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Dókus LE, Yousef M, Bánóczi Z. Modulators of calpain activity: inhibitors and activators as potential drugs. Expert Opin Drug Discov 2020; 15:471-486. [DOI: 10.1080/17460441.2020.1722638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Levente Endre Dókus
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Mo’ath Yousef
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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2
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Pehere AD, Zhang X, Abell AD. Macrocyclic Peptidomimetics Prepared by Ring-Closing Metathesis and Azide–Alkyne Cycloaddition. Aust J Chem 2017. [DOI: 10.1071/ch16532] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Macrocycles are finding increasing use as a means to define the backbone geometries of peptides and peptidomimetics. Ring-closing metathesis and CuI-catalyzed azide–alkyne cycloaddition are particularly useful for introducing such rings and they do so in high yield and with a good functional group tolerance and compatibility. Here, we present an overview of the use of these two methods, with reference to selected examples and particular reference to β-strand peptidomimetics for use as protease inhibitors.
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Abstract
Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Affiliation(s)
- Ashwani Kumar
- Guru Jambheshwar University of Science and Technology, India
| | - Ruchika Goyal
- Guru Jambheshwar University of Science and Technology, India
| | - Sandeep Jain
- Guru Jambheshwar University of Science and Technology, India
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4
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Allen SE, Dokholyan NV, Bowers AA. Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications. ACS Chem Biol 2016; 11:10-24. [PMID: 26575401 DOI: 10.1021/acschembio.5b00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.
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Affiliation(s)
- Scott E. Allen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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5
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Muralidharan AR, Selvaraj C, Singh SK, Sheu JR, Thomas PA, Geraldine P. Structure-Based Virtual Screening and Biological Evaluation of a Calpain Inhibitor for Prevention of Selenite-Induced Cataractogenesis in an in Vitro System. J Chem Inf Model 2015; 55:1686-97. [PMID: 26270943 DOI: 10.1021/acs.jcim.5b00092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Calpains belong to the family of calcium-dependent, structurally related intracellular cysteine proteases that exhibit significant functions in evolution of different types of cataracts in human as well as animal models. Application of calpain inhibitors generated through a virtual screening workflow may provide new avenues for the prevention of cataractogenesis. Hence, in the current study, compounds were first screened for potent calpain inhibitory activity by employing a structure-based approach, and the screening results were then validated through biological experiments in rat lenses. A hit compound, HTS08688, was obtained by structure-based virtual screening. A micromolar concentration of HTS08688 was found to prevent in vitro cataractogenesis in isolated Wistar rat lenses, while maintaining the antioxidant and calcium concentrations at near normal levels. Inhibition of superoxide anion generation, as observed through cytochemical localization studies, and maintenance of structural integrity, as demonstrated by histological analysis of lenticular tissue, also suggested that HTS08688 can ameliorate the cataractous condition induced by selenite in an in vitro rodent model. A cell proliferation assay was performed; the IC 50 value of the screened calpain inhibitor, HTS08688, against human lenticular epithelial cells-b3 was found to be 177 μM/mL. This combined theoretical and experimental approach has demonstrated a potent lead compound, HTS08688, that exhibits putative anticataractogenic activity by virtue of its potential to inhibit calpain.
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Affiliation(s)
| | - Chandrabose Selvaraj
- Department of Bioinformatics, Alagappa University , Karaikudi-630003, Tamilnadu, India
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Alagappa University , Karaikudi-630003, Tamilnadu, India
| | - Joen-Rong Sheu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University , Taipei 110, Taiwan
| | - Philip A Thomas
- Institute of Ophthalmology, Joseph Eye Hospital , Tiruchirappalli-620001, Tamilnadu, India
| | - Pitchairaj Geraldine
- Department of Animal Science, School of Life Sciences, Bharathidasan University , Tiruchirappalli-620024, Tamilnadu, India
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Mechanism of action of thalassospiramides, a new class of calpain inhibitors. Sci Rep 2015; 5:8783. [PMID: 25740631 PMCID: PMC4350077 DOI: 10.1038/srep08783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022] Open
Abstract
Thalassospiramides comprise a large family of lipopeptide natural products produced by Thalassospira and Tistrella marine bacteria. Here we provide further evidence of their nanomolar inhibitory activity against the human calpain 1 protease. Analysis of structure-activity relationship data supported our hypothesis that the rigid 12-membered ring containing an α,β-unsaturated carbonyl moiety is the pharmacologically active functional group, in contrast to classic electrophilic “warheads” in known calpain inhibitors. Using a combination of chemical modifications, mass spectrometric techniques, site-directed mutagenesis, and molecular modeling, we show the covalent binding of thalassospiramide's α,β-unsaturated carbonyl moiety to the thiol group of calpain's catalytic Cys115 residue by a Michael 1,4-addition reaction. As nanomolar calpain inhibitors with promising selectivity and low toxicity from natural sources are rare, we consider thalassospiramides as promising drug leads.
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Jones SA, Duncan J, Aitken SG, Coxon JM, Abell AD. The Preparation of Macrocyclic Calpain Inhibitors by Ring Closing Metathesis and Cross Metathesis. Aust J Chem 2014. [DOI: 10.1071/ch14121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ring closing metathesis and cross metathesis approaches to a new macrocyclic peptidomimetic aldehyde 2 have been developed, with the former route being the most convenient. Aldehyde 2 is a potent inhibitor of calpain II (IC50 of 45 nM) with comparable activity to the benchmark acyclic inhibitor SJA6017 4. Both compounds contain an N-terminal 4-fluorophenylsulfonyl group. The P2 Ile analogue of 2 (16) is significantly less active (IC50 of 2000 nM) which reflects an unusually subtle importance of the P2 residue for active site binding.
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8
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Virtual screening based on pharmacophoric features of known calpain inhibitors to identify potent inhibitors of calpain. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0842-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Jones SA, Neilsen PM, Siew L, Callen DF, Goldfarb NE, Dunn BM, Abell AD. A template-based approach to inhibitors of calpain 2, 20S proteasome, and HIV-1 protease. ChemMedChem 2013; 8:1918-21. [PMID: 24130198 DOI: 10.1002/cmdc.201300387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/07/2013] [Indexed: 01/14/2023]
Abstract
Specificity counts: A template-based approach to protease inhibitors is presented using a core macrocycle that presents a generic β-strand template for binding to protease active sites. This is then specifically functionalized at P2 , and the C and N termini to give inhibitors of calpain 2, 20S proteasome, and HIV-1 protease.
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Affiliation(s)
- Seth A Jones
- School Chemistry and Physics, The University of Adelaide, Adelaide, SA 5005 (Australia)
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Chen H, Jiao W, Jones MA, Coxon JM, Morton JD, Bickerstaffe R, Pehere AD, Zvarec O, Abell AD. New tripeptide-based macrocyclic calpain inhibitors formed by N-alkylation of histidine. Chem Biodivers 2013; 9:2473-84. [PMID: 23161629 DOI: 10.1002/cbdv.201200320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Indexed: 01/14/2023]
Abstract
Two new series of 15-membered macrocyclic peptidomimetics, in which the P1 and P3 residues of the peptide backbone are linked by a bridge containing a 1,4-disubstituted 1H-imidazole, are reported. The structure with an aldehyde at the C-terminus and the imidazole at P3, i.e., 4c, shows significant inhibitory activity against calpain 2, with an IC(50) value of 238 nM. The macrocyclic aldehyde with the imidazole at the alternative P1 position, i.e., 5c, is significantly less active. The relative activities are linked to the ability of the component macrocycles to mimic a β-strand geometry that is known to favor active-site binding. This ability is defined by conformational searches and docking studies with calpain.
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Affiliation(s)
- Hongyuan Chen
- Chemistry Department, University of Canterbury, Christchurch, New Zealand
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11
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Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit 2013; 26:215-39. [PMID: 23526775 DOI: 10.1002/jmr.2266] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville; VIC; 3052; Australia
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Chondrogianni N, Petropoulos I, Grimm S, Georgila K, Catalgol B, Friguet B, Grune T, Gonos ES. Protein damage, repair and proteolysis. Mol Aspects Med 2012; 35:1-71. [PMID: 23107776 DOI: 10.1016/j.mam.2012.09.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 09/26/2012] [Indexed: 01/10/2023]
Abstract
Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression.
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Affiliation(s)
- Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Helenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece.
| | - Isabelle Petropoulos
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4-UPMC, IFR 83, Université Pierre et Marie Curie-Paris 6, 4 Place Jussieu, 75005 Paris, France
| | - Stefanie Grimm
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller University, Dornburger Straße 24, 07743 Jena, Germany
| | - Konstantina Georgila
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Helenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Betul Catalgol
- Department of Biochemistry, Faculty of Medicine, Genetic and Metabolic Diseases Research Center (GEMHAM), Marmara University, Haydarpasa, Istanbul, Turkey
| | - Bertrand Friguet
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4-UPMC, IFR 83, Université Pierre et Marie Curie-Paris 6, 4 Place Jussieu, 75005 Paris, France
| | - Tilman Grune
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller University, Dornburger Straße 24, 07743 Jena, Germany
| | - Efstathios S Gonos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Helenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece.
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Saupe SM, Steinmetzer T. A New Strategy for the Development of Highly Potent and Selective Plasmin Inhibitors. J Med Chem 2012; 55:1171-80. [DOI: 10.1021/jm2011996] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sebastian M. Saupe
- Department of Pharmacy,
Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department of Pharmacy,
Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
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