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Almalki AA, Shafie A, Hazazi A, Banjer HJ, Bakhuraysah MM, Almaghrabi SA, Alsaiari AA, Alsaeedi FA, Ashour AA, Alharthi A, Alharthi NS, Anjum F. Targeting Cathepsin L in Cancer Management: Leveraging Machine Learning, Structure-Based Virtual Screening, and Molecular Dynamics Studies. Int J Mol Sci 2023; 24:17208. [PMID: 38139037 PMCID: PMC10743089 DOI: 10.3390/ijms242417208] [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: 11/15/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Cathepsin L (CTSL) expression is dysregulated in a variety of cancers. Extensive empirical evidence indicates their direct participation in cancer growth, angiogenic processes, metastatic dissemination, and the development of treatment resistance. Currently, no natural CTSL inhibitors are approved for clinical use. Consequently, the development of novel CTSL inhibition strategies is an urgent necessity. In this study, a combined machine learning (ML) and structure-based virtual screening strategy was employed to identify potential natural CTSL inhibitors. The random forest ML model was trained on IC50 values. The accuracy of the trained model was over 90%. Furthermore, we used this ML model to screen the Biopurify and Targetmol natural compound libraries, yielding 149 hits with prediction scores >0.6. These hits were subsequently selected for virtual screening using a structure-based approach, yielding 13 hits with higher binding affinity compared to the positive control (AZ12878478). Two of these hits, ZINC4097985 and ZINC4098355, have been shown to strongly bind CTSL proteins. In addition to drug-like properties, both compounds demonstrated high affinity, ligand efficiency, and specificity for the CTSL binding pocket. Furthermore, in molecular dynamics simulations spanning 200 ns, these compounds formed stable protein-ligand complexes. ZINC4097985 and ZINC4098355 can be considered promising candidates for CTSL inhibition after experimental validation, with the potential to provide therapeutic benefits in cancer management.
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Affiliation(s)
- Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia;
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Maha M. Bakhuraysah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Sarah Abdullah Almaghrabi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Center of Innovations in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Fouzeyyah Ali Alsaeedi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif 21944, Saudi Arabia;
| | - Afaf Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Nahed S. Alharthi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
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Li Q, Wang H, Yang WL, Yang JK. An approach combining deep learning and molecule docking for drug discovery of cathepsin L. Expert Opin Drug Discov 2023; 18:347-356. [PMID: 36852432 DOI: 10.1080/17460441.2023.2174522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
OBJECTIVES Cathepsin L (CTSL) is a promising therapeutic target for metabolic disorders and COVID-19. However, there are still no clinically available CTSL inhibitors. Our objective is to develop an approach for the discovery of potential reversible covalent CTSL inhibitors. METHODS The authors combined Chemprop, a deep learning-based strategy, and the Schrödinger CovDock algorithm to identify potential CTSL inhibitors. First, they used Chemprop to train a deep learning model capable of predicting whether a molecule would inhibit the activity of CTSL and performed predictions on ZINC20 in-stock librarie (~9.2 million molecules). Then, they selected the top-200 predicted molecules and performed the Schrödinger covalent docking algorithm to explore the binding patterns to CTSL (PDB: 5MQY). The authors then calculated the binding energies using Prime MM/GBSA and examined the stability between the best two molecules and CTSL using 100ns molecular dynamics simulations. RESULTS The authors found five molecules that showed better docking results than the well-known cathepsin inhibitor odanacatib. Notably, two of these molecules, ZINC-35287427 and ZINC-1857528743, showed better docking results with CTSL compared to other cathepsins. CONCLUSION Our approach enables drug discovery from large-scale databases with little computational consumption, which will save the cost and time required for drug discovery.
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Affiliation(s)
- Qi Li
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Hao Wang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei-Li Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jin-Kui Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Dana D, Pathak SK. A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L. Molecules 2020; 25:E698. [PMID: 32041276 PMCID: PMC7038230 DOI: 10.3390/molecules25030698] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endopeptidase activity. Although its primary functions were originally thought to be only of a housekeeping enzyme that degraded intracellular and endocytosed proteins in lysosome, numerous recent studies suggest that it plays many critical and specific roles in diverse cellular settings. Not surprisingly, the dysregulated function of cathepsin L has manifested itself in several human diseases, making it an attractive target for drug development. Unfortunately, several redundant and isoform-specific functions have recently emerged, adding complexities to the drug discovery process. To address this, a series of chemical biology tools have been developed that helped define cathepsin L biology with exquisite precision in specific cellular contexts. This review elaborates on the recently developed small molecule inhibitors and probes of human cathepsin L, outlining their mechanisms of action, and describing their potential utilities in dissecting unknown function.
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Affiliation(s)
- Dibyendu Dana
- Chemistry and Biochemistry Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Flushing, NY 11367, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York (CUNY), 365 5th Ave, New York, NY 10016, USA
| | - Sanjai K. Pathak
- Chemistry and Biochemistry Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Flushing, NY 11367, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York (CUNY), 365 5th Ave, New York, NY 10016, USA
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4
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Synthesis and biological evaluation of a water-soluble phosphate prodrug salt and structural analogues of KGP94, a lead inhibitor of cathepsin L. Bioorg Med Chem Lett 2016; 27:1304-1310. [PMID: 28117205 DOI: 10.1016/j.bmcl.2016.12.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 11/22/2022]
Abstract
The magnitude of expression of cathepsin L, often upregulated in the tumor microenvironment, correlates with the invasive and metastatic nature of certain tumors. Inhibition of cathepsin L represents an emerging strategy for the treatment of metastatic cancer. A potent, small-molecule inhibitor (referred to as KGP94) of cathepsin L, and new KGP94 analogues were synthesized. (3,5-Dibromophenyl)-(3-hydroxyphenyl) ketone thiosemicarbazone (22), with an IC50 value of 202nM, exhibited similar inhibitory activity against cathepsin L compared to KGP94 (IC50=189nM). Due to limited aqueous solubility of KGP94, a water-soluble phosphate salt (KGP420) was prepared in order to facilitate future in vivo studies. Enzymatic hydrolysis with alkaline phosphatase (ALP) demonstrated that the phosphate prodrug, KGP420, was readily converted to the parent compound, KGP94.
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Parker EN, Song J, Kishore Kumar GD, Odutola SO, Chavarria GE, Charlton-Sevcik AK, Strecker TE, Barnes AL, Sudhan DR, Wittenborn TR, Siemann DW, Horsman MR, Chaplin DJ, Trawick ML, Pinney KG. Synthesis and biochemical evaluation of benzoylbenzophenone thiosemicarbazone analogues as potent and selective inhibitors of cathepsin L. Bioorg Med Chem 2015; 23:6974-92. [PMID: 26462052 DOI: 10.1016/j.bmc.2015.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/11/2015] [Accepted: 09/22/2015] [Indexed: 12/27/2022]
Abstract
Upregulation of cathepsin L in a variety of tumors and its ability to promote cancer cell invasion and migration through degradation of the extracellular matrix suggest that cathepsin L is a promising biological target for the development of anti-metastatic agents. Based on encouraging results from studies on benzophenone thiosemicarbazone cathepsin inhibitors, a series of fourteen benzoylbenzophenone thiosemicarbazone analogues were designed, synthesized, and evaluated for their inhibitory activity against cathepsins L and B. Thiosemicarbazone inhibitors 3-benzoylbenzophenone thiosemicarbazone 1, 1,3-bis(4-fluorobenzoyl)benzene thiosemicarbazone 8, and 1,3-bis(2-fluorobenzoyl)-5-bromobenzene thiosemicarbazone 32 displayed the greatest potency against cathepsin L with low IC50 values of 9.9 nM, 14.4 nM, and 8.1 nM, respectively. The benzoylbenzophenone thiosemicarbazone analogues evaluated were selective in their inhibition of cathepsin L compared to cathepsin B. Thiosemicarbazone analogue 32 inhibited invasion through Matrigel of MDA-MB-231 breast cancer cells by 70% at 10 μM. Thiosemicarbazone analogue 8 significantly inhibited the invasive potential of PC-3ML prostate cancer cells by 92% at 5 μM. The most active cathepsin L inhibitors from this benzoylbenzophenone thiosemicarbazone series (1, 8, and 32) displayed low cytotoxicity toward normal primary cells [in this case human umbilical vein endothelial cells (HUVECs)]. In an initial in vivo study, 3-benzoylbenzophenone thiosemicarbazone (1) was well-tolerated in a CDF1 mouse model bearing an implanted C3H mammary carcinoma, and showed efficacy in tumor growth delay. Low cytotoxicity, inhibition of cell invasion, and in vivo tolerability are desirable characteristics for anti-metastatic agents functioning through an inhibition of cathepsin L. Active members of this structurally diverse group of benzoylbenzophenone thiosemicarbazone cathepsin L inhibitors show promise as potential anti-metastatic, pre-clinical drug candidates.
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Affiliation(s)
- Erica N Parker
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - Jiangli Song
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - G D Kishore Kumar
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - Samuel O Odutola
- Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798-7224, United States
| | - Gustavo E Chavarria
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - Amanda K Charlton-Sevcik
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - Tracy E Strecker
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - Ashleigh L Barnes
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States
| | - Dhivya R Sudhan
- Department of Radiation Oncology, University of Florida Health Cancer Center, Gainesville, FL 32610, United States
| | - Thomas R Wittenborn
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Dietmar W Siemann
- Department of Radiation Oncology, University of Florida Health Cancer Center, Gainesville, FL 32610, United States; Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Michael R Horsman
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - David J Chaplin
- OXiGENE, Inc., 701 Gateway Blvd, Suite 210, South San Francisco, CA 94080, United States
| | - Mary Lynn Trawick
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States; Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798-7224, United States.
| | - Kevin G Pinney
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, United States; Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798-7224, United States.
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6
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Song J, Jones LM, Chavarria GE, Charlton-Sevcik AK, Jantz A, Johansen A, Bayeh L, Soeung V, Snyder LK, Lade SD, Chaplin DJ, Trawick ML, Pinney KG. Small-molecule inhibitors of cathepsin L incorporating functionalized ring-fused molecular frameworks. Bioorg Med Chem Lett 2013; 23:2801-7. [DOI: 10.1016/j.bmcl.2012.12.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/30/2012] [Accepted: 12/10/2012] [Indexed: 12/29/2022]
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7
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Song J, Jones LM, Kumar GDK, Conner ES, Bayeh L, Chavarria GE, Charlton-Sevcik AK, Chen SE, Chaplin DJ, Trawick ML, Pinney KG. Synthesis and biochemical evaluation of thiochromanone thiosemicarbazone analogues as inhibitors of cathepsin L. ACS Med Chem Lett 2012; 3:450-3. [PMID: 24900494 DOI: 10.1021/ml200299g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/18/2012] [Indexed: 11/29/2022] Open
Abstract
A series of 36 thiosemicarbazone analogues containing the thiochromanone molecular scaffold functionalized primarily at the C-6 position were prepared by chemical synthesis and evaluated as inhibitors of cathepsins L and B. The most promising inhibitors from this group are selective for cathepsin L and demonstrate IC50 values in the low nanomolar range. In nearly all cases, the thiochromanone sulfide analogues show superior inhibition of cathepsin L as compared to their corresponding thiochromanone sulfone derivatives. Without exception, the compounds evaluated were inactive (IC50 > 10000 nM) against cathepsin B. The most potent inhibitor (IC50 = 46 nM) of cathepsin L proved to be the 6,7-difluoro analogue 4. This small library of compounds significantly expands the structure-activity relationship known for small molecule, nonpeptidic inhibitors of cathepsin L.
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Affiliation(s)
- Jiangli Song
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Lindsay M. Jones
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - G. D. Kishore Kumar
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Elizabeth S. Conner
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Liela Bayeh
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Gustavo E. Chavarria
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Amanda K. Charlton-Sevcik
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Shen-En Chen
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - David J. Chaplin
- OXiGENE Inc., 701 Gateway Boulevard, Suite 210, South San Francisco, California, 94080, United States
| | - Mary Lynn Trawick
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
| | - Kevin G. Pinney
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas, 76798-7348 United States
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Azepanone-based inhibitors of human cathepsin S: optimization of selectivity via the P2 substituent. Bioorg Med Chem Lett 2011; 21:4409-15. [PMID: 21733692 DOI: 10.1016/j.bmcl.2011.06.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/07/2011] [Accepted: 06/10/2011] [Indexed: 12/31/2022]
Abstract
A series of azepanone inhibitors of cathepsin S is described. Selectivity over both cathepsin K and cathepsin L was achieved by varying the P2 substituent. Ultimately, a balanced potency and selectivity profile was achieved in compound 39 possessing a 1-methylcyclohexyl alanine at P2 and nicotinamide as the P' substituent. The cellular potency of selected analogs is also described.
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9
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Qin Y, Shi GP. Cysteinyl cathepsins and mast cell proteases in the pathogenesis and therapeutics of cardiovascular diseases. Pharmacol Ther 2011; 131:338-50. [PMID: 21605595 DOI: 10.1016/j.pharmthera.2011.04.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 01/10/2023]
Abstract
The initiation and progression of cardiovascular diseases involve extensive arterial wall matrix protein degradation. Proteases are essential to these pathological events. Recent discoveries suggest that proteases do more than catabolize matrix proteins. During the pathogenesis of atherosclerosis, abdominal aortic aneuryms, and associated complications, cysteinyl cathepsins and mast cell tryptases and chymases participate importantly in vascular cell apoptosis, foam cell formation, matrix protein gene expression, and pro-enzyme, latent cytokine, chemokine, and growth factor activation. Experimental animal disease models have been invaluable in examining each of these protease functions. Deficiency and pharmacological inhibition of cathepsins or mast cell proteases have allowed their in vivo evaluation in the setting of pathological conditions. Recent discoveries of highly selective and potent inhibitors of cathepsins, chymase, and tryptase, and their applications in vascular diseases in animal models and non-vascular diseases in human trials, have led to the hypothesis that selective inhibition of cathepsins, chymases, and tryptase will benefit patients suffering from cardiovascular diseases. This review highlights recent discoveries from in vitro cell-based studies to experimental animal cardiovascular disease models, from protease knockout mice to treatments with recently developed selective and potent protease inhibitors, and from patients with cathepsin-associated non-vascular diseases to those affected by cardiovascular complications.
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Affiliation(s)
- Yanwen Qin
- The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Beijing Anzhen Hospital, Capital Medical University, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
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Kumar GDK, Chavarria GE, Charlton-Sevcik AK, Yoo GK, Song J, Strecker TE, Siim BG, Chaplin DJ, Trawick ML, Pinney KG. Functionalized benzophenone, thiophene, pyridine, and fluorene thiosemicarbazone derivatives as inhibitors of cathepsin L. Bioorg Med Chem Lett 2010; 20:6610-5. [PMID: 20933415 DOI: 10.1016/j.bmcl.2010.09.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
Abstract
A series of thiosemicarbazone analogs based on the benzophenone, thiophene, pyridine, and fluorene molecular frameworks has been prepared by chemical synthesis and evaluated as small-molecule inhibitors of the cysteine proteases cathepsin L and cathepsin B. The two most potent inhibitors of cathepsin L in this series (IC(50)<135 nM) are brominated-benzophenone thiosemicarbazone analogs that are further functionalized with a phenolic moiety (2 and 6). In addition, a bromo-benzophenone thiosemicarbazone acetyl derivative (3) is also strongly inhibitory against cathepsin L (IC(50)=150.8 nM). Bromine substitution in the thiophene series results in compounds that demonstrate only moderate inhibition of cathepsin L. The two most active analogs in the benzophenone thiosemicarbazone series are highly selective for their inhibition of cathepsin L versus cathepsin B.
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Affiliation(s)
- G D Kishore Kumar
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
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Liu Z, Myers MC, Shah PP, Beavers MP, Benedetti PA, Diamond SL, Smith AB, Huryn DM. Design, synthesis and biological evaluation of a library of thiocarbazates and their activity as cysteine protease inhibitors. Comb Chem High Throughput Screen 2010; 13:337-51. [PMID: 20438448 PMCID: PMC2975254 DOI: 10.2174/138620710791054303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2009] [Accepted: 02/01/2010] [Indexed: 11/22/2022]
Abstract
Recently, we identified a novel class of potent cathepsin L inhibitors, characterized by a thiocarbazate warhead. Given the potential of these compounds to inhibit other cysteine proteases, we designed and synthesized a library of thiocarbazates containing diversity elements at three positions. Biological characterization of this library for activity against a panel of proteases indicated a significant preference for members of the papain family of cysteine proteases over serine, metallo-, and certain classes of cysteine proteases, such as caspases. Several potent inhibitors of cathepsin L and S were identified. The SAR data were employed in docking studies in an effort to understand the structural elements required for cathepsin S inhibition. This study provides the basis for the design of highly potent and selective inhibitors of the papain family of cysteine proteases.
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Affiliation(s)
- Zhuqing Liu
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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12
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Kishore Kumar G, Chavarria GE, Charlton-Sevcik AK, Arispe WM, MacDonough MT, Strecker TE, Chen SE, Siim BG, Chaplin DJ, Trawick ML, Pinney KG. Design, synthesis, and biological evaluation of potent thiosemicarbazone based cathepsin L inhibitors. Bioorg Med Chem Lett 2010; 20:1415-9. [PMID: 20089402 PMCID: PMC7125537 DOI: 10.1016/j.bmcl.2009.12.090] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 12/23/2009] [Accepted: 12/24/2009] [Indexed: 11/23/2022]
Abstract
A small library of 36 functionalized benzophenone thiosemicarbazone analogs has been prepared by chemical synthesis and evaluated for their ability to inhibit the cysteine proteases cathepsin L and cathepsin B. Inhibitors of cathepsins L and B have the potential to limit or arrest cancer metastasis. The six most active inhibitors of cathepsin L (IC50<85 nM) in this series incorporate a meta-bromo substituent in one aryl ring along with a variety of functional groups in the second aryl ring. These six analogs are selective for their inhibition of cathepsin L versus cathepsin B (IC50>10,000 nM). The most active analog in the series, 3-bromophenyl-2'-fluorophenyl thiosemicarbazone 1, also efficiently inhibits cell invasion of the DU-145 human prostate cancer cell line.
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Affiliation(s)
- G.D. Kishore Kumar
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Gustavo E. Chavarria
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Amanda K. Charlton-Sevcik
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Wara M. Arispe
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Matthew T. MacDonough
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Tracy E. Strecker
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Shen-En Chen
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Bronwyn G. Siim
- OXiGENE Inc., Magdalen Center, Robert Robinson Avenue, The Oxford Science Park, OX4 4GA, UK
| | - David J. Chaplin
- OXiGENE Inc., Magdalen Center, Robert Robinson Avenue, The Oxford Science Park, OX4 4GA, UK
| | - Mary Lynn Trawick
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
| | - Kevin G. Pinney
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798-7348, USA
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Asaad N, Bethel PA, Coulson MD, Dawson JE, Ford SJ, Gerhardt S, Grist M, Hamlin GA, James MJ, Jones EV, Karoutchi GI, Kenny PW, Morley AD, Oldham K, Rankine N, Ryan D, Wells SL, Wood L, Augustin M, Krapp S, Simader H, Steinbacher S. Dipeptidyl nitrile inhibitors of Cathepsin L. Bioorg Med Chem Lett 2009; 19:4280-3. [PMID: 19515558 DOI: 10.1016/j.bmcl.2009.05.071] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 05/20/2009] [Accepted: 05/21/2009] [Indexed: 10/20/2022]
Abstract
A series of potent Cathepsin L inhibitors with good selectivity with respect to other cysteine Cathepsins is described and SAR is discussed with reference to the crystal structure of a protein-ligand complex.
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Affiliation(s)
- Nabil Asaad
- Respiratory & Inflammation Research Area, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, UK
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14
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Yadav MR, Shinde AK, Chouhan BS, Giridhar R, Menard R. Peptidomimetic 2-cyanopyrrolidines as potent selective cathepsin L inhibitors. J Enzyme Inhib Med Chem 2008; 23:190-7. [PMID: 18343903 DOI: 10.1080/14756360701504842] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Cathepsins have been found to have important physiological roles. The implication of cathepsin L in various types of cancers is well established. In a search for selective cathepsin L inhibitors as anticancer agents, a series of 2-cyanoprrolidine peptidomimetics, carrying a nitrile group as warhead, were designed. Two series of compounds, one with a benzyl moiety and a second with an isobutyl moiety at P(2) position of the enzyme were synthesized. The synthesized compounds were evaluated for inhibitory activity against human cathepsin L and cathepsin B. Although, none of the compounds showed promising inhibitory activity, (E)N-{(S)1-[(S)2-cyano-1-pyrrolidinecarbonyl]-3-methylbutyl}-2,3-diphenylacrylamide (24) with an isobutyl moiety at P(2) was found to show selectivity as a cathepsin L inhibitor (Ki 5.3 microM for cathepsin L and Ki > 100 microM for cathepsin B). This compound could act as a new lead for the further development of improved inhibitors within this inhibitor type.
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Affiliation(s)
- Mange R Yadav
- Pharmacy Department, Faculty of Technology and Engineering, The M S University of Baroda, Vadodara, India.
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15
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Design, synthesis, and evaluation of inhibitors of cathepsin L: Exploiting a unique thiocarbazate chemotype. Bioorg Med Chem Lett 2008; 18:3646-51. [PMID: 18499453 DOI: 10.1016/j.bmcl.2008.04.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/16/2008] [Accepted: 04/21/2008] [Indexed: 11/24/2022]
Abstract
Recently, we identified a thiocarbazate that exhibits potent inhibitory activity against human cathepsin L. Since this structure represents a novel chemotype with potential for activity against the entire cysteine protease family, we designed, synthesized, and assayed a series of analogs to probe the mechanism of action, as well as the structural requirements for cathepsin L activity. Molecular docking studies using coordinates of a papain-inhibitor complex as a model for cathepsin L provided useful insights.
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16
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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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17
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Klon AE, Diller DJ. Library Fingerprints: A Novel Approach to the Screening of Virtual Libraries. J Chem Inf Model 2007; 47:1354-65. [PMID: 17595072 DOI: 10.1021/ci7000204] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose a novel method to prioritize libraries for combinatorial synthesis and high-throughput screening that assesses the viability of a particular library on the basis of the aggregate physical-chemical properties of the compounds using a naïve Bayesian classifier. This approach prioritizes collections of related compounds according to the aggregate values of their physical-chemical parameters in contrast to single-compound screening. The method is also shown to be useful in screening existing noncombinatorial libraries when the compounds in these libraries have been previously clustered according to their molecular graphs. We show that the method used here is comparable or superior to the single-compound virtual screening of combinatorial libraries and noncombinatorial libraries and is superior to the pairwise Tanimoto similarity searching of a collection of combinatorial libraries.
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Affiliation(s)
- Anthony E Klon
- Department of Molecular Modeling, Pharmacopeia, P.O. Box 5350, Princeton, New Jersey 08543-5350, USA.
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18
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Synthesis of 3-oxooxa- and 3-oxoazacycloalk-4-enes by ring-closing metathesis. Application to the synthesis of an inhibitor of cathepsin K. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.03.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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20
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Patterson AW, Wood WJL, Hornsby M, Lesley S, Spraggon G, Ellman JA. Identification of selective, nonpeptidic nitrile inhibitors of cathepsin s using the substrate activity screening method. J Med Chem 2006; 49:6298-307. [PMID: 17034136 DOI: 10.1021/jm060701s] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The substrate activity screening method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain low nanomolar 1,4-disubstituted-1,2,3-triazole-based aldehyde inhibitors (Wood, W. J. L.; Patterson, A. W.; Tsuruoka, H.; Jain, R. K.; Ellman, J. A. J. Am. Chem. Soc. 2005, 127, 15521-15527). Replacement of the metabolically labile aldehyde pharmacophore with the nitrile pharmacophore provided inhibitors with moderate potency for cathepsin S. The inhibitors showed good selectivity over cathepsins B and L but no selectivity over cathepsin K. X-ray structures of two crystal forms (1.5 and 1.9 A) of a complex between cathepsin S and a triazole inhibitor incorporating a chloromethyl ketone pharmacophore guided the design of triazole substrates with increased cleavage efficiency and selectivity for cathepsin S over cathepsins B, L, and K. Conversion of select substrates to nitrile inhibitors yielded a low molecular weight (414 Da) and potent (15 nM) cathepsin S inhibitor that showed >1000-fold selectivity over cathepsins B, L, and K.
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Affiliation(s)
- Andrew W Patterson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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21
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Xue F, Seto CT. Structure–activity studies of cyclic ketone inhibitors of the serine protease plasmin: Design, synthesis, and biological activity. Bioorg Med Chem 2006; 14:8467-87. [PMID: 16971130 DOI: 10.1016/j.bmc.2006.08.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 08/23/2006] [Accepted: 08/28/2006] [Indexed: 11/16/2022]
Abstract
Three series of cyclic ketone inhibitors were synthesized and evaluated against the serine protease plasmin. Peptide inhibitors that incorporated 3-oxotetrahydrofuran and 3-oxotetrahydrothiophene 1,1-dioxide groups had the highest activities. Alkylamino substituents, which were designed to bind in the S1 subsite of plasmin, were attached to the inhibitors. Compounds 5c and 5g, which incorporated 6-aminohexyl substituents, were found to be optimal and demonstrated IC(50) values in the low micromolar range. Incorporating conformationally constrained peptide segments into the inhibitors did not improve their activities.
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Affiliation(s)
- Fengtian Xue
- Department of Chemistry, Brown University, 324 Brook Street, Box H, Providence, RI 02912, USA
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22
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Tully DC, Liu H, Chatterjee AK, Alper PB, Epple R, Williams JA, Roberts MJ, Woodmansee DH, Masick BT, Tumanut C, Li J, Spraggon G, Hornsby M, Chang J, Tuntland T, Hollenbeck T, Gordon P, Harris JL, Karanewsky DS. Synthesis and SAR of arylaminoethyl amides as noncovalent inhibitors of cathepsin S: P3 cyclic ethers. Bioorg Med Chem Lett 2006; 16:5112-7. [PMID: 16876402 DOI: 10.1016/j.bmcl.2006.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 07/07/2006] [Accepted: 07/11/2006] [Indexed: 12/01/2022]
Abstract
The synthesis and structure-activity relationship of a series of arylaminoethyl amide cathepsin S inhibitors are reported. Optimization of P3 and P2 groups to improve overall physicochemical properties resulted in significant improvements in oral bioavailability over early lead compounds. An X-ray structure of compound 37 bound to the active site of cathepsin S is also reported.
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Affiliation(s)
- David C Tully
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, CA 92121, USA.
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