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Schönauer E, Kany AM, Haupenthal J, Hüsecken K, Hoppe IJ, Voos K, Yahiaoui S, Elsässer B, Ducho C, Brandstetter H, Hartmann RW. Discovery of a Potent Inhibitor Class with High Selectivity toward Clostridial Collagenases. J Am Chem Soc 2017; 139:12696-12703. [PMID: 28820255 PMCID: PMC5607459 DOI: 10.1021/jacs.7b06935] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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Secreted virulence
factors like bacterial collagenases are conceptually
attractive targets for fighting microbial infections. However, previous
attempts to develop potent compounds against these metalloproteases
failed to achieve selectivity against human matrix metalloproteinases
(MMPs). Using a surface plasmon resonance-based screening complemented
with enzyme inhibition assays, we discovered an N-aryl mercaptoacetamide-based inhibitor scaffold that showed
sub-micromolar affinities toward collagenase H (ColH) from the human
pathogen Clostridium histolyticum. Moreover, these
inhibitors also efficiently blocked the homologous bacterial collagenases,
ColG from C. histolyticum, ColT from C. tetani, and ColQ1 from the Bacillus cereus strain Q1,
while showing negligible activity toward human MMPs-1, -2, -3, -7,
-8, and -14. The most active compound displayed a more than 1000-fold
selectivity over human MMPs. This selectivity can be rationalized
by the crystal structure of ColH with this compound, revealing a distinct
non-primed binding mode to the active site. The non-primed binding
mode presented here paves the way for the development of selective
broad-spectrum bacterial collagenase inhibitors with potential therapeutic
application in humans.
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Affiliation(s)
- Esther Schönauer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Andreas M Kany
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Kristina Hüsecken
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Isabel J Hoppe
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Katrin Voos
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Samir Yahiaoui
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany
| | - Brigitta Elsässer
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, 66123 Saarbrücken, Germany
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Schönauer E, Brandstetter H. Inhibition and Activity Regulation of Bacterial Collagenases. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Medicinal applications of perfluoroalkylated chain-containing compounds. Future Med Chem 2015; 6:1201-29. [PMID: 25078138 DOI: 10.4155/fmc.14.53] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Compounds with polyfluorinated molecular fragments possess unique properties associated with the presence of a large number of fluorine atoms that affect lipophilicity and conformational rigidity of the parent molecule along with other effects. The aim of this review is to provide an overview of synthesized compounds possessing perfluoroalkylated or polyfluorinated chains that have been tested for bioactivity or as potential drug candidates for the treatment of various diseases. As far as the length of the perfluoroalkylated chain is concerned the focus is centered on the compound bearing perfluoroethyl or tetrafluoroethyl as well as longer chains. The perfluoroalkylated compounds discussed are classified according to their biological activity.
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Eckhard U, Huesgen PF, Brandstetter H, Overall CM. Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen. J Proteomics 2013; 100:102-14. [PMID: 24125730 PMCID: PMC3985423 DOI: 10.1016/j.jprot.2013.10.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 09/27/2013] [Accepted: 10/03/2013] [Indexed: 12/15/2022]
Abstract
Clostridial collagenases are among the most efficient degraders of collagen. Most clostridia are saprophytes and secrete proteases to utilize proteins in their environment as carbon sources; during anaerobic infections, collagenases play a crucial role in host colonization. Several medical and biotechnological applications have emerged utilizing their high collagenolytic efficiency. However, the contribution of the functionally most important peptidase domain to substrate specificity remains unresolved. We investigated the active site sequence specificity of the peptidase domains of collagenase G and H from Clostridium histolyticum and collagenase T from Clostridium tetani. Both prime and non-prime cleavage site specificity were simultaneously profiled using Proteomic Identification of protease Cleavage Sites (PICS), a mass spectrometry-based method utilizing database searchable proteome-derived peptide libraries. For each enzyme we identified > 100 unique-cleaved peptides, resulting in robust cleavage logos revealing collagen-like specificity patterns: a strong preference for glycine in P3 and P1′, proline at P2 and P2′, and a slightly looser specificity at P1, which in collagen is typically occupied by hydroxyproline. This specificity for the classic collagen motifs Gly-Pro-X and Gly-X-Hyp represents a remarkable adaptation considering the complex requirements for substrate unfolding and presentation that need to be fulfilled before a single collagen strand becomes accessible for cleavage. Biological significance We demonstrate the striking sequence specificity of a family of clostridial collagenases using proteome derived peptide libraries and PICS, Proteomic Identification of protease Cleavage Sites. In combination with the previously published crystal structures of these proteases, our results represent an important piece of the puzzle in understanding the complex mechanism underlying collagen hydrolysis, and pave the way for the rational design of specific test substrates and selective inhibitors. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes? Active site specificity profiling of 3 clostridial collagenases—ColG and H from C. histolyticum, and ColT from C. tetani. Their high sequence specificity to collagen-like sequence points towards a co-evolution with the mammalian substrate. Significant differences to MMPs and a more promiscuous cleavage mechanism facilitating rapid collagenolysis were revealed. Human proteome-derived peptide libraries & PICS are suitable for active site specificity profiling of pathogenic proteases. Results pave the way for rational design of test substrates and selective inhibitors.
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Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada; Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstr, 11, 5020 Salzburg, Austria
| | - Pitter F Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hans Brandstetter
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstr, 11, 5020 Salzburg, Austria
| | - Christopher M Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
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Krishnamoorthy G, Sehgal PK, Mandal AB, Sadulla S. Studies on collagen-tannic acid-collagenase ternary system: Inhibition of collagenase against collagenolytic degradation of extracellular matrix component of collagen. J Enzyme Inhib Med Chem 2011; 27:451-7. [PMID: 21823836 DOI: 10.3109/14756366.2011.596834] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We report the detailed studies on the inhibitory effect of tannic acid (TA) on Clostridium histolyticum collagenase (ChC) activity against degradation of extracellular matrix component of collagen. The TA treated collagen exhibited 64% resistance against collagenolytic hydrolysis by ChC, whereas direct interaction of TA with ChC exhibited 99% inhibition against degradation of collagen and the inhibition was found to be concentration dependant. The kinetic inhibition of ChC has been deduced from the extent of hydrolysis of N-[3-(2-furyl) acryloyl]-Leu-Gly-Pro-Ala (FALGPA). This data provides a selective competitive mode of inhibition on ChC activity seems to be influenced strongly by the nature and structure of TA. TA showed inhibitor activity against the ChC by molecular docking method. This result demonstrated that TA containing digalloyl radical possess the ability to inhibit the ChC. The inhibition of ChC in gaining new insight into the mechanism of stabilization of collagen by TA is discussed.
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Affiliation(s)
- Ganesan Krishnamoorthy
- Bioproducts Laboratory-Biomaterial Development Division, Central Leather Research Institute (Council of Scientific & Industrial Research), Chennai, Tamil Nadu, India
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Gupta SP. Quantitative Structure−Activity Relationship Studies on Zinc-Containing Metalloproteinase Inhibitors. Chem Rev 2007; 107:3042-87. [PMID: 17622180 DOI: 10.1021/cr030448t] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Satya P Gupta
- Department of Chemistry, Birla Institute of Technology and Science, Pilani-333031, India.
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Ilies M, Banciu MD, Scozzafava A, Ilies MA, Caproiu MT, Supuran CT. Protease inhibitors: synthesis of bacterial collagenase and matrix metalloproteinase inhibitors incorporating arylsulfonylureido and 5-dibenzo-suberenyl/suberyl moieties. Bioorg Med Chem 2003; 11:2227-39. [PMID: 12713832 DOI: 10.1016/s0968-0896(03)00113-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Novel matrix metalloproteinase (MMP)/bacterial collagenase inhibitors are reported, considering the sulfonylated amino acid hydroxamates as lead molecules. A series of compounds was prepared by reaction of arylsulfonyl isocyanates with N-(5H-dibenzo[a,d]cyclohepten-5-yl)- and N-(10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-yl) methyl glycocolate, respectively, followed by the conversion of the COOMe to the carboxylate/hydroxamate moieties. The corresponding derivatives with methylene and ethylene spacers between the polycyclic moiety and the amino acid functionality were also obtained by related synthetic strategies. These new compounds were assayed as inhibitors of MMP-1, MMP-2, MMP-8 and MMP-9, and of the collagenase isolated from Clostridium histolyticum (ChC). Some of the new derivatives reported here proved to be powerful inhibitors of the four MMPs mentioned above and of ChC, with activities in the low nanomolar range for some of the target enzymes, depending on the substitution pattern at the sulfonylureido moiety and on the length of the spacer through which the dibenzosuberenyl/suberyl group is connected with the rest of the molecule. Several of these inhibitors also showed selectivity for the deep pocket enzymes (MMP-2, MMP-8 and MMP-9) over the shallow pocket ones MMP-1 and ChC.
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Affiliation(s)
- Monica Ilies
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Via della Lastruccia 3, Rm 188, Polo Scientifico, 50019-Sesto Fiorentino, Firenze, Italy
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Abstract
The effects of Aloe barbadensis gel and aloe gel constituents on the activity of microbial and human metalloproteinases have been investigated. Clostridium histolyticum collagenase (ChC) results dose-dependently inhibited by aloe gel and the activity-guided fractionation led to an active fraction enriched in phenolics and aloins. Aloins have been shown to be able to bind and to inhibit ChC reversibly and non-competitively. Aloe gel and aloins are also effective inhibitors of stimulated granulocyte matrix metalloproteinases (MMPs). The remarkable structural resemblances between aloins and the pharmacophore structure of inhibitory tetracyclines, suggest that the inhibitory effects of aloins are via an interaction between the carbonyl group at C(9) and an adjacent hydroxyl group of anthrone (C(1) or C(8)) at the secondary binding site of enzyme, destabilizing the structure of granulocyte MMPs.
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Affiliation(s)
- Esther Barrantes
- Department of Pharmacology, School of Pharmacy, University of Alcalá, Ctra. Madrid-Barcelona Km 33.6, 28871 Alcalá de Henares, Spain
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Scozzafava A, Supuran CT. Protease inhibitors: synthesis of matrix metalloproteinase and bacterial collagenase inhibitors incorporating 5-amino-2-mercapto-1,3,4-thiadiazole zinc binding functions. Bioorg Med Chem Lett 2002; 12:2667-72. [PMID: 12217351 DOI: 10.1016/s0960-894x(02)00564-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Matrix metalloproteinase (MMP)/bacterial collagenase inhibitors incorporating 5-amino-2-mercapto-1,3,4-thiadiazole zinc binding functions are reported. A series of compounds was prepared by reaction of arylsulfonyl isocyanates or arylsulfonyl halides with phenylalanyl-alanine, followed by coupling with 5-amino-2-mercapto-1,3,4-thiadiazole in the presence of carbodiimides. These new compounds were assayed as inhibitors of human MMP-1, MMP-2, MMP-8 and MMP-9, and of the collagenase isolated from the anaerobe Clostridium histolyticum (ChC). The new derivatives proved to be powerful inhibitors of these metalloproteases, with activities in the low micromolar range for some of the target enzymes, depending on the substitution pattern at the arylsulfonyl(ureido) moieties.
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Affiliation(s)
- Andrea Scozzafava
- Università degli Studi di Firenze, Dipartimento di Chimica, Laboratorio di Chimica Bioinorganica, Sesto Fiorentino, Florence, Italy
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Abstract
Serine-, cysteine-, and metalloproteases are widely spread in many pathogenic bacteria, where they play critical functions related to colonization and evasion of host immune defenses, acquisition of nutrients for growth and proliferation, facilitation of dissemination, or tissue damage during infection. Since all the antibiotics used clinically at the moment share a common mechanism of action, acting as inhibitors of the bacterial cell wall biosynthesis or affecting protein synthesis on ribosomes, resistance to these pharmacological agents represents a serious medical problem, which might be resolved by using new generation of antibiotics, possessing a different mechanism of action. Bacterial protease inhibitors constitute an interesting such possibility, due to the fact that many specific as well as ubiquitous proteases have recently been characterized in some detail in both gram-positive as well as gram-negative pathogens. Few potent, specific inhibitors for such bacterial proteases have been reported at this moment except for some signal peptidase, clostripain, Clostridium histolyticum collagenase, botulinum neurotoxin, and tetanus neurotoxin inhibitors. No inhibitors of the critically important and ubiquitous AAA proteases, degP or sortase have been reported, although such compounds would presumably constitute a new class of highly effective antibiotics. This review presents the state of the art in the design of such enzyme inhibitors with potential therapeutic applications, as well as recent advances in the use of some of these proteases in therapy.
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Affiliation(s)
- Claudiu T Supuran
- University of Florence, Dipartimento di Chimica, Laboratorio di Chimica Inorganica e Bioinorganica, Firenze, Italy.
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Scozzafava A, Supuran CT. Carbonic anhydrase activators: high affinity isozymes I, II, and IV activators, incorporating a beta-alanyl-histidine scaffold. J Med Chem 2002; 45:284-91. [PMID: 11784133 DOI: 10.1021/jm010958k] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel class of tight binding carbonic anhydrase (CA) activators was designed by using histamine and histidine as lead molecules. Carnosine (beta-Ala-His) derivatives were synthesized by reaction of appropriately derivatized beta-alanines with imidazole/carboxy-protected histidine in the presence of carbodiimides, followed by removal of the various protecting groups. The derivatized beta-alanines mentioned above were in turn obtained by coupling of 4-fluorophenylsulfonylureido amino acids (fpu-AA) or 2-toluenesulfonylureido amino acids (ots-AA) with beta-Ala. Some structurally related dipeptides with the general formula fpu/ots-AA1-AA2 (AA, AA1, and AA2 represent amino acyl moieties) were also prepared by a similar strategy and used thereafter for obtaining CA activators incorporating a modified tetrapeptide scaffold. Many of the new tri-/tetrapeptide derivatives reported here proved to be efficient in vitro activators of three CA isozymes. Very good activity was detected against hCA I and bCA IV, for which some of the new compounds showed affinities in the 1-20 nM range (h = human; b = bovine isozymes), whereas against hCA II, their affinities were in the range of 10-40 nM. Ex vivo experiments showed some of the new activators to strongly enhance cytosolic red cell CA activity after incubation with human erythrocytes. This new class of CA activators might lead to the development of drugs/diagnostic tools for the management of CA deficiency syndromes, as well as for the pharmacological enhancement of synaptic efficacy, spatial learning, and memory. This may constitute a new approach for the treatment of Alzheimer's disease and other conditions in need of achieving memory therapy.
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Affiliation(s)
- Andrea Scozzafava
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Via Gino Capponi 7, I-50121 Florence, Italy
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Natchus MG, Bookland RG, Laufersweiler MJ, Pikul S, Almstead NG, De B, Janusz MJ, Hsieh LC, Gu F, Pokross ME, Patel VS, Garver SM, Peng SX, Branch TM, King SL, Baker TR, Foltz DJ, Mieling GE. Development of new carboxylic acid-based MMP inhibitors derived from functionalized propargylglycines. J Med Chem 2001; 44:1060-71. [PMID: 11297453 DOI: 10.1021/jm000477l] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of carboxylic acids were prepared from a propargylglycine scaffold and tested for efficacy as matrix metalloproteinase (MMP) inhibitors. Detailed SAR for the series is reported for four enzymes within the MMP family. The inhibitors were typically potent against collagenase-3 (MMP-13) and gelatinase A (MMP-2), while they spared collagenase-1 (MMP-1) and only moderately inhibited stromelysin (MMP-3). Compound 40 represents a typical inhibition profile of a compound with reasonable potency. Introduction of polar groups was required in order to generate inhibitors with acceptable water solubility, and this often resulted in a loss of potency as in compound 63. High serum protein binding proved to be a difficult hurdle with many compounds such as 48 showing >99% binding. Some compounds such as 64 displayed approximately 90% binding, but no reliable method was discovered for designing molecules with low protein binding. Finally, selected data regarding the pharmacokinetic behavior of these compounds is presented.
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Affiliation(s)
- M G Natchus
- Procter and Gamble Pharmaceuticals, 8700 Mason-Montgomery Road, Mason, Ohio 45040, USA.
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