thermally Stable Molybdenum(VI) Dioxide Complexes. J Org Chem 2023; 88:6192-6202. [PMID: 37027833 PMCID: PMC10422866 DOI: 10.1021/acs.joc.3c00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Oxazolines and thiazolines are important constituents of bioactive natural products and pharmaceuticals. Here, we report the development of an effective and practical method of oxazoline and thiazoline formation, which can facilitate the synthesis of natural products, chiral ligands, and pharmaceutical intermediates. This method capitalized on a Mo(VI) dioxide catalyst stabilized by substituted picolinic acid ligands, which is tolerant to many functional groups that would otherwise be sensitive to highly electrophilic alternative reagents.
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Affiliation(s)
- Garrett E Evenson
- University of Colorado, Department of Chemistry, Boulder, Colorado 80309, United States
| | - Wyatt C Powell
- University of Colorado, Department of Chemistry, Boulder, Colorado 80309, United States
| | - Aaron B Hinds
- University of Colorado, Department of Chemistry, Boulder, Colorado 80309, United States
| | - Maciej A Walczak
- University of Colorado, Department of Chemistry, Boulder, Colorado 80309, United States
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5
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Kumar Pal S, Kumar S. LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) inhibitors: A long path explored for potent drug design. Int J Biol Macromol 2023; 234:122960. [PMID: 36565833 DOI: 10.1016/j.ijbiomac.2022.12.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Microbial infections are becoming resistant to traditional antibiotics. As novel resistance mechanisms are developed and disseminated across the world, our ability to treat the most common infectious diseases is becoming increasingly compromised. As existing antibiotics are losing their effectiveness, especially treatment of bacterial infections, is difficult. In order to combat this issue, it is of utmost importance to identify novel pharmacological targets or antibiotics. LpxC, a zinc-dependent metalloamidase that catalyzes the committed step in the biosynthesis of lipid A (endotoxin) in bacteria, is a prime candidate for drug/therapeutic target. So far, the rate-limiting metallo-amidase LpxC has been the most-targeted macromolecule in the Raetz pathway. This is because it is important for the growth of these bacterial infections. This review showcases on the research done to develop efficient drugs in this area before and after the 2015.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
| | - Sanjit Kumar
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
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Basak S, Li Y, Tao S, Daryaee F, Merino J, Gu C, Delker SL, Phan JN, Edwards TE, Walker SG, Tonge PJ. Structure-Kinetic Relationship Studies for the Development of Long Residence Time LpxC Inhibitors. J Med Chem 2022; 65:11854-11875. [PMID: 36037447 PMCID: PMC10182817 DOI: 10.1021/acs.jmedchem.2c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a promising drug target in Gram-negative bacteria. Previously, we described a correlation between the residence time of inhibitors on Pseudomonas aeruginosa LpxC (paLpxC) and the post-antibiotic effect (PAE) caused by the inhibitors on the growth of P. aeruginosa. Given that drugs with prolonged activity following compound removal may have advantages in dosing regimens, we have explored the structure-kinetic relationship for paLpxC inhibition by analogues of the pyridone methylsulfone PF5081090 (1) originally developed by Pfizer. Several analogues have longer residence times on paLpxC than 1 (41 min) including PT913, which has a residence time of 124 min. PT913 also has a PAE of 4 h, extending the original correlation observed between residence time and PAE. Collectively, the studies provide a platform for the rational modulation of paLpxC inhibitor residence time and the potential development of antibacterial agents that cause prolonged suppression of bacterial growth.
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Affiliation(s)
- Sneha Basak
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Yong Li
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Suyuan Tao
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Jonathan Merino
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Chendi Gu
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | - Jenny N. Phan
- McGill University Montreal, Quebec H3A 0G4, Canada Canada
| | | | - Stephen G. Walker
- Department of Oral Biology and Pathology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
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7
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Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
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Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
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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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9
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Galster M, Löppenberg M, Galla F, Börgel F, Agoglitta O, Kirchmair J, Holl R. Phenylethylene glycol-derived LpxC inhibitors with diverse Zn2+-binding groups. Tetrahedron 2019. [DOI: 10.1016/j.tet.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Affiliation(s)
- Dmitrii V. Kalinin
- Institut für Organische Chemie, Universität Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Ralph Holl
- Institut für Organische Chemie, Universität Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems
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11
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Mane YD, Sarnikar YP, Surwase SM, Biradar DO, Gorepatil PB, Shinde VS, Khade BC. Design, synthesis, and antimicrobial activity of novel 5-substituted indole-2-carboxamide derivatives. RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2696-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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12
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Erwin AL. Antibacterial Drug Discovery Targeting the Lipopolysaccharide Biosynthetic Enzyme LpxC. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025304. [PMID: 27235477 DOI: 10.1101/cshperspect.a025304] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The enzyme LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) is broadly conserved across Gram-negative bacteria and is essential for synthesis of lipid A, the membrane anchor of the lipopolysaccharides (LPSs), which are a major component of the outer membrane in nearly all Gram-negative bacteria. LpxC has been the focus of target-directed antibiotic discovery projects in numerous pharmaceutical and academic groups for more than 20 years. Despite intense effort, no LpxC inhibitor has been approved for therapeutic use, and only one has yet reached human studies. This article will summarize the history of LpxC as a drug target and the parallel history of research on LpxC biology. Both academic and industrial researchers have used LpxC inhibitors as tool compounds, leading to increased understanding of the differing mechanisms for regulation of LPS synthesis in Escherichia coli and Pseudomonas aeruginosa.
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Design, synthesis and biological evaluation of LpxC inhibitors with novel hydrophilic terminus. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Wang X, Quinn PJ, Yan A. Kdo2 -lipid A: structural diversity and impact on immunopharmacology. Biol Rev Camb Philos Soc 2014; 90:408-27. [PMID: 24838025 PMCID: PMC4402001 DOI: 10.1111/brv.12114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 04/10/2014] [Accepted: 04/17/2014] [Indexed: 12/11/2022]
Abstract
3-deoxy-d-manno-octulosonic acid-lipid A (Kdo2-lipid A) is the essential component of lipopolysaccharide in most Gram-negative bacteria and the minimal structural component to sustain bacterial viability. It serves as the active component of lipopolysaccharide to stimulate potent host immune responses through the complex of Toll-like-receptor 4 (TLR4) and myeloid differentiation protein 2. The entire biosynthetic pathway of Escherichia coli Kdo2-lipid A has been elucidated and the nine enzymes of the pathway are shared by most Gram-negative bacteria, indicating conserved Kdo2-lipid A structure across different species. Yet many bacteria can modify the structure of their Kdo2-lipid A which serves as a strategy to modulate bacterial virulence and adapt to different growth environments as well as to avoid recognition by the mammalian innate immune systems. Key enzymes and receptors involved in Kdo2-lipid A biosynthesis, structural modification and its interaction with the TLR4 pathway represent a clear opportunity for immunopharmacological exploitation. These include the development of novel antibiotics targeting key biosynthetic enzymes and utilization of structurally modified Kdo2-lipid A or correspondingly engineered live bacteria as vaccines and adjuvants. Kdo2-lipid A/TLR4 antagonists can also be applied in anti-inflammatory interventions. This review summarizes recent knowledge on both the fundamental processes of Kdo2-lipid A biosynthesis, structural modification and immune stimulation, and applied research on pharmacological exploitations of these processes for therapeutic development.
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Affiliation(s)
- Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
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15
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Lee CJ, Liang X, Gopalaswamy R, Najeeb J, Ark ED, Toone EJ, Zhou P. Structural basis of the promiscuous inhibitor susceptibility of Escherichia coli LpxC. ACS Chem Biol 2014; 9:237-46. [PMID: 24117400 DOI: 10.1021/cb400067g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The LpxC enzyme in the lipid A biosynthetic pathway is one of the most promising and clinically unexploited antibiotic targets for treatment of multidrug-resistant Gram-negative infections. Progress in medicinal chemistry has led to the discovery of potent LpxC inhibitors with a variety of chemical scaffolds and distinct antibiotic profiles. The vast majority of these compounds, including the nanomolar inhibitors L-161,240 and BB-78485, are highly effective in suppressing the activity of Escherichia coli LpxC (EcLpxC) but not divergent orthologs such as Pseudomonas aeruginosa LpxC (PaLpxC) in vitro. The molecular basis for such promiscuous inhibition of EcLpxC has remained poorly understood. Here, we report the crystal structure of EcLpxC bound to L-161,240, providing the first molecular insight into L-161,240 inhibition. Additionally, structural analysis of the EcLpxC/L-161,240 complex together with the EcLpxC/BB-78485 complex reveals an unexpected backbone flipping of the Insert I βa-βb loop in EcLpxC in comparison with previously reported crystal structures of EcLpxC complexes with l-threonyl-hydroxamate-based broad-spectrum inhibitors. Such a conformational switch, which has only been observed in EcLpxC but not in divergent orthologs such as PaLpxC, results in expansion of the active site of EcLpxC, enabling it to accommodate LpxC inhibitors with a variety of head groups, including compounds containing single (R- or S-enantiomers) or double substitutions at the neighboring Cα atom of the hydroxamate warhead group. These results highlight the importance of understanding inherent conformational plasticity of target proteins in lead optimization.
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Affiliation(s)
- Chul-Jin Lee
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
| | - Xiaofei Liang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Ramesh Gopalaswamy
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Javaria Najeeb
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
| | - Eugene D. Ark
- Trinity College of Arts & Sciences, Duke University, Durham, North Carolina 27708, United States
| | - Eric J. Toone
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Pei Zhou
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Structural Biology & Biophysics Program, Duke University, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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FtsH-mediated coordination of lipopolysaccharide biosynthesis in Escherichia coli correlates with the growth rate and the alarmone (p)ppGpp. J Bacteriol 2013; 195:1912-9. [PMID: 23417489 DOI: 10.1128/jb.02134-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The outer membrane is the first line of defense for Gram-negative bacteria and serves as a major barrier for antibiotics and other harmful substances. The biosynthesis of lipopolysaccharides (LPS), the essential component of the outer membrane, must be tightly controlled as both too much and too little LPS are toxic. In Escherichia coli, the cellular level of the key enzyme LpxC, which catalyzes the first committed step in LPS biosynthesis, is adjusted by proteolysis carried out by the essential and membrane-bound protease FtsH. Here, we demonstrate that LpxC is degraded in a growth rate-dependent manner with half-lives between 4 min and >2 h. According to the cellular demand for LPS biosynthesis, LpxC is degraded during slow growth but stabilized when cells grow rapidly. Disturbing the balance between LPS and phospholipid biosynthesis in favor of phospholipid production in an E. coli strain encoding a hyperactive FabZ protein abolishes growth rate dependency of LpxC proteolysis. Lack of the alternative sigma factor RpoS or inorganic polyphosphates, which are known to mediate growth rate-dependent gene regulation in E. coli, did not affect proteolysis of LpxC. In contrast, absence of RelA and SpoT, which synthesize the alarmone (p)ppGpp, deregulated LpxC degradation resulting in rapid proteolysis in fast-growing cells and stabilization during slow growth. Our data provide new insights into the essential control of LPS biosynthesis in E. coli.
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Warmus JS, Quinn CL, Taylor C, Murphy ST, Johnson TA, Limberakis C, Ortwine D, Bronstein J, Pagano P, Knafels JD, Lightle S, Mochalkin I, Brideau R, Podoll T. Structure based design of an in vivo active hydroxamic acid inhibitor of P. aeruginosa LpxC. Bioorg Med Chem Lett 2012; 22:2536-43. [PMID: 22401863 DOI: 10.1016/j.bmcl.2012.01.140] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 11/28/2022]
Abstract
Lipid A is an essential component of the Gram negative outer membrane, which protects the bacterium from attack of many antibiotics. The Lipid A biosynthesis pathway is essential for Gram negative bacterial growth and is unique to these bacteria. The first committed step in Lipid A biosynthesis is catalysis by LpxC, a zinc dependent deacetylase. We show the design of an LpxC inhibitor utilizing a robust model which directed efficient design of picomolar inhibitors. Analysis of physiochemical properties drove design to focus on an optimal lipophilicity profile. Further structure based design took advantage of a conserved water network over the active site, and with the optimal lipophilicity profile, led to an improved LpxC inhibitor with in vivo activity against wild type Pseudomonas aeruginosa.
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Affiliation(s)
- Joseph S Warmus
- Department of Chemistry, Pfizer Global Research and Development, Ann Arbor, MI 48105, USA.
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18
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Control of lipopolysaccharide biosynthesis by FtsH-mediated proteolysis of LpxC is conserved in enterobacteria but not in all gram-negative bacteria. J Bacteriol 2010; 193:1090-7. [PMID: 21193611 DOI: 10.1128/jb.01043-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the essential function of lipopolysaccharides (LPS) in Gram-negative bacteria, it is largely unknown how the exact amount of this molecule in the outer membrane is controlled. The first committed step in LPS biosynthesis is catalyzed by the LpxC enzyme. In Escherichia coli, the cellular concentration of LpxC is adjusted by the only essential protease in this organism, the membrane-anchored metalloprotease FtsH. Turnover of E. coli LpxC requires a length- and sequence-specific C-terminal degradation signal. LpxC proteins from Salmonella, Yersinia, and Vibrio species carry similar C-terminal ends and, like the E. coli enzyme, were degraded by FtsH. Although LpxC proteins are highly conserved in Gram-negative bacteria, there are striking differences in their C termini. The Aquifex aeolicus enzyme, which is devoid of the C-terminal extension, was stable in E. coli, whereas LpxC from the alphaproteobacteria Agrobacterium tumefaciens and Rhodobacter capsulatus was degraded by the Lon protease. Proteolysis of the A. tumefaciens protein required the C-terminal end of LpxC. High stability of Pseudomonas aeruginosa LpxC in E. coli and P. aeruginosa suggested that Pseudomonas uses a proteolysis-independent strategy to control its LPS content. The differences in LpxC turnover along with previously reported differences in susceptibility against antimicrobial compounds have important implications for the potential of LpxC as a drug target.
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19
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Antimicrobial activity of CHIR-090, an inhibitor of lipopolysaccharide biosynthesis, against the Burkholderia cepacia complex. Antimicrob Agents Chemother 2010; 54:3531-3. [PMID: 20516283 DOI: 10.1128/aac.01600-09] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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20
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Cuny GD. A new class of UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) inhibitors for the treatment of Gram-negative infections: PCT application WO 2008027466. Expert Opin Ther Pat 2009; 19:893-9. [PMID: 19473108 DOI: 10.1517/13543770902766829] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Human infections due to Gram-negative bacteria cause significant morbidity and mortality. Identification of new strategies, molecular targets, and agents for the treatment of Gram-negative bacterial infections are needed urgently. Lipid A is a necessary component of the lipopolysaccharide-containing outer membrane of Gram-negative bacteria. The zinc-dependent hydrolase UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) involved in the first committed step in the biosynthetic pathway of lipid A has no sequence homology to any known mammalian enzymes and has emerged as an attractive Gram-negative antibacterial molecular target. Most previously described LpxC inhibitors contain a hydroxamic acid, which can lead to low specificity vs. other metal-dependent enzymes and can consequently result in unwanted side effects. OBJECTIVE This review examines a new reported class of nonhydroxamic LpxC inhibitors for the treatment of Gram-negative infections. METHODS The new class of inhibitor is compared with several previously reported LpxC inhibitors. CONCLUSION The LpxC inhibitors disclosed in PCT application WO 2008027466 contain hydantoins in place of the hydroxamic acids commonly found in most previously described inhibitors. These molecules could represent a means of treating Gram-negative infections via a more selective inhibition of LpxC.
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Affiliation(s)
- Gregory D Cuny
- Brigham & Women's Hospital, Harvard Medical School, Partners Center for Drug Discovery, Laboratory for Drug Discovery in Neurodegeneration, 65 Landsdowne Street, Cambridge, MA 02139, USA.
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21
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Ramsden NL, Buetow L, Dawson A, Kemp LA, Ulaganathan V, Brenk R, Klebe G, Hunter WN. A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy. J Med Chem 2009; 52:2531-42. [PMID: 19320487 PMCID: PMC2669732 DOI: 10.1021/jm801475n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria. Virtual screening against Escherichia coli IspF (EcIspF) was performed by combining a hierarchical filtering methodology with molecular docking. Docked compounds were inspected and 10 selected for experimental validation. A surface plasmon resonance assay was developed and two weak ligands identified. Crystal structures of EcIspF complexes were determined to support rational ligand development. Cytosine analogues and Zn2+-binding moieties were characterized. One of the putative Zn2+-binding compounds gave the lowest measured KD to date (1.92 ± 0.18 μM). These data provide a framework for the development of IspF inhibitors to generate lead compounds of therapeutic potential against microbial pathogens.
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Affiliation(s)
- Nicola L Ramsden
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
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22
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Shin H, Gennadios HA, Whittington DA, Christianson DW. Amphipathic benzoic acid derivatives: synthesis and binding in the hydrophobic tunnel of the zinc deacetylase LpxC. Bioorg Med Chem 2007; 15:2617-23. [PMID: 17296300 DOI: 10.1016/j.bmc.2007.01.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/15/2007] [Accepted: 01/26/2007] [Indexed: 11/18/2022]
Abstract
The first committed step in lipid A biosynthesis is catalyzed by uridine diphosphate-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase (LpxC), a zinc-dependent deacetylase, and inhibitors of LpxC may be useful in the development of antibacterial agents targeting a broad spectrum of Gram-negative bacteria. Here, we report the design of amphipathic benzoic acid derivatives that bind in the hydrophobic tunnel in the active site of LpxC. The hydrophobic tunnel accounts for the specificity of LpxC toward substrates and substrate analogues bearing a 3-O-myristoyl substituent. Simple benzoic acid derivatives bearing an aliphatic 'tail' bind in the hydrophobic tunnel with micromolar affinity despite the lack of a glucosamine ring like that of the substrate. However, although these benzoic acid derivatives each contain a negatively charged carboxylate 'warhead' intended to coordinate to the active site zinc ion, the 2.25A resolution X-ray crystal structure of LpxC complexed with 3-(heptyloxy)benzoate reveals 'backward' binding in the hydrophobic tunnel, such that the benzoate moiety does not coordinate to zinc. Instead, it binds at the outer end of the hydrophobic tunnel. Interestingly, these ligands bind with affinities comparable to those measured for more complicated substrate analogue inhibitors containing glucosamine ring analogues and hydroxamate 'warheads' that coordinate to the active site zinc ion. We conclude that the intermolecular interactions in the hydrophobic tunnel dominate enzyme affinity in this series of benzoic acid derivatives.
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Affiliation(s)
- Hyunshun Shin
- Department of Chemistry, University of San Francisco, 2130 Fulton Street, San Francisco, CA 94117-1080, USA
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23
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Mdluli KE, Witte PR, Kline T, Barb AW, Erwin AL, Mansfield BE, McClerren AL, Pirrung MC, Tumey LN, Warrener P, Raetz CRH, Stover CK. Molecular validation of LpxC as an antibacterial drug target in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2006; 50:2178-84. [PMID: 16723580 PMCID: PMC1479155 DOI: 10.1128/aac.00140-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
LpxC [UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase] is a metalloamidase that catalyzes the first committed step in the biosynthesis of the lipid A component of lipopolysaccharide. A previous study (H. R. Onishi, B. A. Pelak, L. S. Gerckens, L. L. Silver, F. M. Kahan, M. H. Chen, A. A. Patchett, S. M. Galloway, S. A. Hyland, M. S. Anderson, and C. R. H. Raetz, Science 274:980-982, 1996) identified a series of synthetic LpxC-inhibitory molecules that were bactericidal for Escherichia coli. These molecules did not inhibit the growth of Pseudomonas aeruginosa and were therefore not developed further as antibacterial drugs. The inactivity of the LpxC inhibitors for P. aeruginosa raised the possibility that LpxC activity might not be essential for all gram-negative bacteria. By placing the lpxC gene of P. aeruginosa under tight control of an arabinose-inducible promoter, we demonstrated the essentiality of LpxC activity for P. aeruginosa. It was found that compound L-161,240, the most potent inhibitor from the previous study, was active against a P. aeruginosa construct in which the endogenous lpxC gene was inactivated and in which LpxC activity was supplied by the lpxC gene from E. coli. Conversely, an E. coli construct in which growth was dependent on the P. aeruginosa lpxC gene was resistant to the compound. The differential activities of L-161,240 against the two bacterial species are thus the result primarily of greater potency toward the E. coli enzyme rather than of differences in the intrinsic resistance of the bacteria toward antibacterial compounds due to permeability or efflux. These data validate P. aeruginosa LpxC as a target for novel antibiotic drugs and should help direct the design of inhibitors against clinically important gram-negative bacteria.
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Affiliation(s)
- Khisimuzi E Mdluli
- Department of Research Biology, Chiron Corporation, Seattle, WA 98119, USA
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24
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Decken A, Gossage RA. Synthesis and characterisation of the first transition metal complex of zoxazolamine (2-amino-5-chlorobenzoxazole): the X-ray crystal structure determination of [ZnCl2(η1-Nbenzoxazole-2-amino-5-chlorobenzoxazole)2]. J Inorg Biochem 2005; 99:664-7. [PMID: 15621301 DOI: 10.1016/j.jinorgbio.2004.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 08/30/2004] [Accepted: 09/03/2004] [Indexed: 11/21/2022]
Abstract
The synthesis and characterisation (NMR, X-ray, elemental analysis) of the first transition metal complex of Zoxazolamine (1: 2-amino-5-chlorobenzoxazole), viz. [ZnCl(2)(1)(2)] (2) is described; complex 2 is obtained in 77% yield from the treatment of 1 with ZnCl(2) in acetone solution. The Zn compound is a mononuclear species (X-ray) with a distorted tetrahedral array of ligands around the metal centre with the title ligand bound to Zn via the benzoxazole ring N-atom. The structural properties of 2 are discussed in relation to other mononuclear Zn halide complexes.
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Affiliation(s)
- Andreas Decken
- Department of Chemistry, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 6E2.
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25
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Schmid MB. Seeing is believing: the impact of structural genomics on antimicrobial drug discovery. Nat Rev Microbiol 2004; 2:739-46. [PMID: 15372084 DOI: 10.1038/nrmicro978] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, the availability of complete microbial genome sequences has led to changes in the strategies that are used to search for novel anti-infectives. However, despite the identification of many new potential drug targets, novel antimicrobial agents have been slow to emerge from these efforts. In part, this reflects the long discovery and development times that are needed to bring new drugs to market and the bottlenecks at the stages of identifying good lead compounds and optimizing these leads into drug candidates. Structural genomics will hopefully provide opportunities to overcome these bottlenecks and populate the antimicrobial pipeline.
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Affiliation(s)
- Molly B Schmid
- MBS Associates, 38 Avenue Road, Suite 601, Toronto, Ontario M5R 2G2, Canada.
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26
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Supuran CT, Briganti F, Mincione G, Scozzafava A. Protease inhibitors: Synthesis of L-alanine hydroxamate sulfonylated derivatives as inhibitors of clostridium histolyticum collagenase. JOURNAL OF ENZYME INHIBITION 2003; 15:111-28. [PMID: 10938538 DOI: 10.1080/14756360009030345] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
L-alanine hydroxamate derivatives were obtained by reaction of alkyl/arylsulfonyl halides with L-alanine, followed by treatment with benzyl chloride, and conversion of the COOH moiety to the CONHOH group with hydroxylamine in the presence of carbodiimides. Other derivatives were obtained by reaction of N-benzyl-alanine with aryl isocyanates, arylsulfonyl isocyanates or benzoyl isothiocyanate, followed by a similar conversion of the COOH to the CONHOH moiety. The obtained compounds were assayed as inhibitors of Clostridium histolyticum collagenase, ChC (EC 3.4.24.3), a zinc enzyme which degrades triple helical collagen. The hydroxamate derivatives were generally 100-500 times more active than the corresponding carboxylates. In the series of synthesized derivatives, substitution patterns leading to the most potent ChC inhibitors were those involving perfluoroalkylsulfonyl- and substituted-arylsulfonyl moieties, such as pentafluorophenylsulfonyl, 3- and 4-protected-aminophenylsulfonyl-, 3- and 4-carboxy-phenylsulfonyl-, 3-trifluoromethyl-phenylsulfonyl-, or 1- and 2-naphthylsulfonyl among others. Similarly to the matrix metalloproteinase (MMP) hydroxamate inhibitors, ChC inhibitors of the type reported here must incorporate hydrophobic moieties at the P(2') and P(3') sites, in order to achieve tight binding to the enzyme.
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Affiliation(s)
- C T Supuran
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Via Gino Capponi 7, I-50121, Florence, Italy.
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27
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Whittington DA, Rusche KM, Shin H, Fierke CA, Christianson DW. Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis. Proc Natl Acad Sci U S A 2003; 100:8146-50. [PMID: 12819349 PMCID: PMC166197 DOI: 10.1073/pnas.1432990100] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer leaflet of the outer membrane of the Gram-negative bacterium serves as a permeability barrier and is composed of lipopolysaccharide, also known as endotoxin. The membrane anchor of lipopolysaccharide is lipid A, the biosynthesis of which is essential for cell viability. The first committed step in lipid A biosynthesis is catalyzed by UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase (LpxC), a zinc-dependent deacetylase. Here we report the crystal structure of LpxC from Aquifex aeolicus, which reveals a new alpha+beta fold reflecting primordial gene duplication and fusion, as well as a new zinc-binding motif. The catalytic zinc ion resides at the base of an active-site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents. Notably, simple inhibitors designed to target interactions in the hydrophobic tunnel bind with micromolar affinity, thereby representing a step toward the structure-based design of a potent, broad-spectrum antibacterial drug.
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Affiliation(s)
- Douglas A. Whittington
- Roy and Diana Vagelos Laboratories, Department
of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; and
Department of Chemistry, University of
Michigan, Ann Arbor, MI 48109-1055
| | - Kristin M. Rusche
- Roy and Diana Vagelos Laboratories, Department
of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; and
Department of Chemistry, University of
Michigan, Ann Arbor, MI 48109-1055
| | - Hyunshun Shin
- Roy and Diana Vagelos Laboratories, Department
of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; and
Department of Chemistry, University of
Michigan, Ann Arbor, MI 48109-1055
| | - Carol A. Fierke
- Roy and Diana Vagelos Laboratories, Department
of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; and
Department of Chemistry, University of
Michigan, Ann Arbor, MI 48109-1055
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department
of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; and
Department of Chemistry, University of
Michigan, Ann Arbor, MI 48109-1055
- To whom correspondence should be addressed. E-mail:
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28
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Abstract
As the prevalence of resistance to multiple antibiotics increases it is progressively more difficult to treat pneumonia in hospitalized patients. Therefore, anti-infectious agents that have new modes of action are needed urgently. Recent advances in DNA sequencing technology make it possible to elucidate the sequences of the entire genomes of pathogenic bacteria. This allows many novel, non-traditional targets for therapeutic intervention to be identified, such as those involved in disease pathogenesis, and in adaptation and growth at sites of infection. In the past few years, inhibitors of new bacterial targets have been developed, including inhibitors of genes that are required for either virulence or pathogenesis. The challenge is to optimize and develop these agents to provide novel approaches to the treatment of pneumonia in hospitalized patients.
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MESH Headings
- Adjuvants, Immunologic/therapeutic use
- Anti-Bacterial Agents/therapeutic use
- Community-Acquired Infections/drug therapy
- Community-Acquired Infections/therapy
- Cross Infection/drug therapy
- Cross Infection/therapy
- Cytokines/therapeutic use
- DNA, Antisense/therapeutic use
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial
- Gene Targeting
- Genes, Bacterial
- Humans
- Pneumonia, Bacterial/drug therapy
- Pneumonia, Bacterial/therapy
- RNA, Antisense/therapeutic use
- RNA, Bacterial/genetics
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Affiliation(s)
- Mario Cazzola
- Cardarelli Hospital, Department of Respiratory Medicine, Unit of Pneumology and Allergology, Via del Parco Margherita 24, 80121 Napoli, Italy.
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29
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Clements JM, Coignard F, Johnson I, Chandler S, Palan S, Waller A, Wijkmans J, Hunter MG. Antibacterial activities and characterization of novel inhibitors of LpxC. Antimicrob Agents Chemother 2002; 46:1793-9. [PMID: 12019092 PMCID: PMC127247 DOI: 10.1128/aac.46.6.1793-1799.2002] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2001] [Revised: 01/14/2002] [Accepted: 03/12/2002] [Indexed: 11/20/2022] Open
Abstract
Lipid A is the hydrophobic anchor of lipopolysaccharide (LPS) and forms the major lipid component of the outer monolayer of the outer membrane of gram-negative bacteria. Lipid A is required for bacterial growth and virulence, and inhibition of its biosynthesis is lethal to bacteria. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme that catalyzes the second step in the biosynthesis of lipid A. Inhibitors of LpxC have previously been shown to have antibiotic activities. We have screened a metalloenzyme inhibitor library for antibacterial activities against an Escherichia coli strain with reduced LpxC activity. From this screen, a series of sulfonamide derivatives of the alpha-(R)-amino hydroxamic acids, exemplified by BB-78484 and BB-78485, have been identified as having potent inhibitory activities against LpxC in an in vitro assay. Leads from this series showed gram-negative selective activities against members of the Enterobacteriaceae, Serratia marcescens, Morganella morganii, Haemophilus influenzae, Moraxella catarrhalis, and Burkholderia cepacia. BB-78484 was bactericidal against E. coli, achieving 3-log killing in 4 h at a concentration 4 times above the MIC, as would be predicted for an inhibitor of lipid A biosynthesis. E. coli mutants with decreased susceptibility to BB-78484 were selected. Analysis of these mutants revealed that resistance arose as a consequence of mutations in the fabZ or lpxC genes. These data confirm the antibacterial target of BB-78484 and BB-78485 and validate LpxC as a target for gram-negative selective antibacterials.
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Affiliation(s)
- John M Clements
- British Biotech Pharmaceuticals Ltd., Oxford OX4 6LY, United Kingdom.
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30
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Wang W, Maniar M, Jain R, Jacobs J, Trias J, Yuan Z. A fluorescence-based homogeneous assay for measuring activity of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase. Anal Biochem 2001; 290:338-46. [PMID: 11237337 DOI: 10.1006/abio.2000.4973] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is one of the key enzymes of bacterial lipid A biosynthesis, catalyzing the removal of the N-acetyl group of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine. The lpxC gene is essential in Gram-negative bacteria but absent from mammalian genomes, making it an attractive target for antibacterial drug discovery. Current assay methods for LpxC are not suitable for high throughput screening, since they require multiple product separation steps and the use of radioactively labeled material that is difficult to prepare. A homogeneous fluorescence-based assay was developed that uses UDP-3-O-(N-hexyl-propionamide)-N-acetylglucosamine as a surrogate substrate. This surrogate can be prepared from commercially available UDP-GlcNAc by enzymatic conversion to UDP-MurNAc, which is then chemically coupled to n-hexylamine. Following the LpxC reaction, the free amine of the deacetylation product can be derivatized by fluorescamine, thus generating a fluorescent signal. This surrogate substrate has a K(m) of 367 microM and k(cat) of 0.36 s(-1), compared to 2 microM and 1.5 s(-1) for the natural substrate. Since no separation is needed, the assay is easily adaptable to high throughput screening. IC(50)s of LpxC inhibitors determined using this assay method is similar to those measured by traditional method with the natural substrate.
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Affiliation(s)
- W Wang
- Versicor, Inc., 34790 Ardentech Court, Fremont, California 94555, USA
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31
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Abstract
So far, two strategies have been applied to develop new anti-infective agents: (a) the synthesis of analogs of classical antibiotics with enhanced activity against resistant pathogens and (b) the screening of naturally occurring substances and libraries of synthetic compounds for antimicrobial activity in whole-cell assays. Today, the same principles are being used; however, the search for antimicrobial compounds with novel modes of action is based on targeting specific resistance and virulence factors. Novel targets for anti-infective agents are currently being discovered as a consequence of a better understanding of cell biology, the molecular basis of bacterial resistance, the gene-pathogenicity relationship and the mechanism of the infection process.
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Affiliation(s)
- E L Setti
- Axys Pharmaceuticals, Inc., South San Francisco, California 94080, USA
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32
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Abstract
Recently, several new drugs for the treatment of bacterial infections have been developed. Quinupristin/dalfopristin, moxifloxacin and gatifloxacin have been approved throughout the world for clinical use. Levofloxacin has been approved for the treatment of community-acquired pneumonia caused by penicillin-resistant Streptococcus pnuemoniae. The Food and Drug Administration has approved linezolid for clinical use, and new drug applications for gemifloxacin and telithromycin were filed. Other new targets have surfaced in the quest for novel antibacterial agents.
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Affiliation(s)
- K Bush
- The RW Johnson Pharmaceutical Research Institute, Raritan, NJ 08869, USA.
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33
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Jackman JE, Fierke CA, Tumey LN, Pirrung M, Uchiyama T, Tahir SH, Hindsgaul O, Raetz CR. Antibacterial agents that target lipid A biosynthesis in gram-negative bacteria. Inhibition of diverse UDP-3-O-(r-3-hydroxymyristoyl)-n-acetylglucosamine deacetylases by substrate analogs containing zinc binding motifs. J Biol Chem 2000; 275:11002-9. [PMID: 10753902 DOI: 10.1074/jbc.275.15.11002] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) catalyzes the second step in the biosynthesis of lipid A, a unique amphiphilic molecule found in the outer membranes of virtually all Gram-negative bacteria. Since lipid A biosynthesis is required for bacterial growth, inhibitors of LpxC have potential utility as antibiotics. The enzymes of lipid A biosynthesis, including LpxC, are encoded by single copy genes in all sequenced Gram-negative genomes. We have now cloned, overexpressed, and purified LpxC from the hyperthermophile Aquifex aeolicus. This heat-stable LpxC variant (the most divergent of all known LpxCs) displays 32% identity and 51% similarity over 277 amino acid residues out of the 305 in Escherichia coli LpxC. Although A. aeolicus LpxC deacetylates the substrate UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine at a rate comparable with E. coli LpxC, a phenyloxazoline-based hydroxamate that inhibits E. coli LpxC with K(i) of approximately 50 nM (Onishi, H. R., Pelak, B. A., Gerckens, L. S., Silver, L. L., Kahan, F. M., Chen, M. H., Patchett, A. A., Galloway, S. M., Hyland, S. A., Anderson, M. S., and Raetz, C. R. H. (1996) Science 274, 980-982) does not inhibit A. aeolicus LpxC. To determine whether or not broad-spectrum deacetylase inhibitors can be found, we have designed a new class of hydroxamate-containing inhibitors of LpxC, starting with the structure of the physiological substrate. Several of these compounds inhibit both E. coli and A. aeolicus LpxC at similar concentrations. We have also identified a phosphinate-containing substrate analog that inhibits both E. coli and A. aeolicus LpxC, suggesting that the LpxC reaction proceeds by a mechanism similar to that described for other zinc metalloamidases, like carboxypeptidase A and thermolysin. The differences between the phenyloxazoline and the substrate-based LpxC inhibitors might be exploited for developing novel antibiotics targeted either against some or all Gram-negative strains. We suggest that LpxC inhibitors with antibacterial activity be termed "deacetylins."
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Affiliation(s)
- J E Jackman
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Scozzafava A, Supuran CT. Protease inhibitors - part 5. Alkyl/arylsulfonyl- and arylsulfonylureido-/arylureido- glycine hydroxamate inhibitors of Clostridium histolyticum collagenase. Eur J Med Chem 2000; 35:299-307. [PMID: 10785556 DOI: 10.1016/s0223-5234(00)00127-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Reaction of alkyl/arylsulfonyl halides with glycine afforded a series of derivatives which were first N-benzylated by treatment with benzyl chloride, and then converted to the corresponding hydroxamic acids with hydroxylamine in the presence of carbodiimide derivatives. Other derivatives were obtained by reaction of N-benzyl-glycine with aryl isocyanates, arylsulfonyl isocyanates or benzoyl isothiocyanate, followed by conversion of their COOH group into the CONHOH moiety, as mentioned above. The 90 new compounds reported here were assayed as inhibitors of the Clostridium histolyticum collagenase (EC 3.4.24.3), a zinc enzyme which degrades triple helical regions of native collagen. The prepared hydroxamate derivatives were generally 100-500 times more active than the corresponding carboxylates. In the series of synthesized hydroxamates, substitution patterns leading to the best inhibitors were those involving perfluoroalkylsulfonyl- and substituted-arylsulfonyl moieties, such as pentafluorophenylsulfonyl, 3- and 4-carboxyphenylsulfonyl-, 3-trifluoromethyl-phenylsulfonyl or 1- and 2-naphthyl among others. Thus, it seems that similarly to the matrix metalloproteinase (MMP) hydroxamate inhibitors, Clostridium histolyticum collagenase inhibitors should incorporate hydrophobic moieties at the P(1') and P(2') sites, whereas the alpha-carbon substituent may be a small and compact moiety (such as H, for the Gly derivatives reported here). Such compounds might lead to the design of collagenase inhibitor-based drugs useful as anti-cancer, anti-arthritis or anti-bacterial agents for the treatment of corneal keratitis.
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Affiliation(s)
- A Scozzafava
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Via Gino Capponi 7, I-50121, Florence, Italy
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Scozzafava A, Supuran CT. Protease inhibitors. Part 8: synthesis of potent Clostridium histolyticum collagenase inhibitors incorporating sulfonylated L-alanine hydroxamate moieties. Bioorg Med Chem 2000; 8:637-45. [PMID: 10732980 DOI: 10.1016/s0968-0896(99)00316-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A series of hydroxamates was prepared by reaction of alkyl/arylsulfonyl halides with N-2-chlorobenzyl-L-alanine, followed by conversion of the COOH moiety to the CONHOH group, with hydroxylamine in the presence of carbodiimides. Other structurally related compounds were obtained by reaction of N-2-chlorobenzyl-L-alanine with aryl isocyanates, arylsulfonyl isocyanates or benzoyl isothiocyanate, followed by the similar conversion of the COOH into the CONHOH moiety. The new compounds were assayed as inhibitors of the Clostridium histolyticum collagenase, ChC (EC 3.4.24.3), a bacterial zinc metallo-peptidase which degrades triple helical collagen as well as a large number of synthetic peptides. The prepared hydroxamate derivatives proved to be 100-500 times more active collagenase inhibitors than the corresponding carboxylates. Substitution patterns leading to best ChC inhibitors (both for carboxylates as well as for the hydroxamates) were those involving perfluoroalkylsulfonyl- and substituted-arylsulfonyl moieties, such as pentafluorophenylsulfonyl; 3- and 4-protected-aminophenylsulfonyl-; 3- and 4-carboxyphenylsulfonyl-; 3-trifluoromethyl-phenylsulfonyl; as well as 1- and 2-naphthyl-, quinoline-8-yl- or substituted-arylsulfonylamidocarboxyl moieties among others. Similarly to the matrix metalloproteinase (MMP) hydroxamate inhibitors, ChC inhibitors of the type reported here must incorporate hydrophobic moieties at the P2' and P3' sites, in order to achieve tight binding to the enzyme. This study also proves that the 2-chlorobenzyl moiety, investigated here for the first time, is an efficient P2' anchoring moiety for obtaining potent ChC inhibitors.
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Affiliation(s)
- A Scozzafava
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Florence, Italy
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