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Chitranshi N, Kumar A, Sheriff S, Gupta V, Godinez A, Saks D, Sarkar S, Shen T, Mirzaei M, Basavarajappa D, Abyadeh M, Singh SK, Dua K, Zhang KYJ, Graham SL, Gupta V. Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer's Disease: Computational Refining and Biochemical Evaluation. Cells 2021; 10:cells10081946. [PMID: 34440715 PMCID: PMC8391575 DOI: 10.3390/cells10081946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Amyloid precursor protein (APP), upon proteolytic degradation, forms aggregates of amyloid β (Aβ) and plaques in the brain, which are pathological hallmarks of Alzheimer’s disease (AD). Cathepsin B is a cysteine protease enzyme that catalyzes the proteolytic degradation of APP in the brain. Thus, cathepsin B inhibition is a crucial therapeutic aspect for the discovery of new anti-Alzheimer’s drugs. In this study, we have employed mixed-feature ligand-based virtual screening (LBVS) by integrating pharmacophore mapping, docking, and molecular dynamics to detect small, potent molecules that act as cathepsin B inhibitors. The LBVS model was generated by using hydrophobic (HY), hydrogen bond acceptor (HBA), and hydrogen bond donor (HBD) features, using a dataset of 24 known cathepsin B inhibitors of both natural and synthetic origins. A validated eight-feature pharmacophore hypothesis (Hypo III) was utilized to screen the Maybridge chemical database. The docking score, MM-PBSA, and MM-GBSA methodology was applied to prioritize the lead compounds as virtual screening hits. These compounds share a common amide scaffold, and showed important interactions with Gln23, Cys29, His110, His111, Glu122, His199, and Trp221. The identified inhibitors were further evaluated for cathepsin-B-inhibitory activity. Our study suggests that pyridine, acetamide, and benzohydrazide compounds could be used as a starting point for the development of novel therapeutics.
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Affiliation(s)
- Nitin Chitranshi
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
- Correspondence: (N.C.); (V.G.); Tel.: +61-(02)-9850-2804 (N.C.)
| | - Ashutosh Kumar
- Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan; (A.K.); (K.Y.J.Z.)
| | - Samran Sheriff
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Veer Gupta
- School of Medicine, Faculty of Health, Deakin University, Geelong, VIC 3220, Australia;
| | - Angela Godinez
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Danit Saks
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Soumalya Sarkar
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Ting Shen
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Mehdi Mirzaei
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Devaraj Basavarajappa
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran;
| | - Sachin K. Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India;
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kam Y. J. Zhang
- Center for Biosystems Dynamics Research, Laboratory for Structural Bioinformatics, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan; (A.K.); (K.Y.J.Z.)
| | - Stuart L. Graham
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
| | - Vivek Gupta
- Faculty of Medicine, Health and Human Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; (S.S.); (A.G.); (D.S.); (S.S.); (T.S.); (M.M.); (D.B.); (S.L.G.)
- Correspondence: (N.C.); (V.G.); Tel.: +61-(02)-9850-2804 (N.C.)
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Dana D, Das TK, Kumar I, Davalos AR, Mark KJ, Ramai D, Chang EJ, Talele TT, Kumar S. Design, synthesis, and evaluation of 2-(arylsulfonyl)oxiranes as cell-permeable covalent inhibitors of protein tyrosine phosphatases. Chem Biol Drug Des 2012; 80:489-99. [PMID: 22726577 DOI: 10.1111/j.1747-0285.2012.01437.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A structure-based design approach has been applied to develop 2-(arylsulfonyl)oxiranes as potential covalent inhibitors of protein tyrosine phosphatases. A detailed kinetic analysis of inactivation by these covalent inhibitors reveals that this class of compounds inhibits a panel of protein tyrosine phosphatases in a time- and dose-dependent manner, consistent with the covalent modification of the enzyme active site. An inactivation experiment in the presence of sodium arsenate, a known competitive inhibitor of protein tyrosine phosphatase, indicated that these inhibitors were active site bound. This finding is consistent with the mass spectrometric analysis of the covalently modified protein tyrosine phosphatase enzyme. Additional experiments indicated that these compounds remained inert toward other classes of arylphosphate-hydrolyzing enzymes, and alkaline and acid phosphatases. Cell-based experiments with human A549 lung cancer cell lines indicated that 2-(phenylsulfonyl)oxirane (1) caused an increase in intracellular pTyr levels in a dose-dependent manner thereby suggesting its cell-permeable nature. Taken together, the newly identified 2-(arylsulfonyl)oxiranyl moiety could serve as a novel chemotype for the development of activity-based probes and therapeutic agents against protein tyrosine phosphatase superfamily of enzymes.
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Affiliation(s)
- Dibyendu Dana
- Department of Chemistry & Biochemistry, Queens College-CUNY, 65-30 Kissena Blvd., Flushing, NY 11367, USA
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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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Baron A, Verdié P, Martinez J, Lamaty F. cis-Apa: A Practical Linker for the Microwave-Assisted Preparation of Cyclic Pseudopeptides via RCM Cyclative Cleavage. J Org Chem 2011; 76:766-72. [DOI: 10.1021/jo101629v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alice Baron
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1-Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pascal Verdié
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1-Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1-Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Frédéric Lamaty
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1-Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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