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Khatua K, Alugubelli YR, Yang KS, Vulupala VR, Blankenship LR, Coleman D, Atla S, Chaki SP, Geng ZZ, Ma XR, Xiao J, Chen PH, Cho CCD, Sharma S, Vatansever EC, Ma Y, Yu G, Neuman BW, Xu S, Liu WR. Azapeptides with unique covalent warheads as SARS-CoV-2 main protease inhibitors. Antiviral Res 2024; 225:105874. [PMID: 38555023 PMCID: PMC11070182 DOI: 10.1016/j.antiviral.2024.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
The main protease (MPro) of SARS-CoV-2, the causative agent of COVID-19, is a pivotal nonstructural protein critical for viral replication and pathogenesis. Its protease function relies on three active site pockets for substrate recognition and a catalytic cysteine for enzymatic activity. To develop potential SARS-CoV-2 antivirals, we successfully synthesized a diverse range of azapeptide inhibitors with various covalent warheads to target MPro's catalytic cysteine. Our characterization identified potent MPro inhibitors, including MPI89 that features an aza-2,2-dichloroacetyl warhead with a remarkable EC50 value of 10 nM against SARS-CoV-2 infection in ACE2+ A549 cells and a selective index of 875. MPI89 is also remarkably selective and shows no potency against SARS-CoV-2 papain-like protease and several human proteases. Crystallography analyses demonstrated that these inhibitors covalently engaged the catalytic cysteine and used the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 stands as one of the most potent MPro inhibitors, suggesting the potential for further exploration of azapeptides and the aza-2,2-dichloroacetyl warhead for developing effective therapeutics against COVID-19.
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Affiliation(s)
- Kaustav Khatua
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Yugendar R Alugubelli
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Kai S Yang
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Veerabhadra R Vulupala
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Lauren R Blankenship
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Demonta Coleman
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Sandeep Atla
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Sankar P Chaki
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhi Zachary Geng
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Xinyu R Ma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Jing Xiao
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Peng-Hsun Chen
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Chia-Chuan D Cho
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Shivangi Sharma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Erol C Vatansever
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Yuying Ma
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Ge Yu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA
| | - Benjamin W Neuman
- Department of Biology, Texas A&M University, College Station, TX 77843, USA; Texas A&M Global Health Research Complex, Texas A&M University, College Station, TX 77843, USA; Health Science Centre, Department of Molecular Pathogenesis and Immunology, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA; Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA.
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Center and Department of Chemistry, Texas A&M University, College Station, TX 77854, USA; Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
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2
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Khatua K, Alugubelli YR, Yang KS, Vulupala VR, Blankenship LR, Coleman DD, Atla S, Chaki SP, Geng ZZ, Ma XR, Xiao J, Chen PHC, Cho CCD, Vatansever EC, Ma Y, Yu G, Neuman BW, Xu S, Liu WR. An Azapeptide Platform in Conjunction with Covalent Warheads to Uncover High-Potency Inhibitors for SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536467. [PMID: 37090597 PMCID: PMC10120698 DOI: 10.1101/2023.04.11.536467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Main protease (M Pro ) of SARS-CoV-2, the viral pathogen of COVID-19, is a crucial nonstructural protein that plays a vital role in the replication and pathogenesis of the virus. Its protease function relies on three active site pockets to recognize P1, P2, and P4 amino acid residues in a substrate and a catalytic cysteine residue for catalysis. By converting the P1 Cα atom in an M Pro substrate to nitrogen, we showed that a large variety of azapeptide inhibitors with covalent warheads targeting the M Pro catalytic cysteine could be easily synthesized. Through the characterization of these inhibitors, we identified several highly potent M Pro inhibitors. Specifically, one inhibitor, MPI89 that contained an aza-2,2-dichloroacetyl warhead, displayed a 10 nM EC 50 value in inhibiting SARS-CoV-2 from infecting ACE2 + A549 cells and a selectivity index of 875. The crystallography analyses of M Pro bound with 6 inhibitors, including MPI89, revealed that inhibitors used their covalent warheads to covalently engage the catalytic cysteine and the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 represents one of the most potent M Pro inhibitors developed so far, suggesting that further exploration of the azapeptide platform and the aza-2,2-dichloroacetyl warhead is needed for the development of potent inhibitors for the SARS-CoV-2 M Pro as therapeutics for COVID-19.
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3
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Mijanović O, Jakovleva A, Branković A, Zdravkova K, Pualic M, Belozerskaya TA, Nikitkina AI, Parodi A, Zamyatnin AA. Cathepsin K in Pathological Conditions and New Therapeutic and Diagnostic Perspectives. Int J Mol Sci 2022; 23:ijms232213762. [PMID: 36430239 PMCID: PMC9698382 DOI: 10.3390/ijms232213762] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022] Open
Abstract
Cathepsin K (CatK) is a part of the family of cysteine proteases involved in many important processes, including the degradation activity of collagen 1 and elastin in bone resorption. Changes in levels of CatK are associated with various pathological conditions, primarily related to bone and cartilage degradation, such as pycnodysostosis (associated with CatK deficiency), osteoporosis, and osteoarthritis (associated with CatK overexpression). Recently, the increased secretion of CatK is being highly correlated to vascular inflammation, hypersensitivity pneumonitis, Wegener granulomatosis, berylliosis, tuberculosis, as well as with tumor progression. Due to the wide spectrum of diseases in which CatK is involved, the design and validation of active site-specific inhibitors has been a subject of keen interest in pharmaceutical companies in recent decades. In this review, we summarized the molecular background of CatK and its involvement in various diseases, as well as its clinical significance for diagnosis and therapy.
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Affiliation(s)
- Olja Mijanović
- Dia-M, LCC, 7 b.3 Magadanskaya Str., 129345 Moscow, Russia
- The Human Pathology Department, Sechenov First Moscow State University, 119991 Moscow, Russia
| | | | - Ana Branković
- Department of Forensics Engineering, University of Criminal Investigation and Police Studies, Cara Dusana 196, 11000 Belgrade, Serbia
| | - Kristina Zdravkova
- AD Alkaloid Skopje, Boulevar Alexander the Great 12, 1000 Skopje, North Macedonia
| | - Milena Pualic
- Institute Cardiovascular Diseases Dedinje, Heroja Milana Tepica 1, 11000 Belgrade, Serbia
| | - Tatiana A. Belozerskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Angelina I. Nikitkina
- ArhiMed Clinique for New Medical Technologies, Vavilova St. 68/2, 119261 Moscow, Russia
| | - Alessandro Parodi
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Andrey A. Zamyatnin
- Scientific Center for Translation Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7X, UK
- Correspondence: ; Tel.: +7-9261180220
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5
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Cathepsin K: A Versatile Potential Biomarker and Therapeutic Target for Various Cancers. Curr Oncol 2022; 29:5963-5987. [PMID: 36005209 PMCID: PMC9406569 DOI: 10.3390/curroncol29080471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/15/2022] [Accepted: 08/21/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer, a common malignant disease, is one of the predominant causes of diseases that lead to death. Additionally, cancer is often detected in advanced stages and cannot be radically cured. Consequently, there is an urgent need for reliable and easily detectable markers to identify and monitor cancer onset and progression as early as possible. Our aim was to systematically review the relevant roles of cathepsin K (CTSK) in various possible cancers in existing studies. CTSK, a well-known key enzyme in the bone resorption process and most studied for its roles in the effective degradation of the bone extracellular matrix, is expressed in various organs. Nowadays, CTSK has been involved in various cancers such as prostate cancer, breast cancer, bone cancer, renal carcinoma, lung cancer and other cancers. In addition, CTSK can promote tumor cells proliferation, invasion and migration, and its mechanism may be related to RANK/RANKL, TGF-β, mTOR and the Wnt/β-catenin signaling pathway. Clinically, some progress has been made with the use of cathepsin K inhibitors in the treatment of certain cancers. This paper reviewed our current understanding of the possible roles of CTSK in various cancers and discussed its potential as a biomarker and/or novel molecular target for various cancers.
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6
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Pharmacological Therapies for the Management of Inflammatory Bone Resorption in Periodontal Disease: A Review of Preclinical Studies. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5832009. [PMID: 35547360 PMCID: PMC9085331 DOI: 10.1155/2022/5832009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/28/2022] [Accepted: 04/13/2022] [Indexed: 02/06/2023]
Abstract
Periodontitis, a highly prevalent multicausal chronic inflammatory and destructive disease, develops as a result of complex host-parasite interactions. Dysbiotic bacterial biofilm in contact with the gingival tissues initiates a cascade of inflammatory events, mediated and modulated by the host's immune response, which is characterized by increased expression of several inflammatory mediators such as cytokines and chemokines in the connective tissue. If periodontal disease (PD) is left untreated, it results in the destruction of the supporting tissues around the teeth, including periodontal ligament, cementum, and alveolar bone, which lead to a wide range of disabilities and poor quality of life, thus imposing significant burdens. This process depends on the differentiation and activity of osteoclasts, the cells responsible for reabsorbing the bone tissue. Therefore, the inhibition of differentiation or activity of these cells is a promising strategy for controlling bone resorption. Several pharmacological drugs that target osteoclasts and inflammatory cells with immunomodulatory and anti-inflammatory effects, such as bisphosphonates, anti-RANK-L antibody, strontium ranelate, cathepsin inhibitors, curcumin, flavonoids, specialized proresolving mediators, and probiotics, were already described to manage inflammatory bone resorption during experimental PD progression in preclinical studies. Meantime, a growing number of studies have described the beneficial effects of herbal products in inhibiting bone resorption in experimental PD. Therefore, this review summarizes the role of several pharmacological drugs used for PD prevention and treatment and highlights the targeted action of all those drugs with antiresorptive properties. In addition, our review provides a timely and critical appraisal for the scientific rationale use of the antiresorptive and immunomodulatory medications in preclinical studies, which will help to understand the basis for its clinical application.
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7
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Bianco G, Goodsell DS, Forli S. Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors. Trends Pharmacol Sci 2020; 41:1038-1049. [PMID: 33153778 PMCID: PMC7669701 DOI: 10.1016/j.tips.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors are currently showing great promise for systems that are normally difficult to target with small molecule therapies. This renewed interest has spurred the refinement of existing computational methods as well as the designof new ones, expanding the toolbox for discovery and optimization of selectiveand effective covalent inhibitors. Commonly applied approaches are covalentdocking methods that predict the conformation of the covalent complex with known residues. More recently, a new predictive method, reactive docking, was developed, building on the growing corpus of data generated by large proteomics experiments. This method was successfully used in several 'inverse drug discovery' programs that use high-throughput techniques to isolate effective compounds based on screening of entire compound libraries based on desired phenotypes.
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Affiliation(s)
- Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Research Collaboratory for Structure Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Petushkova AI, Zamyatnin AA. Redox-Mediated Post-Translational Modifications of Proteolytic Enzymes and Their Role in Protease Functioning. Biomolecules 2020; 10:biom10040650. [PMID: 32340246 PMCID: PMC7226053 DOI: 10.3390/biom10040650] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/13/2022] Open
Abstract
Proteolytic enzymes play a crucial role in metabolic processes, providing the cell with amino acids through the hydrolysis of multiple endogenous and exogenous proteins. In addition to this function, proteases are involved in numerous protein cascades to maintain cellular and extracellular homeostasis. The redox regulation of proteolysis provides a flexible dose-dependent mechanism for proteolytic activity control. The excessive reactive oxygen species (ROS) and reactive nitrogen species (RNS) in living organisms indicate pathological conditions, so redox-sensitive proteases can swiftly induce pro-survival responses or regulated cell death (RCD). At the same time, severe protein oxidation can lead to the dysregulation of proteolysis, which induces either protein aggregation or superfluous protein hydrolysis. Therefore, oxidative stress contributes to the onset of age-related dysfunction. In the present review, we consider the post-translational modifications (PTMs) of proteolytic enzymes and their impact on homeostasis.
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Affiliation(s)
- Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence:
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9
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Mons E, Jansen IDC, Loboda J, van Doodewaerd BR, Hermans J, Verdoes M, van Boeckel CAA, van Veelen PA, Turk B, Turk D, Ovaa H. The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K. J Am Chem Soc 2019; 141:3507-3514. [PMID: 30689386 PMCID: PMC6396318 DOI: 10.1021/jacs.8b11027] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 12/21/2022]
Abstract
Irreversible covalent inhibitors can have a beneficial pharmacokinetic/pharmacodynamics profile but are still often avoided due to the risk of indiscriminate covalent reactivity and the resulting adverse effects. To overcome this potential liability, we introduced an alkyne moiety as a latent electrophile into small molecule inhibitors of cathepsin K (CatK). Alkyne-based inhibitors do not show indiscriminate thiol reactivity but potently inhibit CatK protease activity by formation of an irreversible covalent bond with the catalytic cysteine residue, confirmed by crystal structure analysis. The rate of covalent bond formation ( kinact) does not correlate with electrophilicity of the alkyne moiety, indicative of a proximity-driven reactivity. Inhibition of CatK-mediated bone resorption is validated in human osteoclasts. Together, this work illustrates the potential of alkynes as latent electrophiles in small molecule inhibitors, enabling the development of irreversible covalent inhibitors with an improved safety profile.
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Affiliation(s)
- Elma Mons
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Division
of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ineke D. C. Jansen
- Department
of Periodontology, Academic Center For Dentistry
Amsterdam (ACTA), 1081 LA Amsterdam, The Netherlands
| | - Jure Loboda
- Department
of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana 1000, Slovenia
- Jožef
Stefan International Postgraduate School, Ljubljana 1000, Slovenia
| | - Bjorn R. van Doodewaerd
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Jill Hermans
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Martijn Verdoes
- Department
of Tumor Immunology, Institute for Molecular
Life Sciences Radboud UMC, 6525 GA Nijmegen, The Netherlands
| | | | - Peter A. van Veelen
- Centre for
Proteomics and Metabolomics, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Boris Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana 1000, Slovenia
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Ljubljana 1000, Slovenia
| | - Dusan Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana 1000, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Ljubljana 1000, Slovenia
| | - Huib Ovaa
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Division
of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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10
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Galibert M, Wartenberg M, Lecaille F, Saidi A, Mavel S, Joulin-Giet A, Korkmaz B, Brömme D, Aucagne V, Delmas AF, Lalmanach G. Substrate-derived triazolo- and azapeptides as inhibitors of cathepsins K and S. Eur J Med Chem 2018; 144:201-210. [DOI: 10.1016/j.ejmech.2017.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/15/2017] [Accepted: 12/03/2017] [Indexed: 12/17/2022]
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Kumar N, Devineni SR, Aggile K, Gajjala PR, Kumar P, Dubey SK. Facile new industrial process for synthesis of teneligliptin through new intermediates and its optimization with control of impurities. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3120-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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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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13
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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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14
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Ali AR, El-Bendary ER, Ghaly MA, Shehata IA. Novel acetamidothiazole derivatives: synthesis and in vitro anticancer evaluation. Eur J Med Chem 2013; 69:908-19. [PMID: 24125851 DOI: 10.1016/j.ejmech.2013.08.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/09/2013] [Accepted: 08/12/2013] [Indexed: 01/07/2023]
Abstract
A novel series of acetamide derivatives possessing both 2-imino-4-arylthiazoles and morpholine or different piperazines were synthesized and characterized by IR, (1)H NMR, (13)C NMR, elemental and mass spectral analyses. Twelve compounds were granted NSC codes at National Cancer Institute (NCI), USA for anticancer activity at a single high dose (10(-5) M) in full NCI 60 cell panel. Among the compounds tested, compounds 5a and 6b were found to be the most active candidates of the synthesized series. Assessment of toxicities, druglikeness, and drug score profiles of compounds 5a and 6b are promising. Some of the synthesized compounds showed a good docking score with potential anticancer targets, chosen based on pharmacophore mapping of the established derivatives.
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Affiliation(s)
- Ahmed R Ali
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt.
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15
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Schröder J, Klinger A, Oellien F, Marhöfer RJ, Duszenko M, Selzer PM. Docking-based virtual screening of covalently binding ligands: an orthogonal lead discovery approach. J Med Chem 2013; 56:1478-90. [PMID: 23350811 DOI: 10.1021/jm3013932] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In pharmaceutical industry, lead discovery strategies and screening collections have been predominantly tailored to discover compounds that modulate target proteins through noncovalent interactions. Conversely, covalent linkage formation is an important mechanism for a quantity of successful drugs in the market, which are discovered in most cases by hindsight instead of systematical design. In this article, the implementation of a docking-based virtual screening workflow for the retrieval of covalent binders is presented considering human cathepsin K as a test case. By use of the docking conditions that led to the best enrichment of known actives, 44 candidate compounds with unknown activity on cathepsin K were finally selected for experimental evaluation. The most potent inhibitor, 4-(N-phenylanilino)-6-pyrrolidin-1-yl-1,3,5-triazine-2-carbonitrile (CP243522), showed a K(i) of 21 nM and was confirmed to have a covalent reversible mechanism of inhibition. The presented approach will have great potential in cases where covalent inhibition is the desired drug discovery strategy.
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Affiliation(s)
- Jörg Schröder
- MSD Animal Health Innovation GmbH, Zur Propstei, D-55270 Schwabenheim, Germany
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16
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Low SA, Kopeček J. Targeting polymer therapeutics to bone. Adv Drug Deliv Rev 2012; 64:1189-204. [PMID: 22316530 DOI: 10.1016/j.addr.2012.01.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 01/16/2012] [Accepted: 01/18/2012] [Indexed: 12/13/2022]
Abstract
An aging population in the developing world has led to an increase in musculoskeletal diseases such as osteoporosis and bone metastases. Left untreated many bone diseases cause debilitating pain and in the case of cancer, death. Many potential drugs are effective in treating diseases but result in side effects preventing their efficacy in the clinic. Bone, however, provides a unique environment of inorganic solids, which can be exploited in order to effectively target drugs to diseased tissue. By integration of bone targeting moieties to drug-carrying water-soluble polymers, the payload to diseased area can be increased while side effects decreased. The realization of clinically relevant bone targeted polymer therapeutics depends on (1) understanding bone targeting moiety interactions, (2) development of controlled drug delivery systems, as well as (3) understanding drug interactions. The latter makes it possible to develop bone targeted synergistic drug delivery systems.
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Affiliation(s)
- Stewart A Low
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
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17
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Scaffa P, Vidal C, Barros N, Gesteira T, Carmona A, Breschi L, Pashley D, Tjäderhane L, Tersariol I, Nascimento F, Carrilho M. Chlorhexidine Inhibits the Activity of Dental Cysteine Cathepsins. J Dent Res 2012; 91:420-5. [DOI: 10.1177/0022034511435329] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The co-expression of MMPs and cysteine cathepsins in the human dentin-pulp complex indicates that both classes of enzymes can contribute to the endogenous proteolytic activity of dentin. Chlorhexidine (CHX) is an efficient inhibitor of MMP activity. This study investigated whether CHX could also inhibit cysteine cathepsins present in dentin. The inhibitory profile of CHX on the activity of dentin-extracted and recombinant cysteine cathepsins (B, K, and L) was monitored in fluorogenic substrates. The rate of substrate hydrolysis was spectrofluorimetrically measured, and inhibitory constants were calculated. Molecular docking was performed to predict the binding affinity between CHX and cysteine cathepsins. The results showed that CHX inhibited the proteolytic activity of dentin-extracted cysteine cathepsins in a dose-dependent manner. The proteolytic activity of human recombinant cathepsins was also inhibited by CHX. Molecular docking analysis suggested that CHX strongly interacts with the subsites S2 to S2′ of cysteine cathepsins B, K, and L in a very similar manner. Taken together, these results clearly showed that CHX is a potent inhibitor of the cysteine cathepsins-proteolytic enzymes present in the dentin-pulp complex.
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Affiliation(s)
- P.M.C. Scaffa
- Department of Restorative Dentistry, Piracicaba Dental School, State University of Campinas, Piracicaba, Brazil
| | - C.M.P. Vidal
- Department of Restorative Dentistry, Piracicaba Dental School, State University of Campinas, Piracicaba, Brazil
| | - N. Barros
- Department of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - T.F. Gesteira
- Department of Biochemistry, Federal University of São Paulo, São Paulo, Brazil
| | - A.K. Carmona
- Department of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - L. Breschi
- Department of Biomedicine, University of Trieste, and IGM-CNR and Unit of Bologna c/o IOR, Bologna, Italy
| | - D.H. Pashley
- Department of Oral Biology, College of Dental Medicine, Georgia Health Sciences University, Augusta, GA, USA
| | - L. Tjäderhane
- Institute of Dentistry, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - I.L.S. Tersariol
- Department of Biochemistry, Federal University of São Paulo, São Paulo, Brazil
- Centro Interdisciplinar de Investigação Bioquímica, University of Mogi das Cruzes, Mogi das Cruzes, Brazil
| | - F.D. Nascimento
- Biomaterials Research Group, Bandeirante University of São Paulo, Rua Maria Cândida, 1813, 6 andar, São Paulo, 02071-013, Brazil
| | - M.R. Carrilho
- Biomaterials Research Group, Bandeirante University of São Paulo, Rua Maria Cândida, 1813, 6 andar, São Paulo, 02071-013, Brazil
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18
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Eldridge GM, Weiss GA. Hydrazide reactive peptide tags for site-specific protein labeling. Bioconjug Chem 2011; 22:2143-53. [PMID: 21905743 DOI: 10.1021/bc200415v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New site-specific protein labeling (SSPL) reactions for targeting-specific, short peptides could be useful for the real-time detection of proteins inside of living cells. One SSPL approach matches bioorthogonal reagents with complementary peptides. Here, hydrazide reactive peptides were selected from phage-displayed libraries using reaction-based selections. Selection conditions included washes of varying pH and treatment with NaCNBH(3) in order to specifically select reactive carbonyl-containing peptides. Selected peptides were fused to T4 lysozyme or synthesized on filter paper for colorimetric assays of the peptide-hydrazide interaction. A peptide-lysozyme protein fusion demonstrated specific, covalent labeling by the hydrazide reactive (HyRe) peptides in crude bacterial cell lysates, sufficient for the specific detection of an overexpressed protein fusion. Chemical synthesis of a short HyRe tag variant and subsequent reaction with two structurally distinct hydrazide probes produced covalent adducts observable by MALDI-TOF MS and MS/MS. Rather than isolating reactive carbonyl-containing peptides, we observed reaction with the N-terminal His of HyRe tag 114, amino acid sequence HKSNHSSKNRE, which attacks the hydrazide carbonyl at neutral pH. However, at the pH used during selection wash steps (<6.0), an alternative imine-containing product is formed that can be reduced with sodium cyanoborohydride. MSMS further reveals that this low pH product forms an adduct on Ser6. Further optimization of the novel bimolecular reaction described here could provide a useful tool for in vivo protein labeling and bioconjugate synthesis. The reported selection and screening methods could be widely applicable to the identification of peptides capable of other site-specific protein labeling reactions with bioorthogonal reagents.
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Affiliation(s)
- Glenn M Eldridge
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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19
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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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20
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Kiss G, Röthlisberger D, Baker D, Houk KN. Evaluation and ranking of enzyme designs. Protein Sci 2011; 19:1760-73. [PMID: 20665693 DOI: 10.1002/pro.462] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechanics (QM) on truncated model systems to the treatment of the full protein with ONIOM QM/MM and AMBER molecular dynamics (MD) were explored. The most effective procedure involved molecular dynamics, and a general MD protocol was established. Substantial deviations from the ideal catalytic geometries were observed for a number of designs. Penetration of water into the catalytic site and insufficient residue-packing around the active site are the main factors that can cause enzyme designs to be inactive. Where in the past, computational evaluations of designed enzymes were too time-extensive for practical considerations, it has now become feasible to rank and refine candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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21
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Antagonists of inhibitor of apoptosis proteins based on thiazole amide isosteres. Bioorg Med Chem Lett 2010; 20:2229-33. [PMID: 20189383 DOI: 10.1016/j.bmcl.2010.02.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/03/2010] [Accepted: 02/03/2010] [Indexed: 11/22/2022]
Abstract
A series of IAP antagonists based on thiazole or benzothiazole amide isosteres was designed and synthesized. These compounds were tested for binding to the XIAP-BIR3 and ML-IAP BIR using a fluorescence polarization assay. The most potent of these compounds, 19a and 33b, were found to have K(i)'s of 20-30 nM against ML-IAP and 50-60 nM against XIAP-BIR3.
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22
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Affiliation(s)
- Bimal K. Banik
- Dept. Chemistry, University of Texas-Pan American, W. University Drive 1201, Edinburg, 78539 USA
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23
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Je JE, Ahn SJ, Kim NY, Seo JS, Kim MS, Park NG, Kim JK, Chung JK, Lee HH. Molecular cloning, expression analysis and enzymatic characterization of cathepsin K from olive flounder (Paralichthys olivaceus). Comp Biochem Physiol A Mol Integr Physiol 2009; 154:474-85. [DOI: 10.1016/j.cbpa.2009.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 07/28/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022]
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24
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Cunha RL, Gouvêa IE, Feitosa GP, Alves MF, Brömme D, Comasseto JV, Tersariol IL, Juliano L. Irreversible inhibition of human cathepsins B, L, S and K by hypervalent tellurium compounds. Biol Chem 2009; 390:1205-12. [DOI: 10.1515/bc.2009.125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Abstract
The inhibition of human cysteine cathepsins B, L, S and K was evaluated by a set of hypervalent tellurium compounds (telluranes) comprising both organic and inorganic derivatives. All telluranes studied showed a time- and concentration-dependent irreversible inhibition of the cathepsins, and their second-order inactivation rate constants were determined. The organic derivatives were potent inhibitors of the cathepsins and clear specificities were detected, which were parallel to their known substrate specificities. In all cases, the activity of the tellurane-inhibited cathepsins was recovered by treatment of the inactivated enzymes with reducing agents. The maximum stoichiometry of the reaction between cysteine residues and telluranes were also determined. The presented data indicate that it is possible to design organic compounds with a tellurium(IV) moiety as a novel warhead that covalently modifies the catalytic cysteine, and which also form strong interactions with subsites of cathepsins B, L, S and K, resulting in more specific inhibition.
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25
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Tada S, Tsutsumi K, Ishihara H, Suzuki K, Gohda K, Teno N. Species differences between human and rat in the substrate specificity of cathepsin K. J Biochem 2008; 144:499-506. [PMID: 18664521 DOI: 10.1093/jb/mvn093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cathepsin K is known to play an important role in bone resorption, and it has the P2 specificity for proline. Rat cathepsin K has 88% identity with the human enzyme. However, it has been reported that its enzymatic activity for a Cbz-Leu-Arg-MCA substrate is lower than that of human cathepsin K, and that the rat enzyme is not well inhibited by human cathepsin K inhibitors. For this study, we prepared recombinant enzyme to investigate the substrate specificity of rat cathepsin K. Cleavage experiments using the fragment of type I collagen and peptidic libraries demonstrated that rat cathepsin K preferentially hydrolyses the substrates at the P2 Hyp position. Comparison of the S2 site between rat and human cathepsin K sequences indicated that two S2 residues at Ser134 and Val160 in rat are varied to Ala and Leu, respectively, in the human enzyme. Cleavage experiments using two single mutants, S134A and V160L, and one double mutant, S134A/V160L, of rat cathepsin K showed that all the rat mutants lost the P2 Hyp specificity. The information obtained from our comparative studies on rat and human cathepsin K should make a significant impact on developing specific inhibitors of human cathepsin K since rat is usually used as test species.
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Affiliation(s)
- Sachiyo Tada
- Novartis Institutes for BioMedical Research, Tsukuba, Ibaraki, Japan
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26
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Markt P, McGoohan C, Walker B, Kirchmair J, Feldmann C, De Martino G, Spitzer G, Distinto S, Schuster D, Wolber G, Laggner C, Langer T. Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening. J Chem Inf Model 2008; 48:1693-705. [PMID: 18637674 DOI: 10.1021/ci800101j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cysteine protease cathepsin S (CatS) is involved in the pathogenesis of autoimmune disorders, atherosclerosis, and obesity. Therefore, it represents a promising pharmacological target for drug development. We generated ligand-based and structure-based pharmacophore models for noncovalent and covalent CatS inhibitors to perform virtual high-throughput screening of chemical databases in order to discover novel scaffolds for CatS inhibitors. An in vitro evaluation of the resulting 15 structures revealed seven CatS inhibitors with kinetic constants in the low micromolar range. These compounds can be subjected to further chemical modifications to obtain drugs for the treatment of autoimmune disorders and atherosclerosis.
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Affiliation(s)
- Patrick Markt
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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27
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Abstract
The name "cysteine protease" refers to the protease's nucleophilic cysteine residue that forms a covalent bond with the carbonyl group of the scissile peptide bond in substrates. The papain-like cysteine proteases, classified as the "C1 family" are the most predominant cysteine proteases. These proteases are found in viruses, plants, primitive parasites, invertebrates, and vertebrates alike. Mammalian papain-like cysteine proteases are also known as cathepsins. This unit discusses cathepsins, and their subcellular and tissue localization, catalytic mechanism, and substrate specificity. Several tables illustrate the properties of the various cathepsins.
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Affiliation(s)
- D Brömme
- Mount Sinai School of Medicine, New York, New York, USA
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28
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Shah PP, Myers MC, Beavers MP, Purvis JE, Jing H, Grieser HJ, Sharlow ER, Napper AD, Huryn DM, Cooperman BS, Smith AB, Diamond SL. Kinetic characterization and molecular docking of a novel, potent, and selective slow-binding inhibitor of human cathepsin L. Mol Pharmacol 2008; 74:34-41. [PMID: 18403718 DOI: 10.1124/mol.108.046219] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A novel small molecule thiocarbazate (PubChem SID 26681509), a potent inhibitor of human cathepsin L (EC 3.4.22.15) with an IC(50) of 56 nM, was developed after a 57,821-compound screen of the National Institutes of Health Molecular Libraries Small Molecule Repository. After a 4-h preincubation with cathepsin L, this compound became even more potent, demonstrating an IC(50) of 1.0 nM. The thiocarbazate was determined to be a slow-binding and slowly reversible competitive inhibitor. Through a transient kinetic analysis for single-step reversibility, inhibition rate constants were k(on) = 24,000 M(-1)s(-1) and k(off) = 2.2 x 10(-5) s(-1) (K(i) = 0.89 nM). Molecular docking studies were undertaken using the experimentally derived X-ray crystal structure of papain/CLIK-148 (1cvz. pdb). These studies revealed critical hydrogen bonding patterns of the thiocarbazate with key active site residues in papain. The thiocarbazate displayed 7- to 151-fold greater selectivity toward cathepsin L than papain and cathepsins B, K, V, and S with no activity against cathepsin G. The inhibitor demonstrated a lack of toxicity in human aortic endothelial cells and zebrafish. In addition, the thiocarbazate inhibited in vitro propagation of malaria parasite Plasmodium falciparum with an IC(50) of 15.4 microM and inhibited Leishmania major with an IC(50) of 12.5 microM.
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Affiliation(s)
- Parag P Shah
- Penn Center for Molecular Discovery, University of Pennsylvania, 1024 Vagelos Laboratories, Philadelphia, PA 19104-6383, USA
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Chowdhury SF, Joseph L, Kumar S, Tulsidas SR, Bhat S, Ziomek E, Ménard R, Sivaraman J, Purisima EO. Exploring inhibitor binding at the S' subsites of cathepsin L. J Med Chem 2008; 51:1361-8. [PMID: 18278855 DOI: 10.1021/jm701190v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a series of noncovalent, reversible inhibitors of cathepsin L that have been designed to explore additional binding interactions with the S' subsites. The design was based on our previously reported crystal structure that suggested the possibility of engineering increased interactions with the S' subsites ( Chowdhury et al. J. Med. Chem. 2002, 45, 5321-5329 ). A representative of these new inhibitors has been co-crystallized with mature cathepsin L, and the structure has been solved and refined at 2.2 A. The inhibitors described in this work extend farther into the S' subsites of cathepsins than any inhibitors reported in the literature thus far. These interactions appear to make use of a S3' subsite that can potentially be exploited for enhanced specificity and/or affinity.
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31
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Ma S, Devi-Kesavan LS, Gao J. Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K. J Am Chem Soc 2007; 129:13633-45. [PMID: 17935329 PMCID: PMC2556303 DOI: 10.1021/ja074222+] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
| | - Lakshmi S. Devi-Kesavan
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
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32
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Myers MC, Shah PP, Diamond SL, Huryn DM, Smith AB. Identification and synthesis of a unique thiocarbazate cathepsin L inhibitor. Bioorg Med Chem Lett 2007; 18:210-4. [PMID: 18060772 DOI: 10.1016/j.bmcl.2007.10.107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 10/22/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022]
Abstract
Library samples containing 2,5-disubstituted oxadiazoles were identified as potent hits in a high throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR) directed at discovering inhibitors of cathepsin L. However, when synthesized in pure form, the putative actives were found to be devoid of biological activity. Analyses by LC-MS of original library samples indicated the presence of a number of impurities, in addition to the oxadiazoles. Synthesis and bioassay of the probable impurities led to the identification of a thiocarbazate that likely originated via ring opening of the oxadiazole. Previously unknown, thiocarbazates (-)-11 and (-)-12 were independently synthesized as single enantiomers and found to inhibit cathepsin L in the low nanomolar range.
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Affiliation(s)
- Michael C Myers
- Penn Center for Molecular Discovery, University of Pennsylvania, 1024 Vagelos Research Laboratories, Philadelphia, PA 19104-6383, USA
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33
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Lecaille F, Brömme D, Lalmanach G. Biochemical properties and regulation of cathepsin K activity. Biochimie 2007; 90:208-26. [PMID: 17935853 DOI: 10.1016/j.biochi.2007.08.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/24/2007] [Indexed: 02/02/2023]
Abstract
Cysteine cathepsins (11 in humans) are mostly located in the acidic compartments of cells. They have been known for decades to be involved in intracellular protein degradation as housekeeping proteases. However, the discovery of new cathepsins, including cathepsins K, V and F, has provided strong evidence that they also participate in specific biological events. This review focuses on the current knowledge of cathepsin K, the major bone cysteine protease, which is a drug target of clinical interest. Nevertheless, we will not discuss recent developments in cathepsin K inhibitor design since they have been extensively detailed elsewhere. We will cover features of cathepsin K structure, cellular and tissue distribution, substrate specificity, and regulation (pH, propeptide, glycosaminoglycans, oxidants), and its putative roles in physiological or pathophysiological processes. Finally, we will review the kinetic data of its inhibition by natural endogenous inhibitors (stefin B, cystatin C, H- and L-kininogens).
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Affiliation(s)
- Fabien Lecaille
- INSERM, U618, Protéases et Vectorisation Pulmonaires, Equipe Protéases et Pathologies Pulmonaires, Faculté de Médecine, Université François Rabelais, 10 Boulevard Tonnellé, F-37032 Tours Cedex, France.
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34
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Lecaille F, Chowdhury S, Purisima E, Brömme D, Lalmanach G. The S2 subsites of cathepsins K and L and their contribution to collagen degradation. Protein Sci 2007; 16:662-70. [PMID: 17384231 PMCID: PMC2203344 DOI: 10.1110/ps.062666607] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The exchange of residues 67 and 205 of the S2 pocket of human cysteine cathepsins K and L induces a permutation of their substrate specificity toward fluorogenic peptide substrates. While the cathepsin L-like cathepsin K (Tyr67Leu/Leu205Ala) mutant has a marked preference for Phe, the Leu67Tyr/Ala205Leu cathepsin L variant shows an effective cathepsin K-like preference for Leu and Pro. A similar turnaround of inhibition was observed by using specific inhibitors of cathepsin K [1-(N-Benzyloxycarbonyl-leucyl)-5-(N-Boc-phenylalanyl-leucyl)carbohydrazide] and cathepsin L [N-(4-biphenylacetyl)-S-methylcysteine-(D)-Arg-Phe-beta-phenethylamide]. Molecular modeling studies indicated that mutations alter the character of both S2 and S3 subsites, while docking calculations were consistent with kinetics data. The cathepsin K-like cathepsin L was unable to mimic the collagen-degrading activity of cathepsin K against collagens I and II, DQ-collagens I and IV, and elastin-Congo Red. In summary, double mutations of the S2 pocket of cathepsins K (Y67L/L205A) and L (L67Y/A205L) induce a switch of their enzymatic specificity toward small selective inhibitors and peptidyl substrates, confirming the key role of residues 67 and 205. However, mutations in the S2 subsite pocket of cathepsin L alone without engineering of binding sites to chondroitin sulfate are not sufficient to generate a cathepsin K-like collagenase, emphasizing the pivotal role of the complex formation between glycosaminoglycans and cathepsin K for its unique collagenolytic activity.
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35
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Shinozuka T, Shimada K, Matsui S, Yamane T, Ama M, Fukuda T, Taki M, Takeda Y, Otsuka E, Yamato M, Mochizuki SI, Ohhata K, Naito S. Potent and selective cathepsin K inhibitors. Bioorg Med Chem 2006; 14:6789-806. [PMID: 16842999 DOI: 10.1016/j.bmc.2006.06.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 06/20/2006] [Accepted: 06/21/2006] [Indexed: 11/16/2022]
Abstract
A novel series of cathepsin K inhibitors derived from Novartis compound I is described. Optimization of the P1, P3, and P1' units led to the identification of 4-aminophenoxyacetic acid 24b with an IC(50) value of 4.8 nM, which possessed an excellent selectivity over other human cathepsins and good pharmacokinetic (PK) properties. Oral administration of compound 24b to ovariectomized (OVX) rats showed a trend toward an improvement of bone mineral density (BMD) in the femur bone.
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Affiliation(s)
- Tsuyoshi Shinozuka
- Medicinal Chemistry Research Laboratories, Sankyo Co., Ltd, Shinagawa-ku, Tokyo 140-8710, Japan.
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36
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Ramjee MK, Flinn NS, Pemberton TP, Quibell M, Wang Y, Watts JP. Substrate mapping and inhibitor profiling of falcipain-2, falcipain-3 and berghepain-2: implications for peptidase anti-malarial drug discovery. Biochem J 2006; 399:47-57. [PMID: 16776649 PMCID: PMC1570174 DOI: 10.1042/bj20060422] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 06/07/2006] [Accepted: 06/15/2006] [Indexed: 11/17/2022]
Abstract
The Plasmodium falciparum cysteine peptidases FP-2 (falcipain-2) and FP-3 (falcipain-3), members of the papain-like CAC1 family, are essential haemoglobinases and are therefore potential anti-malarial drug targets. To facilitate a rational drug discovery programme, in the current study we analysed the synthetic substrate and model inhibitor profiles of FP-2 and FP-3 as well as BP-2 (berghepain-2), an orthologue from the rodent parasite Plasmodium berghei. With respect to substrate catalysis, FP-2 exhibited a promiscuous substrate profile based around a consensus non-primeside motif, FP-3 was somewhat more restricted and BP-2 was comparatively specific. Substrate turnover for FP-2 was driven by a basic or acidic P1 residue, whereas for FP-3 turnover occurred predominately through a basic P1 residue only, and for BP-2, turnover was again mainly through a basic P1 residue for some motifs and surprisingly a glycine in the P1 position for other motifs. Within these P1 binding elements, additional recognition motifs were observed with subtle nuances that switched substrate turnover on or off through specific synergistic combinations. The peptidases were also profiled against reversible and irreversible cysteine peptidase inhibitors. The results re-iterated the contrasting kinetic behaviour of each peptidase as observed through the substrate screens. The results showed that the substrate and inhibitor preferences of BP-2 were markedly different from those of FP-2 and FP-3. When FP-2 and FP-3 were compared to each other they also displayed similarities and some significant differences. In conclusion, the in vitro data highlights the current difficulties faced by a peptidase directed anti-malarial medicinal chemistry programme where compounds need to be identified with potent activity against at least three peptidases, each of which displays distinct biochemical traits.
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Key Words
- cysteine protease
- inhibitor
- malaria
- mapping
- substrate
- abz, 2-amino benzoic acid
- amc, 7-amino-4-methyl coumarin
- bp, berghepain
- dtt, dithiothreitol
- fmoc/tbu, fluoren-9-ylmethoxycarbonyl/t-butyl
- fp, falcipain
- fret, fluorescence resonance energy transfer
- hbtu, 2-(1h-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate
- hobt, 1-hydroxybenzotriazole
- nle, norleucine
- nmm, n-methylmorpholine
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Affiliation(s)
- Manoj K Ramjee
- Amura Therapeutics Limited, Horizon Park, Barton Road, Comberton, CB3 7AJ, UK.
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37
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Perez-Amodio S, Jansen DC, Schoenmaker T, Vogels IMC, Reinheckel T, Hayman AR, Cox TM, Saftig P, Beertsen W, Everts V. Calvarial osteoclasts express a higher level of tartrate-resistant acid phosphatase than long bone osteoclasts and activation does not depend on cathepsin K or L activity. Calcif Tissue Int 2006; 79:245-54. [PMID: 17033726 DOI: 10.1007/s00223-005-0289-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2005] [Accepted: 06/01/2006] [Indexed: 10/24/2022]
Abstract
Bone resorption by osteoclasts depends on the activity of various proteolytic enzymes, in particular those belonging to the group of cysteine proteinases. Next to these enzymes, tartrate-resistant acid phosphatase (TRAP) is considered to participate in this process. TRAP is synthesized as an inactive proenzyme, and in vitro studies have shown its activation by cysteine proteinases. In the present study, the possible involvement of the latter enzyme class in the in vivo modulation of TRAP was investigated using mice deficient for cathepsin K and/or L and in bones that express a high (long bone) or low (calvaria) level of cysteine proteinase activity. The results demonstrated, in mice lacking cathepsin K but not in those deficient for cathepsin L, significantly higher levels of TRAP activity in long bone. This higher activity was due to a higher number of osteoclasts. Next, we found considerable differences in TRAP activity between calvarial and long bones. Calvarial bones contained a 25-fold higher level of activity than long bones. This difference was seen in all mice, irrespective of genotype. Osteoclasts isolated from the two types of bone revealed that calvarial osteoclasts expressed higher enzyme activity as well as a higher level of mRNA for the enzyme. Analysis of TRAP-deficient mice revealed higher levels of nondigested bone matrix components in and around calvarial osteoclasts than in long bone osteoclasts. Finally, inhibition of cysteine proteinase activity by specific inhibitors resulted in increased TRAP activity. Our data suggest that neither cathepsin K nor L is essential in activating TRAP. The findings also point to functional differences between osteoclasts from different bone sites in terms of participation of TRAP in degradation of bone matrix. We propose that the higher level of TRAP activity in calvarial osteoclasts compared to that in long bone cells may partially compensate for the lower cysteine proteinase activity found in calvarial osteoclasts and TRAP may contribute to the degradation of noncollagenous proteins during the digestion of this type of bone.
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Affiliation(s)
- S Perez-Amodio
- Experimental Periodontology, Academic Center for Dentistry Amsterdam, Universiteit van Amsterdam and Vrije Universiteit, Louwesweg 1, 1066 EA Amsterdam, The Netherlands
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38
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Pan X, Tan N, Zeng G, Han H, Huang H. 3D-QSAR and docking studies of aldehyde inhibitors of human cathepsin K. Bioorg Med Chem 2006; 14:2771-8. [PMID: 16377193 DOI: 10.1016/j.bmc.2005.11.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 11/24/2005] [Accepted: 11/29/2005] [Indexed: 11/30/2022]
Abstract
In order to better understand the structural and chemical features of human cathepsin K (CatK), which is an important cysteine protease in the pathogenesis of osteoporosis, the 3D-QSAR (CoMFA) studies were conducted on recently explored aldehyde compounds with known CatK inhibitory activities. The genetic algorithm of GOLD2.2 has been employed to position 59 aldehyde compounds into the active sites of CatK to determine the probable binding conformation. Good correlations between the predicted binding free energies and the experimental inhibitory activities suggested that the identified binding conformations of these potential inhibitors are reliable. The docking results also provided a reliable conformational alignment scheme for 3D-QSAR model. Based on the docking conformations, highly predictive comparative molecular field analysis (CoMFA) was performed with q2 value of 0.723. The predictive ability was validated by some compounds that were not included in the training set. Furthermore, the CoMFA model was mapped back to the binding sites of CatK, to get a better understanding of vital interactions between the aldehyde compounds and the protease. The CoMFA field distributions are in good agreement with the structural characteristics of the binding groove of the CatK, which suggested that the n-Bu in R4 position is the favor group substitute at P1 and moderate groups in R2 group are required on P2 substitute. In addition, 3D-QSAR results also demonstrated that aldehyde is an important pharmacophore because of electrostatic effect. These results, together with the good correlations between the inhibitory activities and the binding free energies predicted by GOLD2.2, demonstrated the power of combining docking/QSAR approach to explore the probable binding conformations of compounds at the active sites of the protein target, and further provided useful information in understanding the structural and chemical features of CatK in designing and finding new potential inhibitors.
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Affiliation(s)
- Xulin Pan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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39
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Shinozuka T, Shimada K, Matsui S, Yamane T, Ama M, Fukuda T, Taki M, Naito S. 4-Aminophenoxyacetic acids as a novel class of reversible cathepsin K inhibitors. Bioorg Med Chem Lett 2006; 16:1502-5. [PMID: 16380250 DOI: 10.1016/j.bmcl.2005.12.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 12/07/2005] [Accepted: 12/12/2005] [Indexed: 11/16/2022]
Abstract
We have designed and synthesized a novel series of 3-biphenylamino acid amides as cathepsin K inhibitors based on compound I. In these inhibitors, we have discovered 4-aminophenoxyacetic acids 43 and 47 with good IC(50) values, although lipophilic groups are favorable for the hydrophobic S1' pocket.
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Affiliation(s)
- Tsuyoshi Shinozuka
- Medicinal Chemistry Research Laboratories, Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
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40
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Boeglin D, Lubell WD. Aza-Amino Acid Scanning of Secondary Structure Suited for Solid-Phase Peptide Synthesis with Fmoc Chemistry and Aza-Amino Acids with Heteroatomic Side Chains. ACTA ACUST UNITED AC 2005; 7:864-78. [PMID: 16283795 DOI: 10.1021/cc050043h] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aza-peptides, peptide analogues in which the alpha-carbon of one or more of the amino acid residues is replaced with a nitrogen atom, exhibit a propensity for adopting beta-turn conformations. A general Fmoc-protection protocol for the stepwise solid-phase synthesis of aza-peptides has now been developed based on the activation of N'-alkyl fluoren-9-ylmethyl carbazates with phosgene for coupling the aza-amino acid residues. This method has proven effective for introducing aza-amino acid residues with aliphatic (Ala, Leu, Val, and Gly) and aromatic (Phe, Tyr, and Trp) side chains. Acid promoted loss of aromatic side chains was noted with aza-Trp and aza-Tyr residues during peptide cleavage and suppressed by temperature control in the case of the latter. In addition, aza-peptides with heteroatomic side chain residues (Lys, Orn, Arg, and Asp) were conveniently synthesized using this protocol. Partial aza-amino acid scans were performed on three biologically active peptides: the potent tetrapeptide melanocortin receptor agonist, Ac-His-d-Phe-Arg-Trp-NH2; the growth hormone secretagogue hexapeptide, GHRP-6, His-d-Trp-Ala-Trp-d-Phe-Lys-NH2; and the human calcitonin gene-related peptide (hCGRP) antagonist, FVPTDVGPFAF-NH2. This practical procedure for aza-amino acid scanning using Fmoc-based solid-phase synthesis should find general utility for probing the existence and importance of beta-turn conformations in bioactive peptides.
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Affiliation(s)
- Damien Boeglin
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, Canada
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41
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Brage M, Abrahamson M, Lindström V, Grubb A, Lerner UH. Different cysteine proteinases involved in bone resorption and osteoclast formation. Calcif Tissue Int 2005; 76:439-47. [PMID: 15906014 DOI: 10.1007/s00223-004-0043-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Accepted: 01/13/2005] [Indexed: 02/05/2023]
Abstract
Cysteine proteinases, especially cathepsin K, play an important role in osteoclastic degradation of bone matrix proteins and the process can, consequently, be significantly inhibited by cysteine proteinase inhibitors. We have recently reported that cystatin C and other cysteine proteinase inhibitors also reduce osteoclast formation. However, it is not known which cysteine proteinase(s) are involved in osteoclast differentiation. In the present study, we compared the relative potencies of cystatins C and D as inhibitors of bone resorption in cultured mouse calvariae, osteoclastogenesis in mouse bone marrow cultures, and cathepsin K activity. Inhibition of cathepsin K activity was assessed by determining equilibrium constants for inhibitor complexes in fluorogenic substrate assays. The data demonstrate that whereas human cystatins C and D are equipotent as inhibitors of bone resorption, cystatin D is 10-fold less potent as an inhibitor of osteoclastogenesis and 200-fold less potent as an inhibitor of cathepsin K activity. A recombinant human cystatin C variant with Gly substitutions for residues Arg8, Leu9, Val10, and Trp106 did not inhibit bone resorption, had 1,000-fold decreased inhibitory effect on cathepsin K activity compared to wildtype cystatin C, but was equipotent with wildtype cystatin C as an inhibitor of osteoclastogenesis. It is concluded that (i) different cysteine proteinases are likely to be involved in bone resorption and osteoclast formation, (ii) cathepsin K may not be an exclusive target enzyme in any of the two systems, and (iii) the enzyme(s) involved in osteoclastogenesis might not be a typical papain-like cysteine proteinase.
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Affiliation(s)
- M Brage
- Department of Oral Cell Biology, Umeå University, S-90187 Umeå, Sweden
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42
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43
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44
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Filipek R, Potempa J, Bochtler M. A comparison of staphostatin B with standard mechanism serine protease inhibitors. J Biol Chem 2005; 280:14669-74. [PMID: 15644332 DOI: 10.1074/jbc.m411792200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphostatins are the endogenous, highly specific inhibitors of staphopains, the major secreted cysteine proteases from Staphylococcus aureus. We have previously shown that staphostatins A and B are competitive, active site-directed inhibitors that span the active site clefts of their target proteases in the same orientation as substrates. We now report the crystal structure of staphostatin B in complex with wild-type staphopain B at 1.9 A resolution. In the complex structure, the catalytic residues are found in exactly the positions that would be expected for uncomplexed papain-type proteases. There is robust, continuous density for the staphostatin B binding loop and no indication for cleavage of the peptide bond that comes closest to the active site cysteine of staphopain B. The carbonyl carbon atom C of this peptide bond is 4.1 A away from the active site cysteine sulfur Sgamma atom. The carbonyl oxygen atom O of this peptide bond points away from the putative oxyanion hole and lies almost on a line from the Sgamma atom to the C atom. The arrangement is strikingly similar to the "ionmolecule" arrangement for the complex of papain-type enzymes with their substrates but differs significantly from the arrangement conventionally assumed for the Michaelis complex of papain-type enzymes with their substrates and also from the arrangement that is crystallographically observed for complexes of standard mechanism inhibitors and their target serine proteases.
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Affiliation(s)
- Renata Filipek
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
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45
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Štern I, Schaschke N, Moroder L, Turk D. Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft. Biochem J 2004; 381:511-7. [PMID: 15084146 PMCID: PMC1133859 DOI: 10.1042/bj20040237] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 04/05/2004] [Accepted: 04/15/2004] [Indexed: 11/17/2022]
Abstract
The crystal structure of the inhibitor NS-134 in complex with bovine cathepsin B reveals that functional groups attached to both sides of the epoxysuccinyl reactive group bind to the part of active-site cleft as predicted. The -Leu-Pro-OH side binds to the primed binding sites interacting with the His110 and His111 residues with its C-terminal carboxy group, whereas the -Leu-Gly-Meu (-Leu-Gly-Gly-OMe) part (Meu, methoxycarbonylmethyl) binds along the non-primed binding sites. Comparison with the propeptide structures of cathepsins revealed that the binding of the latter part is least similar to the procathepsin B structure; this result, together with the two-residue shift in positioning of the Leu-Gly-Gly part, suggests that the propeptide structures of the cognate enzymes may not be the best starting point for the design of reverse binding inhibitors.
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Affiliation(s)
- Igor Štern
- *Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Norbert Schaschke
- †Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany
| | - Luis Moroder
- †Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany
| | - Dušan Turk
- *Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
- To whom correspondence should be addressed (e-mail )
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46
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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47
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Wang D, Li W, Pechar M, Kopecková P, Brömme D, Kopecek J. Cathepsin K inhibitor–polymer conjugates: potential drugs for the treatment of osteoporosis and rheumatoid arthritis. Int J Pharm 2004; 277:73-9. [PMID: 15158970 DOI: 10.1016/j.ijpharm.2003.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Revised: 02/05/2003] [Accepted: 03/23/2003] [Indexed: 10/26/2022]
Abstract
The role of the newly discovered cysteine protease, cathepsin K, in osteoporosis and rheumatoid arthritis is reviewed. The current development of cathepsin K inhibitors and their targeted delivery using synthetic polymer carriers are discussed. Future challenges and possible strategies to improve these delivery systems are addressed.
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Affiliation(s)
- D Wang
- Department of Pharmaceutics and Pharmaceutical Chemistry/CCCD, University of Utah, 30 S 2000 E Rm. 301, Salt Lake City, UT 84112, USA
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48
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Inhibition of the Cysteine Protease Cathepsin K (EC 3.4.22.38). ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2004. [DOI: 10.1016/s0065-7743(04)39007-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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49
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Deaton DN, Kumar S. Cathepsin K Inhibitors: Their Potential as Anti-Osteoporosis Agents. PROGRESS IN MEDICINAL CHEMISTRY 2004; 42:245-375. [PMID: 15003723 DOI: 10.1016/s0079-6468(04)42006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- David N Deaton
- Medicinal Chemistry Department, GlaxoSmithKline Inc., 5 Moore Drive, Research Triangle Park, NC 27709, USA
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50
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Lecaille F, Weidauer E, Juliano MA, Brömme D, Lalmanach G. Probing cathepsin K activity with a selective substrate spanning its active site. Biochem J 2003; 375:307-12. [PMID: 12837132 PMCID: PMC1223680 DOI: 10.1042/bj20030468] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2003] [Revised: 06/27/2003] [Accepted: 07/01/2003] [Indexed: 11/17/2022]
Abstract
The limited availability of highly selective cathepsin substrates seriously impairs studies designed to monitor individual cathepsin activities in biological samples. Among mammalian cysteine proteases, cathepsin K has a unique preference for a proline residue at P2, the primary determinant of its substrate specificity. Interestingly, congopain from Trypanosoma congolense also accommodates a proline residue in its S2 subsite. Analysis of a congopain model showed that amino acids forming its S2 subsite are identical with those of cathepsin K, except Leu67 which is replaced by a tyrosine residue in cathepsin K. Furthermore, amino acid residues of the congopain S2' binding pocket, which accepts a proline residue, are strictly identical with those of cathepsin K. Abz-HPGGPQ-EDN2ph [where Abz represents o-aminobenzoic acid and EDN2ph (=EDDnp) represents N -(2,4-dinitrophenyl)-ethylenediamine], a substrate initially developed for trypanosomal enzymes, was efficiently cleaved at the Gly-Gly bond by cathepsin K (kcat/ K(m)=426000 M(-1) x s(-1)). On the other hand, Abz-HPGGPQ-EDN2ph was resistant to hydrolysis by cathepsins B, F, H, L, S and V (20 nM enzyme concentration) and the Y67L (Tyr67-->Leu)/L205A cathepsin K mutant (20 nM), but still acted as a competitive inhibitor. Taken together, the selectivity of Abz-HPGGPQ-EDN2ph to cathepsin K primarily depends on the S2 and S2' subsite specificities of cathepsin K and the ionization state of histidine at P3. Whereas Abz-HPGGPQ-EDN2ph was hydrolysed by wild-type mouse fibroblast lysates, its hydrolysis was completely abolished in the cathepsin K-deficient samples, indicating that Abz-HPGGPQ-EDN2ph can be used to monitor selectively cathepsin K activity in physiological fluids and cell lysates.
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Affiliation(s)
- Fabien Lecaille
- INSERM EMI-U 00-10 Protéases et Vectorisation, Laboratoire d'Enzymologie et Chimie des Protéines, Faculté de Médecine, Université François Rabelais, 2 bis, Boulevard Tonnellé, F-37032 Tours Cedex, France
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