201
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Estácio SG, Moreira R, Guedes RC. Characterizing the Dynamics and Ligand-Specific Interactions in the Human Leukocyte Elastase through Molecular Dynamics Simulations. J Chem Inf Model 2011; 51:1690-702. [DOI: 10.1021/ci200076k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sílvia G. Estácio
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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202
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Crauste C, Froeyen M, Anné J, Herdewijn P. Asymmetric Synthesis of New β-Lactam Lipopeptides as Bacterial Signal Peptidase I Inhibitors. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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203
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Sela-Passwell N, Trahtenherts A, Krüger A, Sagi I. New opportunities in drug design of metalloproteinase inhibitors: combination between structure-function experimental approaches and systems biology. Expert Opin Drug Discov 2011; 6:527-42. [PMID: 22646077 DOI: 10.1517/17460441.2011.560936] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION MMPs (matrix metalloproteinases) and ADAMs (a disintegrin and metalloproteinases) are endopeptidases central to the degradation and remodeling of the extracellular matrix. These proteases also exhibit regulatory activity in cell signaling pathways and thus tissue homeostasis under normal conditions and in many diseases. Consequently, individual members of the MMP and ADAM protein families were identified as important therapeutic targets. However, designing effective inhibitors in vivo for this class of enzymes appears to be extremely challenging. This is attributed to the broad structural similarity of their active sites and to the dynamic functional interconnectivity of MMPs with other proteases, their inhibitors, and substrates (the so-called degradome) in healthy and disease tissues. AREAS COVERED The article covers the progress in designing metalloproteinase inhibitors, based on recent advancements in our understanding of enzyme structures and their function as master regulators. It also discusses the potential of utilizing structure-based drug design strategies in conjunction with systems biology experimental approaches for designing potent and therapeutically effective metalloproteinase inhibitors. EXPERT OPINION We highlight the use of protein-based drug design strategies, for example, antibodies and protein scaffolds, targeting extracatalytic domains, which are central to proteolytic and non-proteolytic enzyme functions. Such rationally designed function-blocking inhibitors may create new opportunities in disease management and in emerging therapies that require control of dysregulated MMP activity without causing severe side effects. Importantly, the lessons learned from studying these protein-based inhibitors can be implemented to design new and effective small or medium sized synthetic antagonists.
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Affiliation(s)
- Netta Sela-Passwell
- The Weizmann Institute of Science, Department of Biological Regulation , Rehovot 76100 , Israel
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204
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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205
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Madala PK, Tyndall JDA, Nall T, Fairlie DP. Update 1 of: Proteases Universally Recognize Beta Strands In Their Active Sites. Chem Rev 2011; 110:PR1-31. [DOI: 10.1021/cr900368a] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Praveen K. Madala
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Tessa Nall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - David P. Fairlie
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
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206
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Rueeger H, Rondeau JM, McCarthy C, Möbitz H, Tintelnot-Blomley M, Neumann U, Desrayaud S. Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors. Bioorg Med Chem Lett 2011; 21:1942-7. [DOI: 10.1016/j.bmcl.2011.02.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/09/2011] [Accepted: 02/10/2011] [Indexed: 01/16/2023]
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207
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Bo Y, Singh S, Duong HQ, Cao C, Sieburth SM. Efficient, enantioselective assembly of silanediol protease inhibitors. Org Lett 2011; 13:1787-9. [PMID: 21381688 PMCID: PMC3064730 DOI: 10.1021/ol2002978] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A five-step assembly of silicon-protected dipeptide mimics from commercially available reagents is described. This methodology makes silanediol protease inhibitors readily available for the first time. The sequence features asymmetric hydrosilylation, a novel reduction of a silyl ether to a silyllithium reagent, and addition of this dianion to a sulfinimine, to produce the complete inhibitor skeleton with full control of stereochemistry. Oxidation of the primary alcohol to an acid completes the synthesis.
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Affiliation(s)
- Yingjian Bo
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122
| | - Swapnil Singh
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122
| | - Hoan Quoc Duong
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122
| | - Cui Cao
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122
| | - Scott McN. Sieburth
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122
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208
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Helix-mediated protein--protein interactions as targets for intervention using foldamers. Amino Acids 2011; 41:743-54. [PMID: 21409387 DOI: 10.1007/s00726-011-0880-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 03/04/2011] [Indexed: 10/18/2022]
Abstract
Protein--protein interactions (PPIs) play a central role in virtually all biological processes and have been the focus of intense investigation from structural molecular biology to cell biology for the majority of the last two decades and, more recently, are emerging as important targets for pharmaceutical intervention. A common motif found at the interface of PPIs is the α-helix, suggesting that, in the same way as the "lock and key" model has evolved for competitive inhibition of enzymes, it should be possible to elaborate "rule-based" approaches for inhibition of helix-mediated PPIs. This review will describe the biological function and structural features of a series of representative helix-mediated PPIs and discuss approaches that are being developed to target these interactions with small molecules that employ non-natural amino acids.
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209
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Saha R, Biswas S, Steele IM, Dey K, Mostafa G. A supramolecular spin crossover Fe(III) complex and its Cr(III) isomer: stabilization of water-chloride cluster within supramolecular host. Dalton Trans 2011; 40:3166-75. [PMID: 21340091 DOI: 10.1039/c0dt01256d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metal complexes, [M(Hdammthiol)(2)]Cl·3H(2)O [M = Cr(III) (1), Fe(III) (2)] [where H(2)dammthiol is the thiol form of the ligand, diacetylmonoxime morpholine N-thiohydrazone] were synthesized by metal template reactions of diacetylemonoxime with morpholine N-thiohydrazide in the presence of CrCl(3)·6H(2)O and FeCl(3)·6H(2)O. Both the complexes (1 and 2) were characterized by single crystal X-ray crystallography, spectroscopic (IR and UV-vis), Mössbauer and TGA analyses. The single crystal X-ray studies of both complexes show that the supramolecular hosts, constructed by the discrete mononuclear complexes, form supramolecular channels along the c-axis which are filled up by water-chloride clusters. In both complexes, the 1D water-chloride chain with chair-like architecture within the supramolecular hosts presents novelty. The magnetic measurement study of Fe(III) complex shows a spin crossover from S = 1/2 at 2.5 K to S = 5/2 at 300 K. At very low temperature, the presence of strong cooperative hydrogen bonding interactions stabilizes the S = 1/2 state.
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Affiliation(s)
- Rajat Saha
- Department of Physics, Jadavpur University, Jadavpur, Kolkata-700032, India
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210
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Olivieri L, Gardebien F. Molecular Dynamics Simulations of a Binding Intermediate between FKBP12 and a High-Affinity Ligand. J Chem Theory Comput 2011; 7:725-41. [DOI: 10.1021/ct100394d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lilian Olivieri
- DSIMB, INSERM, U665, Paris, F-75015, France, DSIMB, INSERM, U665, Faculté des Sciences et Technologies, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France, INTS, Paris, F-75015, France, and Laboratoire de Biochimie et Génétique Moléculaire, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France
| | - Fabrice Gardebien
- DSIMB, INSERM, U665, Paris, F-75015, France, DSIMB, INSERM, U665, Faculté des Sciences et Technologies, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France, INTS, Paris, F-75015, France, and Laboratoire de Biochimie et Génétique Moléculaire, Université de la Réunion, 15, avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09, La Réunion, France
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211
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Tandon A, Sinha S. Structural insights into the binding of MMP9 inhibitors. Bioinformation 2011; 5:310-4. [PMID: 21383916 PMCID: PMC3046033 DOI: 10.6026/97320630005310] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 12/02/2010] [Indexed: 02/02/2023] Open
Abstract
Matrix Metalloproteinase are family of enzymes responsible for degradation of extracellular matrix. MMP9 (gelatinase B) is one of the common matrix
metalloproteinase that is associated with tissue destruction in a number of disease states such as rheumatoid arthiritis, fibrotic lung disease, dilated
cardiomyopathy, as well as cancer invasion and metastasis. Recent study demonstrates that increased expression of MMP9 results in augmentation of
myopathy with increased inflammation and fibernecrosis. Previous studies do not provide any conclusive information related to structural specificity of
MMP9 inhibitors towards its active site, but with the availability of experimental structures it is now possible to study the structural specificity of MMP9
inhibitors. In light of availability of this information, we have applied docking and molecular dynamics approach to study the binding of inhibitors to the
active site of MMP9. Three categories of inhibitor consisting of sulfonamide hydroxamate, thioester, and carboxylic moieties as zinc binding groups
(ZBG) were chosen in the present study. Our docking results demonstrate that thioester based zinc binding group gives favourable docking scores as
compared to other two groups. Molecular Dynamics simulations further reveal that tight binding conformation for thioester group has high specificity for
MMP9 active site. Our study provides valuable insights on inhibitor specificity of MMP9 which provides valuable hints for future design of potent
inhibitors and drugs.
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Affiliation(s)
- Arpit Tandon
- Amity Institute of Biotechnology, Amity University Lucknow Campus, Gomti Nagar, Lucknow 226010, India
- Arpit Tandon:
| | - Siddharth Sinha
- ACS BioInformatics, Biotech Park, Janki Puram, Lucknow 226021, Indi
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212
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Bartoli G, Marcantoni E, Marcolini M, Sambri L. Applications of CeCl(3) as an environmental friendly promoter in organic chemistry. Chem Rev 2011; 110:6104-43. [PMID: 20731375 DOI: 10.1021/cr100084g] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Giuseppe Bartoli
- Department of Organic Chemistry A. Mangini, University of Bologna, viale Risorgimento 4, I-40156 Bologna, Italy
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213
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Zhao JF, Tan BH, Loh TP. In(iii)-pybox complex catalyzed enantioselective Mukaiyama aldol reactions between polymeric or hydrated glyoxylates and enolsilanes derived from aryl ketones. Chem Sci 2011. [DOI: 10.1039/c0sc00454e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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214
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Sexto A, Iglesias E. S-Nitrosocaptopril formation in aqueous acid and basic medium. A vasodilator and angiotensin converting enzyme inhibitor. Org Biomol Chem 2011; 9:7207-16. [DOI: 10.1039/c1ob05747b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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215
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Electronic and steric effects of substituents on the conformational diversity and hydrogen bonding of N-(4-X-phenyl)-N′,N″-bis(piperidinyl) phosphoric triamides (X=F, Cl, Br, H, CH3): A combined experimental and DFT study. Polyhedron 2011. [DOI: 10.1016/j.poly.2010.09.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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216
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Fleming FF, Yao L, Ravikumar PC, Funk L, Shook BC. Nitrile-containing pharmaceuticals: efficacious roles of the nitrile pharmacophore. J Med Chem 2010; 53:7902-17. [PMID: 20804202 PMCID: PMC2988972 DOI: 10.1021/jm100762r] [Citation(s) in RCA: 1119] [Impact Index Per Article: 79.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fraser F Fleming
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282-1530, USA.
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217
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Devel L, Garcia S, Czarny B, Beau F, Lajeunesse E, Vera L, Georgiadis D, Stura E, Dive V. Insights from selective non-phosphinic inhibitors of MMP-12 tailored to fit with an S1' loop canonical conformation. J Biol Chem 2010; 285:35900-9. [PMID: 20817735 PMCID: PMC2975213 DOI: 10.1074/jbc.m110.139634] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 07/21/2010] [Indexed: 01/28/2023] Open
Abstract
After the disappointment of clinical trials with early broad spectrum synthetic inhibitors of matrix metalloproteinases (MMPs), the field is now resurging with a new focus on the development of selective inhibitors that fully discriminate between different members of the MMP family with several therapeutic applications in perspective. Here, we report a novel class of highly selective MMP-12 inhibitors, without a phosphinic zinc-binding group, designed to plunge deeper into the S(1)' cavity of the enzyme. The best inhibitor from this series, identified through a systematic chemical exploration, displays nanomolar potency toward MMP-12 and selectivity factors that range between 2 and 4 orders of magnitude toward a large set of MMPs. Comparison of the high resolution x-ray structures of MMP-12 in free state or bound to this new MMP-12 selective inhibitor reveals that this compound fits deeply within the S(1)' specificity cavity, maximizing surface/volume ratios, without perturbing the S(1)' loop conformation. This is in contrast with highly selective MMP-13 inhibitors that were shown to select a particular S(1)' loop conformation. The search for such compounds that fit precisely to preponderant S(1)' loop conformation of a particular MMP may prove to be an alternative effective strategy for developing selective inhibitors of MMPs.
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Affiliation(s)
- Laurent Devel
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Sandra Garcia
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Bertrand Czarny
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Fabrice Beau
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Evelyne Lajeunesse
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Laura Vera
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Dimitris Georgiadis
- the Laboratory of Organic Chemistry, Department of Organic Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Enrico Stura
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
| | - Vincent Dive
- From the Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France and
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218
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Third generation of matrix metalloprotease inhibitors: Gain in selectivity by targeting the depth of the S1′ cavity. Biochimie 2010; 92:1501-8. [DOI: 10.1016/j.biochi.2010.07.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 07/29/2010] [Indexed: 01/14/2023]
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219
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Lee KS. A New Synthesis of Triphenylphosphorane Ylide Precursors to α-Keto Amide/Ester and Tricarbonyl Units via Horner-Wadsworth-Emmons Reaction. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.10.2776] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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220
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Hooley RJ, Shenoy SR, Rebek J. Electronic and steric effects in binding of deep cavitands. Org Lett 2010; 10:5397-400. [PMID: 18989966 DOI: 10.1021/ol8022775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A deep, self-folding cavitand responds to minor electronic differences between suitably sized adamantane guests. Binding constants range from <0.5 to 4000 M(-1) for guests as similar as 1-bromoadamantane and 1-cyanoadamantane. The barriers to guest exchange also vary up to 3 kcal mol(-1).
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Affiliation(s)
- Richard J Hooley
- Department of Chemistry, The Scripps Research Institute MB-26, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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221
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Soeta T, Kojima Y, Ukaji Y, Inomata K. O-Silylative Passerini Reaction: A New One-Pot Synthesis of α-Siloxyamides. Org Lett 2010; 12:4341-3. [DOI: 10.1021/ol101763w] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takahiro Soeta
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yuuki Kojima
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yutaka Ukaji
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Katsuhiko Inomata
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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222
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Singh S, Singh S, Shukla P. Modeling of novel HIV-1 protease inhibitors incorporating N-Aryl-oxazolidinone-5-carboxamides as P2 ligands using quantum chemical and topological finger print descriptors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9416-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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223
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224
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Webb RL, Schiering N, Sedrani R, Maibaum J. Direct Renin Inhibitors as a New Therapy for Hypertension. J Med Chem 2010; 53:7490-520. [DOI: 10.1021/jm901885s] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Randy L. Webb
- Novartis Pharmaceuticals Corp., Institutes for BioMedical Research, East Hanover, New Jersey
| | - Nikolaus Schiering
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard Sedrani
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Jürgen Maibaum
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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225
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Hanessian S, Maji DK, Govindan S, Matera R, Tintelnot-Blomley M. Substrate-controlled and organocatalytic asymmetric synthesis of carbocyclic amino acid dipeptide mimetics. J Org Chem 2010; 75:2861-76. [PMID: 20392053 DOI: 10.1021/jo100017t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The asymmetric synthesis of a carbocyclic delta-amino acid representing the P(2)/P(3) subunit of a nonpeptidic truncated peptidomimetic molecule is described relying on two independent approaches.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Station Centre-ville, Montréal, QC H3C 3J7, Canada.
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226
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Bourguignon SC, Cavalcanti DFB, de Souza AMT, Castro HC, Rodrigues CR, Albuquerque MG, Santos DO, da Silva GG, da Silva FC, Ferreira VF, de Pinho RT, Alves CR. Trypanosoma cruzi: insights into naphthoquinone effects on growth and proteinase activity. Exp Parasitol 2010; 127:160-6. [PMID: 20647011 DOI: 10.1016/j.exppara.2010.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/18/2022]
Abstract
In this study we compared the effects of naphthoquinones (α-lapachone, β-lapachone, nor-β-lapachone and Epoxy-α-lap) on growth of Trypanosoma cruzi epimastigotes forms, and on viability of VERO cells. In addition we also experimentally analyzed the most active compounds inhibitory profile against T. cruzi serine- and cysteine-proteinases activity and theoretically evaluated them against cruzain, the major T. cruzi cysteine proteinase by using a molecular docking approach. Our results confirmed β-lapachone and Epoxy-α-lap with a high trypanocidal activity in contrast to α-lapachone and nor-β-lapachone whereas Epoxy-α-lap presented the safest toxicity profile against VERO cells. Interestingly the evaluation of the active compounds effects against T. cruzi cysteine- and serine-proteinases activities revealed different targets for these molecules. β-Lapachone is able to inhibit the cysteine-proteinase activity of T. cruzi proteic whole extract and of cruzain, similar to E-64, a classical cysteine-proteinase inhibitor. Differently, Epoxy-α-lap inhibited the T. cruzi serine-proteinase activity, similar to PMSF, a classical serine-proteinase inhibitor. In agreement to these biological profiles in the enzymatic assays, our theoretical analysis showed that E-64 and β-lapachone interact with the cruzain specific S2 pocket and active site whereas Epoxy-α-lap showed no important interactions. Overall, our results infer that β-lapachone and Epoxy-α-lap compounds may inhibit T. cruzi epimastigotes growth by affecting T. cruzi different proteinases. Thus the present data shows the potential of these compounds as prototype of protease inhibitors on drug design studies for developing new antichagasic compounds.
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Affiliation(s)
- Saulo C Bourguignon
- Universidade Federal Fluminense, Instituto de Biologia, 24020-150 Niterói, RJ, Brazil
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227
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Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM. On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins 2010; 78:1120-36. [PMID: 19927322 DOI: 10.1002/prot.22633] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Most function prediction methods that identify cognate ligands from binding site analyses work on the assumption of molecular complementarity. These approaches build on the conjectured complementarity of geometrical and physicochemical properties between ligands and binding sites so that similar binding sites will bind similar ligands. We found that this assumption does not generally hold for protein-ligand interactions and observed that it is not the chemical composition of ligand molecules that dictates the complementarity between protein and ligand molecules, but that the ligand's share within the functional mechanism of a protein determines the degree of complementarity. Here, we present for a set of cognate ligands a descriptive analysis and comparison of the physicochemical properties that each ligand experiences in various nonhomologous binding pockets. The comparisons in each ligand set reveal large variations in their experienced physicochemical properties, suggesting that the same ligand can bind to distinct physicochemical environments. In some protein ligand complexes, the variation was found to correlate with the electrochemical characteristic of ligand molecules, whereas in others it was disclosed as a prerequisite for the biochemical function of the protein. To achieve binding, proteins were observed to engage in subtle balancing acts between electrostatic and hydrophobic interactions to generate stabilizing free energies of binding. For the presented analysis, a new method for scoring hydrophobicity from molecular environments was developed showing high correlations with experimental determined desolvation energies. The presented results highlight the complexities of molecular recognition and underline the challenges of computational structural biology in developing methods to detect these important subtleties.
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Affiliation(s)
- Abdullah Kahraman
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.
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228
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Tatsumi T, Awahara C, Naka H, Aimoto S, Konno H, Nosaka K, Akaji K. Evaluation of retro-inverso modifications of HTLV-1 protease inhibitors containing a hydroxyethylamine isoster. Bioorg Med Chem 2010; 18:2720-7. [DOI: 10.1016/j.bmc.2010.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Revised: 02/10/2010] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
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229
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Abstract
Triple-helical peptides (THPs) have been utilized as collagen models since the 1960s. The original focus for THP-based research was to unravel the structural determinants of collagen. In the last two decades, virtually all aspects of collagen structural biochemistry have been explored with THP models. More specifically, secondary amino acid analogs have been incorporated into THPs to more fully understand the forces that stabilize triple-helical structure. Heterotrimeric THPs have been utilized to better appreciate the contributions of chain sequence diversity on collagen function. The role of collagen as a cell signaling protein has been dissected using THPs that represent ligands for specific receptors. The mechanisms of collagenolysis have been investigated using THP substrates and inhibitors. Finally, THPs have been developed for biomaterial applications. These aspects of THP-based research are overviewed herein.
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Affiliation(s)
- Gregg B Fields
- University of Texas Health Science Center, Department of Biochemistry, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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230
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Matsuoka D, Nakasako M. Prediction of Hydration Structures around Hydrophilic Surfaces of Proteins by Using the Empirical Hydration Distribution Functions from a Database Analysis. J Phys Chem B 2010; 114:4652-63. [DOI: 10.1021/jp9100224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
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231
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Tan Q, Dong D, Ye L, Huo C, Huang F, Li R. Pre-fractionation of rat liver cytosol proteins prior to mass spectrometry-based proteomic analysis using tandem biomimetic affinity chromatography. J Mol Recognit 2010; 23:93-100. [PMID: 19862701 DOI: 10.1002/jmr.995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Efficient and high resolution separation of the protein mixture prior to trypsin digestion and mass spectrometry (MS) analysis is generally used to reduce the complexity of samples, an approach that highly increases the probability of detecting low-copy-number proteins. Our laboratory has constructed an affinity ligand library composed of thousands of ligands with different protein absorbance effects. Structural differences between these ligands result in different non-bonded protein-ligand interactions, thus each ligand exhibits a specific affinity to some protein groups. In this work, we first selected out several synthetic affinity ligands showing large band distribution differences in proteins absorbance profiles, and a tandem composition of these affinity ligands was used to distribute complex rat liver cytosol into simple subgroups. Ultimately, all the fractions collected from tandem affinity pre-fractionation were digested and then analyzed by LC-MS/MS, which resulted in high confidence identification of 665 unique rat protein groups, 1.8 times as many proteins as were detected in the un-fractionated sample (371 protein groups). Of these, 375 new proteins were identified in tandem fractions, and most of the proteins identified in un-fractionated sample (290, 80%) also emerged in tandem fractions. Most importantly, 430 unique proteins (64.7%) only characterized in specific fractions, indicating that the crude tissue extract was well distributed by tandem affinity fractionation. All detected proteins were bioinformatically annotated according to their physicochemical characteristics (such as MW, pI, GRAVY value, TM Helices). This approach highlighted the sensitivity of this method to a wide variety of protein classes. Combined usage of tandem affinity pre-fractionation with MS-based proteomic analysis is simple, low-cost, and effective, providing the prospect of broad application in proteomics.
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Affiliation(s)
- Qingqiao Tan
- MOE Key Laboratory of Microbial Metabolism, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200241, China
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232
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Muldoon J, Ashcroft AE, Wilson AJ. Selective protein-surface sensing using ruthenium(II) tris(bipyridine) complexes. Chemistry 2010; 16:100-3. [PMID: 19946912 DOI: 10.1002/chem.200902368] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James Muldoon
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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233
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Zulkefeli M, Sogon T, Takeda K, Kimura E, Aoki S. Design and synthesis of a stable supramolecular trigonal prism formed by the self-assembly of a linear tetrakis(Zn2+-cyclen) complex and trianionic trithiocyanuric acid in aqueous solution and its complexation with DNA (cyclen = 1,4,7,10-tetraazacyclododecane). Inorg Chem 2010; 48:9567-78. [PMID: 19743814 DOI: 10.1021/ic901407d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new supramolecular complex, {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+), was designed and synthesized by the 3:4 self-assembly of a linear tetrakis(Zn(2+)-cyclen) complex (Zn(4)L(4))(8+) and trianionic trithiocyanurate (TCA(3-)) in aqueous solution (cyclen = 1,4,7,10-tetraazacyclododecane). The {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+) complex, which should have a trigonal prism configuration, was found to be very stable in aqueous solution at neutral pH and 25 degrees C, as evidenced by (1)H NMR titration, potentiometric pH and UV titrations, and MS measurements. The complex does not dissociate into the starting building blocks in the presence of Zn(2+)-binding anions such as phosphates and double-stranded DNA. The results of the competitive binding assays with ethidium bromide and calf-thymus DNA, thermal melting experiments, gel mobility shift assays, and dynamic light-scattering data strongly indicated that the trigonal prism functions as a polycationic template to induce the aggregation of double-stranded DNA.
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Affiliation(s)
- Mohd Zulkefeli
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan
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234
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Bai SQ, Quek GYH, Koh LL, Andy Hor TS. Crystallographic analysis of different water–halidecluster blends in cationic [(SNS)PdII] pincer complexes. CrystEngComm 2010. [DOI: 10.1039/b917189b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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235
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Mou J, Fang H, Liu Y, Shang L, Wang Q, Zhang L, Xu W. Design, synthesis and primary activity assay of bi- or tri-peptide analogues with the scaffold l-arginine as amino-peptidase N/CD13 inhibitors. Bioorg Med Chem 2009; 18:887-95. [PMID: 19969464 DOI: 10.1016/j.bmc.2009.11.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 11/16/2009] [Accepted: 11/17/2009] [Indexed: 10/20/2022]
Abstract
A series of bi- or tri-peptide analogues with the scaffold l-arginine were designed, synthesized and evaluated for their inhibitory activities against amino-peptidase N (APN) and metalloproteinase-2 (MMP-2). The primary activity assay showed that all the compounds exhibited higher inhibitory activities against APN than MMP-2. Within this series, compounds C6 and C7 (IC(50)=4.2 and 4.3microM) showed comparable APN inhibitory activities with the positive control bestatin (IC(50)=3.8microM).
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Affiliation(s)
- Jiajia Mou
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, 44, Wenhuaxi Road, Ji'nan, Shandong 250012, PR China
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236
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Liu N, Cao S, Wu J, Shen L, Yu J, Zhang J, Li H, Qian X. A mild and efficient synthesis of monofluorinated α-lactam pseudopeptides via a novel dehydrofluorination of Ugi products. Mol Divers 2009; 14:501-6. [PMID: 19921454 DOI: 10.1007/s11030-009-9209-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 10/24/2009] [Indexed: 10/20/2022]
Abstract
Six novel monofluorinated α-lactam pseudopeptide derivatives were synthesized via Ugi reaction using gem-difluoromethylene-containing isocyanide as a key component, followed by dehydrofluorination of Ugi products in one pot without additional base.
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Affiliation(s)
- Nianjin Liu
- Shanghai Key Laboratory of Chemical Biology, Center of Fluorine Chemical Technology, School of Pharmacy, East China University of Science and Technology, 200237, Shanghai, China
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237
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Russo F, Wångsell F, Sävmarker J, Jacobsson M, Larhed M. Synthesis and evaluation of a new class of tertiary alcohol based BACE-1 inhibitors. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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238
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Kumar BRP, Soni M, Bhikhalal UB, Kakkot IR, Jagadeesh M, Bommu P, Nanjan MJ. Analysis of physicochemical properties for drugs from nature. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9244-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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239
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Bertini I, Calderone V, Fragai M, Luchinat C, Talluri E. Structural basis of serine/threonine phosphatase inhibition by the archetypal small molecules cantharidin and norcantharidin. J Med Chem 2009; 52:4838-43. [PMID: 19601647 DOI: 10.1021/jm900610k] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The inhibition of a subgroup of human serine/threonine protein phosphatases is responsible for the cytotoxicity of cantharidin and norcantharidin against tumor cells. It is shown that the anhydride rings of cantharidin and norcantharidin are hydrolyzed when bound to the catalytic domain of the human serine/threonine protein phosphatases 5 (PP5c), and the high-resolution crystal structures of PP5c complexed with the corresponding dicarboxylic acid derivatives of the two molecules are reported. Norcantharidin shows a unique binding conformation with the catalytically active Mn2PP5c, while cantharidin is characterized by a double conformation in its binding mode to the protein. Different binding modes of norcantharidin are observed depending of whether the starting ligand is in the anhydride or in the dicarboxylic acid form. All these structures will provide the basis for the rational design of new cantharidin-based drugs.
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Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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240
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Podstawka E, Olszewski TK, Boduszek B, Proniewicz LM. Adsorbed States of Phosphonate Derivatives of N-Heterocyclic Aromatic Compounds, Imidazole, Thiazole, and Pyridine on Colloidal Silver: Comparison with a Silver Electrode. J Phys Chem B 2009; 113:12013-8. [DOI: 10.1021/jp9050116] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edyta Podstawka
- Regional Laboratory of Physicochemical Analysis and Structural Research, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland, Organic Chemistry Division, Faculty of Chemistry, Wroclaw University of Technology, ul. Wybrzeże S. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Tomasz K. Olszewski
- Regional Laboratory of Physicochemical Analysis and Structural Research, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland, Organic Chemistry Division, Faculty of Chemistry, Wroclaw University of Technology, ul. Wybrzeże S. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Bogdan Boduszek
- Regional Laboratory of Physicochemical Analysis and Structural Research, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland, Organic Chemistry Division, Faculty of Chemistry, Wroclaw University of Technology, ul. Wybrzeże S. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Leonard M. Proniewicz
- Regional Laboratory of Physicochemical Analysis and Structural Research, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland, Organic Chemistry Division, Faculty of Chemistry, Wroclaw University of Technology, ul. Wybrzeże S. Wyspiańskiego 27, 50-370 Wrocław, Poland, and Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
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241
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Chiummiento L, Funicello M, Lupattelli P, Tramutola F, Campaner P. New indolic non-peptidic HIV protease inhibitors from (S)-glycidol: synthesis and preliminary biological activity. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.05.089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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242
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Wilson AJ. Inhibition of protein-protein interactions using designed molecules. Chem Soc Rev 2009; 38:3289-300. [PMID: 20449049 DOI: 10.1039/b807197g] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although many cellular processes depend upon enzymatic reactions, protein-protein interactions (PPIs) mediate a large number of important regulatory pathways and thus play a central role in disease development. In order to understand and selectively inhibit cellular signalling pathways, there is a pressing need for small molecules that target PPIs, particularly in the context of pharmaceutical development. This tutorial review will introduce the relevance of PPIs to chemical biology and highlight the key challenges in designing inhibitors. Some of the successes using conventional approaches to the identification of small-molecule PPI inhibitors will be highlighted, and also the reasons why these approaches have not always proven successful. Several general approaches tailored to particular protein topologies are emerging for the design of scaffolds that inhibit PPIs-these will form the major content of this review. Finally a summary of the challenges to be faced in developing inhibitors of PPIs into drug leads and how these challenges may differ from those encountered with enzyme-like targets will be given.
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Affiliation(s)
- Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, LS2 9JT, Leeds, UK.
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243
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Discovery of novel selective HER-2 sheddase inhibitors through optimization of P1 moiety. Bioorg Med Chem Lett 2009; 19:5037-42. [PMID: 19635666 DOI: 10.1016/j.bmcl.2009.07.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 11/20/2022]
Abstract
A novel series of carbamates was discovered as potent and selective HER-2 sheddase inhibitors. Significant enhancement in potency and selectivity was achieved through attenuating the P1 moiety, which was conventionally believed to be exposed to solvent.
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244
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Characterization of alpha-nitromethyl ketone as a new zinc-binding group based on structural analysis of its complex with carboxypeptidase A. Bioorg Med Chem Lett 2009; 19:5009-11. [PMID: 19646864 DOI: 10.1016/j.bmcl.2009.07.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/22/2009] [Accepted: 07/09/2009] [Indexed: 01/12/2023]
Abstract
Zinc-binding groups (ZBGs) are exhaustively applied in the development of the new inhibitors against a wide variety of physiologically and pathologically important zinc proteases. Here the alpha-nitro ketone was presented as a new ZBG, which is a transition-state analog featured by the unique bifurcated hydrogen bonds at the active site of carboxypeptidase A based on the structural analysis. Introduction of a nitro group at the alpha-position of the ketone could provide more non-covalent interactions without loss of the abilities to form a tetrahedral transition-state analog.
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245
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Pochetti G, Montanari R, Gege C, Chevrier C, Taveras AG, Mazza F. Extra binding region induced by non-zinc chelating inhibitors into the S1' subsite of matrix metalloproteinase 8 (MMP-8). J Med Chem 2009; 52:1040-9. [PMID: 19173605 DOI: 10.1021/jm801166j] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mode of binding and the activity of the first two non-zinc chelating, potent, and selective inhibitors of human neutrophil collagenase are reported. The crystal structures of the catalytic domain of MMP-8, respectively complexed with each inhibitor, reveals that both ligands are deeply inserted into the primary specificity subsite S(1)', where they induce a similar conformational change of the surrounding loop that is endowed with the main specificity determinants of MMPs. Accord to this rearrangement, both inhibitors remove the floor of the pocket formed by the Y227 side-chain, rendering available an extra binding region never explored before. The present data show that potent and more selective inhibitors can be obtained by developing ligands able to interact with the selectivity regions of the enzyme rather than with the catalytic zinc ion, which is the common feature of all MMP members.
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Affiliation(s)
- Giorgio Pochetti
- Istituto di Cristallografia-CNR, Area della Ricerca Roma 1, Via Salaria Km.29,300, I-00016 Monterotondo Stazione, Roma, Italy.
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246
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Solid-phase synthesis of linear and cyclic peptides containing a calix[4]arene amino acid. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.02.198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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247
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Burns DM, Li YL, Shi E, He C, Xu M, Zhuo J, Zhang C, Qian DQ, Li Y, Wynn R, Covington MB, Katiyar K, Marando CA, Fridman JS, Scherle P, Friedman S, Metcalf B, Yao W. Compelling P1 substituent affect on metalloprotease binding profile enables the design of a novel cyclohexyl core scaffold with excellent MMP selectivity and HER-2 sheddase inhibition. Bioorg Med Chem Lett 2009; 19:3525-30. [PMID: 19457660 DOI: 10.1016/j.bmcl.2009.04.143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 04/27/2009] [Accepted: 04/30/2009] [Indexed: 11/16/2022]
Abstract
A serendipitous discovery that the metalloprotease binding profile of a novel class of 2-carboxamide-3-hydroxamic acid piperidines could be significantly attenuated by the modification of the unexplored P1 substituent enabled the design and synthesis of a novel 2-carboxamide-1-hydroxamic acid cyclohexyl scaffold core that exhibited excellent HER-2 potency and unprecedented MMP-selectivity that we believe would not have been possible via conventional P1' perturbations.
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Affiliation(s)
- David M Burns
- Incyte Corporation, Department of Medicinal Chemistry, Wilmington, DE 19880, USA.
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248
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Waibel M, Pitrat D, Hasserodt J. On the inhibition of HIV-1 protease by hydrazino-ureas displaying the N→CO interaction. Bioorg Med Chem 2009; 17:3671-9. [DOI: 10.1016/j.bmc.2009.03.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/23/2009] [Accepted: 03/29/2009] [Indexed: 01/23/2023]
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249
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Klein T, P Geurink P, S Overkleeft H, K Kauffman H, Bischoff R. Functional proteomics on zinc-dependent metalloproteinases using inhibitor probes. ChemMedChem 2009; 4:164-70. [PMID: 19072819 DOI: 10.1002/cmdc.200800284] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Metzincins are a family of zinc(II)-dependent metalloproteinases with well known members such as the matrix metalloproteinases (MMPs) and A disintegrin and metalloproteinases (ADAMs). Metzincins are largely responsible for the modulation and regulation of the extracellular matrix by proteolytic degradation of extracellular matrix (ECM) proteins, and by liberation or production of biologically active proteins from their pro-forms. Since metzincin activity is strictly regulated in vivo, novel analysis methods are necessary to elucidate the role of the active enzymes in health and disease. This concept gives an overview of available methods, and describes an approach to use synthetic metzincin inhibitors as affinity probes for selective determination of active metzincins in biological and clinical samples.
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Affiliation(s)
- Theo Klein
- Center of Pharmacy, University of Groningen, The Netherlands
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250
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Li X, Wang Y, Wu J, Li Y, Wang Q, Xu W. Novel aminopeptidase N inhibitors derived from antineoplaston AS2–5 (Part II). Bioorg Med Chem 2009; 17:3061-71. [DOI: 10.1016/j.bmc.2009.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 03/05/2009] [Accepted: 03/06/2009] [Indexed: 10/21/2022]
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