1
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Patra J, Rana D, Arora S, Pal M, Mahindroo N. Falcipains: Biochemistry, target validation and structure-activity relationship studies of inhibitors as antimalarials. Eur J Med Chem 2023; 252:115299. [PMID: 36996716 DOI: 10.1016/j.ejmech.2023.115299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Malaria is a tropical disease with significant morbidity and mortality burden caused by Plasmodium species in Africa, the Middle East, Asia, and South America. Pathogenic Plasmodium species have lately become increasingly resistant to approved chemotherapeutics and combination therapies. Therefore, there is an emergent need for identifying new druggable targets and novel chemical classes against the parasite. Falcipains, cysteine proteases required for heme metabolism in the erythrocytic stage, have emerged as promising drug targets against Plasmodium species that infect humans. This perspective discusses the biology, biochemistry, structural features, and genetics of falcipains. The efforts to identify selective or dual inhibitors and their structure-activity relationships are reviewed to give a perspective on the design of novel compounds targeting falcipains for antimalarial activity evaluating reasons for hits and misses for this important target.
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Affiliation(s)
- Jeevan Patra
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Devika Rana
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India
| | - Smriti Arora
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Mintu Pal
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Bathinda, Punjab, 151001, India
| | - Neeraj Mahindroo
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India; School of Health Sciences and Technology, Dr. Vishwanath Karad MIT World Peace University, 124 Paud Road, Kothrud, Pune, Maharashtra, 411038, India.
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2
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Mueller NPF, Carloni P, Alfonso-Prieto M. Molecular determinants of acrylamide neurotoxicity through covalent docking. Front Pharmacol 2023; 14:1125871. [PMID: 36937867 PMCID: PMC10018202 DOI: 10.3389/fphar.2023.1125871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Acrylamide (ACR) is formed during food processing by Maillard reaction between sugars and proteins at high temperatures. It is also used in many industries, from water waste treatment to manufacture of paper, fabrics, dyes and cosmetics. Unfortunately, cumulative exposure to acrylamide, either from diet or at the workplace, may result in neurotoxicity. Such adverse effects arise from covalent adducts formed between acrylamide and cysteine residues of several neuronal proteins via a Michael addition reaction. The molecular determinants of acrylamide reactivity and its impact on protein function are not completely understood. Here we have compiled a list of acrylamide protein targets reported so far in the literature in connection with neurotoxicity and performed a systematic covalent docking study. Our results indicate that acrylamide binding to cysteine is favored in the presence of nearby positively charged amino acids, such as lysines and arginines. For proteins with more than one reactive Cys, docking scores were able to discriminate between the primary ACR modification site and secondary sites modified only at high ACR concentrations. Therefore, docking scores emerge as a potential filter to predict Cys reactivity against acrylamide. Inspection of the ACR-protein complex structures provides insights into the putative functional consequences of ACR modification, especially for non-enzyme proteins. Based on our study, covalent docking is a promising computational tool to predict other potential protein targets mediating acrylamide neurotoxicity.
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Affiliation(s)
- Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Department of Physics, RWTH Aachen University, Aachen, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Mercedes Alfonso-Prieto,
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3
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In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V. J Mol Graph Model 2022; 113:108153. [DOI: 10.1016/j.jmgm.2022.108153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022]
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4
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Multitarget-Based Virtual Screening for Identification of Herbal Substances toward Potential Osteoclastic Targets. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Osteoporosis is a complex bone disease indicating porous bone with low bone mass density and fragility. Cathepsin K, V-ATPase, and αVβ3 integrin are exhibited as novel targets for osteoporosis treatment. Our preliminary study uses a state-of-the-art method, including target-based virtual screening and clustering methods to determine promising candidates with multitarget properties. Phytochemicals with osteoprotective properties from the literature are used to elucidate the molecular interactions toward three targets. The binding scores of compounds are normalized and rescored. The K-means and hierarchical clustering methods are applied to filter and define the promising compounds, and the silhouette analysis is supposed to validate the clustering method. We explore 108 herbal compounds by virtual screening and the cluster approach, and find that rutin, sagittatoside A, icariin, and kaempferitrin showed strong binding affinities against Cathepsin K, V-ATPase, and αVβ3 integrin. Dockings of candidates toward three targets also provide the protein-ligand interactions and crucial amino acids for binding. Our study provides a straightforward and less time-consuming approach to exploring the new multitarget candidates for further investigations, using a combination of in silico methods.
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5
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Lemke C, Benýšek J, Brajtenbach D, Breuer C, Jílková A, Horn M, Buša M, Ulrychová L, Illies A, Kubatzky KF, Bartz U, Mareš M, Gütschow M. An Activity-Based Probe for Cathepsin K Imaging with Excellent Potency and Selectivity. J Med Chem 2021; 64:13793-13806. [PMID: 34473502 DOI: 10.1021/acs.jmedchem.1c01178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cysteine protease cathepsin K is a target for the treatment of diseases associated with high bone turnover. Cathepsin K is mainly expressed in osteoclasts and responsible for the destruction of the proteinaceous components of the bone matrix. We designed various fluorescent activity-based probes (ABPs) and their precursors that bind to and inactivate cathepsin K. ABP 25 exhibited extraordinary potency (kinac/Ki = 35,300 M-1s-1) and selectivity for human cathepsin K. Crystal structures of cathepsin K in complex with ABP 25 and its nonfluorescent precursor 21 were determined to characterize the binding mode of this new type of acrylamide-based Michael acceptor with the particular orientation of the dibenzylamine moiety to the primed subsite region. The cyanine-5 containing probe 25 allowed for sensitive detection of cathepsin K, selective visualization in complex proteomes, and live cell imaging of a human osteosarcoma cell line, underlining its applicability in a pathophysiological environment.
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Affiliation(s)
- Carina Lemke
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Jakub Benýšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 16610, Czech Republic.,First Faculty of Medicine, Charles University, Kateřinská 32, Prague 12108, Czech Republic
| | - Dominik Brajtenbach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Christian Breuer
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany.,Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, Rheinbach 53359, Germany
| | - Adéla Jílková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 16610, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 16610, Czech Republic
| | - Michal Buša
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 12800, Czech Republic
| | - Lenka Ulrychová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 16610, Czech Republic
| | - Annika Illies
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Katharina F Kubatzky
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, Rheinbach 53359, Germany
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 16610, Czech Republic
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
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6
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Coscia F, Taler-Verčič A. Cryo-EM: A new dawn in thyroid biology. Mol Cell Endocrinol 2021; 531:111309. [PMID: 33964321 PMCID: PMC8316605 DOI: 10.1016/j.mce.2021.111309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 11/09/2022]
Abstract
The thyroid gland accumulates the rare dietary element iodine and incorporates it into iodinated thyroid hormones, utilising several tightly regulated reactions and molecular mechanisms. Thyroid hormones are essential in vertebrates and play a central role in many biological processes, such as development, thermogenesis and growth. The control of these functions is exerted through the binding of hormones to nuclear thyroid hormone receptors that rule the transcription of numerous metabolic genes. Over the last 50 years, thyroid biology has been studied extensively at the cellular and organismal levels, revealing its multiple clinical implications, yet, a complete molecular understanding is still lacking. This includes the atomic structures of crucial pathway components that would be needed to elucidate molecular mechanisms. Here we review the currently known protein structures involved in thyroid hormone synthesis, regulation, transport, and actions. We also highlight targets for future investigations that will significantly benefit from recent advances in macromolecular structure determination by electron cryo-microscopy (cryo-EM). As an example, we demonstrate how cryo-EM was crucial to obtain the structure of the large thyroid hormone precursor protein, thyroglobulin. We discuss modern cryo-EM compared to other structure determination methods and how an integrated structural and cell biological approach will help filling the molecular knowledge gap in our understanding of thyroid hormone metabolism. Together with clinical, cellular and high-throughput 'omics' studies, atomic structures of thyroid components will provide an important framework to map disease mutations and to interpret and predict thyroid phenotypes.
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Affiliation(s)
- Francesca Coscia
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK; Human Technopole, Via Cristina Belgioioso 171, 20157, Milano, Italy.
| | - Ajda Taler-Verčič
- University of Ljubljana, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Vrazov Trg 2, 1000, Ljubljana, Slovenia
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7
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Schade M, Merla B, Lesch B, Wagener M, Timmermanns S, Pletinckx K, Hertrampf T. Highly Selective Sub-Nanomolar Cathepsin S Inhibitors by Merging Fragment Binders with Nitrile Inhibitors. J Med Chem 2020; 63:11801-11808. [PMID: 32880457 DOI: 10.1021/acs.jmedchem.0c00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pharmacological inhibition of cathepsin S (CatS) allows for a specific modulation of the adaptive immune system and many major diseases. Here, we used NMR fragment screening and crystal structure-aided merging to synthesize novel, highly selective CatS inhibitors with picomolar enzymatic Ki values and nanomolar functional activity in human Raji cells. Noncovalent fragment hits revealed binding hotspots, while the covalent inhibitor structure-activity relationship enabled efficient potency optimization.
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Affiliation(s)
- Markus Schade
- Grünenthal GmbH, Zieglerstr. 6, 52078 Aachen, Germany
| | - Beatrix Merla
- Grünenthal GmbH, Zieglerstr. 6, 52078 Aachen, Germany
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8
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Vieira RP, Santos VC, Ferreira RS. Structure-based Approaches Targeting Parasite Cysteine Proteases. Curr Med Chem 2019; 26:4435-4453. [PMID: 28799498 DOI: 10.2174/0929867324666170810165302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 12/17/2022]
Abstract
Cysteine proteases are essential hydrolytic enzymes present in the majority of organisms, including viruses and unicellular parasites. Despite the high sequence identity displayed among these proteins, specific structural features across different species grant distinct functions to these biomolecules, frequently related to pathological conditions. Consequently, their relevance as promising targets for potential specific inhibitors has been highlighted and occasionally validated in recent decades. In this review, we discuss the recent outcomes of structure-based campaigns aiming the discovery of new inhibitor prototypes against cruzain and falcipain, as alternative therapeutic tools for Chagas disease and malaria treatments, respectively. Computational and synthetic approaches have been combined on hit optimization strategies and are also discussed herein. These rationales are extended to additional tropical infectious and neglected pathologies, such as schistosomiasis, leishmaniasis and babesiosis, and also to Alzheimer's Disease, a widespread neurodegenerative disease poorly managed by currently available drugs and recently linked to particular physiopathological roles of human cysteine proteases.
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Affiliation(s)
- Rafael Pinto Vieira
- Departamento de Bioquimica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.,CAPES Foundation, Ministry of Education of Brazil, 70040-020 Brasília, DF, Brazil
| | - Viviane Corrêa Santos
- Departamento de Bioquimica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquimica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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9
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Synthesis and biological evaluation of 7-(aminoalkyl)pyrazolo[1,5-a]pyrimidine derivatives as cathepsin K inhibitors. Bioorg Chem 2019; 84:226-238. [DOI: 10.1016/j.bioorg.2018.11.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/13/2018] [Accepted: 11/17/2018] [Indexed: 12/14/2022]
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10
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Zwicker JD, Diaz NA, Guerra AJ, Kirchhoff PD, Wen B, Sun D, Carruthers VB, Larsen SD. Optimization of dipeptidic inhibitors of cathepsin L for improved Toxoplasma gondii selectivity and CNS permeability. Bioorg Med Chem Lett 2018; 28:1972-1980. [PMID: 29650289 PMCID: PMC5938124 DOI: 10.1016/j.bmcl.2018.03.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
The neurotropic protozoan Toxoplasma gondii is the second leading cause of death due to foodborne illness in the US, and has been designated as one of five neglected parasitic infections by the Center for Disease Control and Prevention. Currently, no treatment options exist for the chronic dormant-phase Toxoplasma infection in the central nervous system (CNS). T. gondii cathepsin L (TgCPL) has recently been implicated as a novel viable target for the treatment of chronic toxoplasmosis. In this study, we report the first body of SAR work aimed at developing potent inhibitors of TgCPL with selectivity vs the human cathepsin L. Starting from a known inhibitor of human cathepsin L, and guided by structure-based design, we were able to modulate the selectivity for Toxoplasma vs human CPL by nearly 50-fold while modifying physiochemical properties to be more favorable for metabolic stability and CNS penetrance. The overall potency of our inhibitors towards TgCPL was improved from 2 μM to as low as 110 nM and we successfully demonstrated that an optimized analog 18b is capable of crossing the BBB (0.5 brain/plasma). This work is an important first step toward development of a CNS-penetrant probe to validate TgCPL as a feasible target for the treatment of chronic toxoplasmosis.
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Affiliation(s)
- Jeffery D Zwicker
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Nicolas A Diaz
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Alfredo J Guerra
- Department of Immunology and Microbiology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Paul D Kirchhoff
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Bo Wen
- Pharmacokinetics Core, Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States
| | - Duxin Sun
- Pharmacokinetics Core, Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, United States
| | - Vern B Carruthers
- Department of Immunology and Microbiology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States.
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11
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Lu J, Wang M, Wang Z, Fu Z, Lu A, Zhang G. Advances in the discovery of cathepsin K inhibitors on bone resorption. J Enzyme Inhib Med Chem 2018; 33:890-904. [PMID: 29723068 PMCID: PMC6010086 DOI: 10.1080/14756366.2018.1465417] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cathepsin K (Cat K), highly expressed in osteoclasts, is a cysteine protease member of the cathepsin lysosomal protease family and has been of increasing interest as a target of medicinal chemistry efforts for its role in bone matrix degradation. Inhibition of the Cat K enzyme reduces bone resorption and thus, has rendered the enzyme as an attractive target for anti-resorptive osteoporosis therapy. Over the past decades, considerable efforts have been made to design and develop highly potent, excellently selective and orally applicable Cat K inhibitors. These inhibitors are derived from synthetic compounds or natural products, some of which have passed preclinical studies and are presently in clinical trials at different stages of advancement. In this review, we briefly summarised the historic development of Cat K inhibitors and discussed the relationship between structures of inhibitors and active sites in Cat K for the purpose of guiding future development of inhibitors.
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Affiliation(s)
- Jun Lu
- a Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China.,b Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China
| | - Maolin Wang
- a Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China.,b Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China
| | - Ziyue Wang
- a Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China
| | - Zhongqi Fu
- a Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China
| | - Aiping Lu
- a Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China.,b Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China
| | - Ge Zhang
- a Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China.,b Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University , Hong Kong SAR , China
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12
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Almeida S, Marti R, Vanoli E, Abele S, Tortoioli S. One-Pot Synthesis of Trifluoromethylated Quinazolin-4(3H)-ones with Trifluoroacetic Acid as CF3 Source. J Org Chem 2018; 83:5104-5113. [DOI: 10.1021/acs.joc.8b00389] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sofia Almeida
- Chemical Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123 Allschwil, Switzerland
- HES-SO, University of Applied Sciences Western Switzerland, Haute Ecole d’Ingénierie et d’Architecture Fribourg, Institute of Chemical Technology, Boulevard de Pérolles 80, CH-1700 Fribourg, Switzerland
| | - Roger Marti
- HES-SO, University of Applied Sciences Western Switzerland, Haute Ecole d’Ingénierie et d’Architecture Fribourg, Institute of Chemical Technology, Boulevard de Pérolles 80, CH-1700 Fribourg, Switzerland
| | - Ennio Vanoli
- HES-SO, University of Applied Sciences Western Switzerland, Haute Ecole d’Ingénierie et d’Architecture Fribourg, Institute of Chemical Technology, Boulevard de Pérolles 80, CH-1700 Fribourg, Switzerland
| | - Stefan Abele
- Chemical Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123 Allschwil, Switzerland
| | - Simone Tortoioli
- Chemical Development, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, 4123 Allschwil, Switzerland
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13
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Salas-Sarduy E, Landaburu LU, Karpiak J, Madauss KP, Cazzulo JJ, Agüero F, Alvarez VE. Novel scaffolds for inhibition of Cruzipain identified from high-throughput screening of anti-kinetoplastid chemical boxes. Sci Rep 2017; 7:12073. [PMID: 28935948 PMCID: PMC5608908 DOI: 10.1038/s41598-017-12170-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/04/2017] [Indexed: 11/16/2022] Open
Abstract
American Trypanosomiasis or Chagas disease is a prevalent, neglected and serious debilitating illness caused by the kinetoplastid protozoan parasite Trypanosoma cruzi. The current chemotherapy is limited only to nifurtimox and benznidazole, two drugs that have poor efficacy in the chronic phase and are rather toxic. In this scenario, more efficacious and safer drugs, preferentially acting through a different mechanism of action and directed against novel targets, are particularly welcome. Cruzipain, the main papain-like cysteine peptidase of T. cruzi, is an important virulence factor and a chemotherapeutic target with excellent pre-clinical validation evidence. Here, we present the identification of new Cruzipain inhibitory scaffolds within the GlaxoSmithKline HAT (Human African Trypanosomiasis) and Chagas chemical boxes, two collections grouping 404 non-cytotoxic compounds with high antiparasitic potency, drug-likeness, structural diversity and scientific novelty. We have adapted a continuous enzymatic assay to a medium-throughput format and carried out a primary screening of both collections, followed by construction and analysis of dose-response curves of the most promising hits. Using the identified compounds as a starting point a substructure directed search against CHEMBL Database revealed plausible common scaffolds while docking experiments predicted binding poses and specific interactions between Cruzipain and the novel inhibitors.
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Affiliation(s)
- Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina
| | - Lionel Urán Landaburu
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina
| | - Joel Karpiak
- GlaxoSmithKline R&D, Molecular Design US, Pennsylvania, Upper Providence PA, USA
| | - Kevin P Madauss
- GlaxoSmithKline R&D, Trust in Science, Pennsylvania, Upper Providence PA, USA
| | - Juan José Cazzulo
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina.
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad Nacional de San Martín - CONICET, San Martin, B1650HMP, Buenos Aires, Argentina.
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14
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Raghav N, Singh M. SAR studies of some acetophenone phenylhydrazone based pyrazole derivatives as anticathepsin agents. Bioorg Chem 2017; 75:38-49. [PMID: 28915464 DOI: 10.1016/j.bioorg.2017.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/18/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022]
Abstract
Cathepsins have emerged as promising molecular targets in a number of diseases such as Alzeimer's, inflammation and cancer. Elevated cathepsin's levels and decreased cellular inhibitor concentrations have emphasized the search for novel inhibitors of cathepsins. The present work is focused on the design and synthesis of some acetophenone phenylhydrazone based pyrazole derivatives as novel non peptidyl inhibitors of cathepsins B, H and L. The synthesized compounds after characterization have been explored for their inhibitory potency against cathepsins B, H and L. The results show that some of the synthesized compounds exhibit anti-catheptic activity with Ki value of the order of 10-10M. Differential inhibitory effects have been observed for cathepsins B, H and L. Cathepsin L is inhibited more pronounced than cathepsin B and cathepsin H in that order.
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Affiliation(s)
- Neera Raghav
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India.
| | - Mamta Singh
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
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15
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Kramer L, Turk D, Turk B. The Future of Cysteine Cathepsins in Disease Management. Trends Pharmacol Sci 2017; 38:873-898. [PMID: 28668224 DOI: 10.1016/j.tips.2017.06.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/23/2017] [Accepted: 06/05/2017] [Indexed: 02/06/2023]
Abstract
Since the discovery of the key role of cathepsin K in bone resorption, cysteine cathepsins have been investigated by pharmaceutical companies as drug targets. The first clinical results from targeting cathepsins by activity-based probes and substrates are paving the way for the next generation of molecular diagnostic imaging, whereas the majority of antibody-drug conjugates currently in clinical trials depend on activation by cathepsins. Finally, cathepsins have emerged as suitable vehicles for targeted drug delivery. It is therefore timely to review the future of cathepsins in drug discovery. We focus here on inflammation-associated diseases because dysregulation of the immune system accompanied by elevated cathepsin activity is a common feature of these conditions.
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Affiliation(s)
- Lovro Kramer
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, 1000 Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, 1000 Ljubljana, Slovenia
| | - Dušan Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, 1000 Ljubljana, Slovenia; Center of Excellence CIPKEBIP, Jamova 39, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, 1000 Ljubljana, Slovenia; Center of Excellence CIPKEBIP, Jamova 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
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16
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Evaluation of dipeptide nitriles as inhibitors of rhodesain, a major cysteine protease of Trypanosoma brucei. Bioorg Med Chem Lett 2017; 27:45-50. [DOI: 10.1016/j.bmcl.2016.11.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/11/2016] [Accepted: 11/13/2016] [Indexed: 12/21/2022]
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17
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Novič M, Tibaut T, Anderluh M, Borišek J, Tomašič T. The Comparison of Docking Search Algorithms and Scoring Functions. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This chapter, composed of two parts, firstly provides molecular docking overview and secondly two molecular docking case studies are described. In overview, basic information about molecular docking are presented such as description of search algorithms and scoring functions applied in various docking programs. Brief description of methods utilized in some of the most popular docking programs also applied in our experimental work is provided. AutoDock, CDOCKER, GOLD, FlexX and FRED were used for docking studies of the DC-SIGN protein, while GOLD was further used for docking studies of cathepsin K protein. Methods and results of our studies with their contribution to science and medicine are presented. Content of the chapter is therefore appropriate for public of Medicinal and Organic Chemistry as an overview of docking studies, and also for Computational Chemists at the beginning of their work as the introduction to application of molecular docking programs.
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18
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Schmitz J, Li T, Bartz U, Gütschow M. Cathepsin B Inhibitors: Combining Dipeptide Nitriles with an Occluding Loop Recognition Element by Click Chemistry. ACS Med Chem Lett 2016; 7:211-6. [PMID: 26985300 DOI: 10.1021/acsmedchemlett.5b00474] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 12/27/2015] [Indexed: 12/21/2022] Open
Abstract
An active site mapping of human cathepsin B with dipeptide nitrile inhibitors was performed for a combinatorial approach by introducing several points of diversity and stepwise optimizing the inhibitor structure. To address the occluding loop of cathepsin B by a carboxylate moiety, click chemistry to generate linker-connected molecules was applied. Inhibitor 17 exhibited K i values of 41.3 nM, 27.3 nM, or 19.2 nM, depending on the substrate and pH of the assay. Kinetic data were discussed with respect to the conformational selection and induced fit models.
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Affiliation(s)
- Janina Schmitz
- Pharmaceutical Institute, Pharmaceutical
Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Strasse 20, D-53359 Rheinbach, Germany
| | - Tianwei Li
- Pharmaceutical Institute, Pharmaceutical
Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Strasse 20, D-53359 Rheinbach, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical
Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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19
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Wang Y, Li R, Zheng Z, Yi H, Li Z. Identification of novel cathepsin K inhibitors using ligand-based virtual screening and structure-based docking. RSC Adv 2016. [DOI: 10.1039/c6ra14251f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Compound 21 was identified as a cathepsin K (Cat K) inhibitor through pharmacophore virtual screening and molecular docking studies.
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Affiliation(s)
- Yali Wang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science and Peking Union Medical College
- Beijing 100050
- China
| | - Ruolan Li
- New Drug Research & Development Center
- North China Pharmaceutical Group Corporation
- Shijiazhuang 050015
- China
| | - Zhihui Zheng
- New Drug Research & Development Center
- North China Pharmaceutical Group Corporation
- Shijiazhuang 050015
- China
| | - Hong Yi
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science and Peking Union Medical College
- Beijing 100050
- China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science and Peking Union Medical College
- Beijing 100050
- China
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