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Farag PS, AboulMagd AM, Hemdan MM, Hassaballah AI. Annulated pyrazole derivatives as a novel class of urokinase (uPA) inhibitors: Green synthesis, anticancer activity, DNA-damage evaluation, and molecular modelling study. Bioorg Chem 2022; 130:106231. [DOI: 10.1016/j.bioorg.2022.106231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/08/2022] [Accepted: 10/26/2022] [Indexed: 11/15/2022]
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2
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El Salamouni NS, Buckley BJ, Ranson M, Kelso MJ, Yu H. Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity. Biophys Rev 2022; 14:277-301. [PMID: 35340592 PMCID: PMC8921380 DOI: 10.1007/s12551-021-00921-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/18/2021] [Indexed: 01/09/2023] Open
Abstract
The urokinase plasminogen activator (uPA) is a widely studied anticancer drug target with multiple classes of inhibitors reported to date. Many of these inhibitors contain amidine or guanidine groups, while others lacking these groups show improved oral bioavailability. Most of the X-ray co-crystal structures of small molecule uPA inhibitors show a key salt bridge with the side chain carboxylate of Asp189 in the S1 pocket of uPA. This review summarises the different classes of uPA inhibitors, their binding interactions and experimentally measured inhibitory potencies and highlights species selectivity issues with attention to recently described 6-substituted amiloride and 5‑N,N-(hexamethylene)amiloride (HMA) derivatives.
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Affiliation(s)
- Nehad S El Salamouni
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522 Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Benjamin J. Buckley
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522 Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522 Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Michael J. Kelso
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522 Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522 Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
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3
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Milani G, Cavalluzzi MM, Altamura C, Santoro A, Perrone M, Muraglia M, Colabufo NA, Corbo F, Casalino E, Franchini C, Pisano I, Desaphy J, Carrieri A, Carocci A, Lentini G. Bioisosteric Modification of To042: Synthesis and Evaluation of Promising Use-Dependent Inhibitors of Voltage-Gated Sodium Channels. ChemMedChem 2021; 16:3588-3599. [PMID: 34519427 PMCID: PMC9293070 DOI: 10.1002/cmdc.202100496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/01/2021] [Indexed: 11/07/2022]
Abstract
Three analogues of To042, a tocainide-related lead compound recently reported for the treatment of myotonia, were synthesized and evaluated in vitro as skeletal muscle sodium channel blockers possibly endowed with enhanced use-dependent behavior. Patch-clamp experiments on hNav1.4 expressed in HEK293 cells showed that N-[(naphthalen-1-yl)methyl]-4-[(2,6-dimethyl)phenoxy]butan-2-amine, the aryloxyalkyl bioisostere of To042, exerted a higher use-dependent block than To042 thus being able to preferentially block the channels in over-excited membranes while preserving healthy tissue function. It also showed the lowest active transport across BBB according to the results of P-glycoprotein (P-gp) interacting activity evaluation and the highest cytoprotective effect on HeLa cells. Quantum mechanical calculations and dockings gave insights on the most probable conformation of the aryloxyalkyl bioisostere of To042 in solution and the target residues involved in the binding, respectively. Both approaches indicated the conformations that might be adopted in both the unbound and bound state of the ligand. Overall, N-[(naphthalen-1-yl)methyl]-4-[(2,6-dimethyl)phenoxy]butan-2-amine exhibits an interesting toxico-pharmacological profile and deserves further investigation.
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Affiliation(s)
- Gualtiero Milani
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Concetta Altamura
- Department of Biomedical Sciences and Human OncologySchool of MedicineUniversity of Bari Aldo Moro PoliclinicoPiazza Giulio Cesare70124BariItaly
| | - Antonella Santoro
- Department of Bioscience, Biotechnology and BiopharmaceuticsUniversity of Bari Aldo MoroVia Orabona 470125BariItaly
| | - Mariagrazia Perrone
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Marilena Muraglia
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Nicola Antonio Colabufo
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Filomena Corbo
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Elisabetta Casalino
- Department of Veterinary MedicineUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Carlo Franchini
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Isabella Pisano
- Department of Bioscience, Biotechnology and BiopharmaceuticsUniversity of Bari Aldo MoroVia Orabona 470125BariItaly
| | - Jean‐François Desaphy
- Department of Biomedical Sciences and Human OncologySchool of MedicineUniversity of Bari Aldo Moro PoliclinicoPiazza Giulio Cesare70124BariItaly
| | - Antonio Carrieri
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Alessia Carocci
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Giovanni Lentini
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
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4
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St Denis JD, Hall RJ, Murray CW, Heightman TD, Rees DC. Fragment-based drug discovery: opportunities for organic synthesis. RSC Med Chem 2020; 12:321-329. [PMID: 34041484 PMCID: PMC8130625 DOI: 10.1039/d0md00375a] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 12/28/2022] Open
Abstract
This Review describes the increasing demand for organic synthesis to facilitate fragment-based drug discovery (FBDD), focusing on polar, unprotected fragments. In FBDD, X-ray crystal structures are used to design target molecules for synthesis with new groups added onto a fragment via specific growth vectors. This requires challenging synthesis which slows down drug discovery, and some fragments are not progressed into optimisation due to synthetic intractability. We have evaluated the output from Astex's fragment screenings for a number of programs, including urokinase-type plasminogen activator, hematopoietic prostaglandin D2 synthase, and hepatitis C virus NS3 protease-helicase, and identified fragments that were not elaborated due, in part, to a lack of commercially available analogues and/or suitable synthetic methodology. This represents an opportunity for the development of new synthetic research to enable rapid access to novel chemical space and fragment optimisation.
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Affiliation(s)
| | - Richard J Hall
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Tom D Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - David C Rees
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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5
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Huggins DJ. Structural analysis of experimental drugs binding to the SARS-CoV-2 target TMPRSS2. J Mol Graph Model 2020; 100:107710. [PMID: 32829149 PMCID: PMC7417922 DOI: 10.1016/j.jmgm.2020.107710] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022]
Abstract
The emergence of SARS-CoV-2 has prompted a worldwide health emergency. There is an urgent need for therapeutics, both through the repurposing of approved drugs and the development of new treatments. In addition to the viral drug targets, a number of human drug targets have been suggested. In theory, targeting human proteins should provide an advantage over targeting viral proteins in terms of drug resistance, which is commonly a problem in treating RNA viruses. This paper focuses on the human protein TMPRSS2, which supports coronavirus life cycles by cleaving viral spike proteins. The three-dimensional structure of TMPRSS2 is not known and so we have generated models of the TMPRSS2 in the apo state as well as in complex with a peptide substrate and putative inhibitors to aid future work. Importantly, many related human proteases have 80% or higher identity with TMPRSS2 in the S1-S1' subsites, with plasminogen and urokinase-type plasminogen activator (uPA) having 95% identity. We highlight 376 approved, investigational or experimental drugs targeting S1A serine proteases that may also inhibit TMPRSS2. Whilst the presence of a relatively uncommon lysine residue in the S2/S3 subsites means that some serine protease inhibitors will not inhibit TMPRSS2, this residue is likely to provide a handle for selective targeting in a focused drug discovery project. We discuss how experimental drugs targeting related serine proteases might be repurposed as TMPRSS2 inhibitors to treat coronaviruses.
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Affiliation(s)
- David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA.
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6
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Mohammadi M, Rezaie E, Sakhteman A, Zarei N. A highly potential cleavable linker for tumor targeting antibody-chemokines. J Biomol Struct Dyn 2020; 40:2546-2556. [PMID: 33118476 DOI: 10.1080/07391102.2020.1841025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chemokines are the large family of chemotactic cytokines that play an important role in leukocyte movement and migration stimulation. Until now, several antibody-cytokine (chemokine) fusion proteins have been investigated in clinical trials because of their ability to evoke the circulating leukocytes far from the tumor site. In this case, creating the concentration gradient regarding the chemokine is very important to recruit the circulating leukocytes with maximum performance to the tumor environment. To achieve a proper gradient, the chemokine separation from the tumor antigen-bounded antibody can be very crucial. Thus, we designed a novel linker that can be cleaved by enzymes presented around the tumor site including cathepsin B, urokinase-type plasminogen activator (uPA) and matrix metalloproteinases (MMPs). Also, it can inhibit tumor progression by competing with the native substrate of key proteases in the tumor microenvironment. The proposed linker was evaluated using some bioinformatics approaches. In silico results showed that the linker is structurally stable and could be detected and cleaved using the mentioned enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mozafar Mohammadi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ehsan Rezaie
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Neda Zarei
- Department of Biology, Farhangian University, Tehran, Iran
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7
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Wang D, Yang Y, Jiang L, Wang Y, Li J, Andreasen PA, Chen Z, Huang M, Xu P. Suppression of Tumor Growth and Metastases by Targeted Intervention in Urokinase Activity with Cyclic Peptides. J Med Chem 2019; 62:2172-2183. [PMID: 30707839 DOI: 10.1021/acs.jmedchem.8b01908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Urokinase-type plasminogen activator (uPA) is a diagnostic marker for breast and prostate cancers recommended by American Society for Clinical Oncology and German Breast Cancer Society. Inhibition of uPA was proposed as an efficient strategy for cancer treatments. In this study, we report peptide-based uPA inhibitors with high potency and specificity comparable to monoclonal antibodies. We revealed the binding and inhibitory mechanisms by combining crystallography, molecular dynamic simulation, and other biophysical and biochemical approaches. Besides, we showed that our peptides efficiently inhibited the invasion of cancer cells via intervening with the processes of the degradation of extracellular matrices. Furthermore, our peptides significantly suppressed the tumor growth and the cancer metastases in tumor-bearing mice. This study demonstrates that these uPA peptides are highly potent anticancer agents and reveals the mechanistic insights of these uPA inhibitors, which can be useful for developing other serine protease inhibitors.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,University of Chinese Academy of Sciences , No.19 (A) Yuquan Road , Shijingshan District, Beijing 100049 , China
| | - Yongshuai Yang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,University of Chinese Academy of Sciences , No.19 (A) Yuquan Road , Shijingshan District, Beijing 100049 , China.,College of Life Science , Fujian Agriculture and Forestry University , Fuzhou , Fujian 350002 , China
| | - Longguang Jiang
- College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Yu Wang
- College of Life Science , Fujian Agriculture and Forestry University , Fuzhou , Fujian 350002 , China
| | - Jinyu Li
- College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics , Aarhus University , Aarhus C 8000 , Denmark
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.,College of Chemistry , Fuzhou University , Fuzhou , Fujian 350116 , China
| | - Peng Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China
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8
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Buckley BJ, Aboelela A, Minaei E, Jiang LX, Xu Z, Ali U, Fildes K, Cheung CY, Cook SM, Johnson DC, Bachovchin DA, Cook GM, Apte M, Huang M, Ranson M, Kelso MJ. 6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer. J Med Chem 2018; 61:8299-8320. [PMID: 30130401 DOI: 10.1021/acs.jmedchem.8b00838] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastasis is the cause of death in the majority (∼90%) of malignant cancers. The oral potassium-sparing diuretic amiloride and its 5-substituted derivative 5 -N, N-(hexamethylene)amiloride (HMA) reportedly show robust antitumor/metastasis effects in multiple in vitro and animal models. These effects are likely due, at least in part, to inhibition of the urokinase plasminogen activator (uPA), a key protease determinant of cell invasiveness and metastasis. This study reports the discovery of 6-substituted HMA analogs that show nanomolar potency against uPA, high selectivity over related trypsin-like serine proteases, and minimal inhibitory effects against epithelial sodium channels (ENaC), the diuretic and antikaliuretic target of amiloride. Reductions in lung metastases were demonstrated for two analogs in a late-stage experimental mouse metastasis model, and one analog completely inhibited formation of liver metastases in an orthotopic xenograft mouse model of pancreatic cancer. The results support further evaluation of 6-substituted HMA derivatives as uPA-targeting anticancer drugs.
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Affiliation(s)
- Benjamin J Buckley
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Ashraf Aboelela
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Elahe Minaei
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Longguang X Jiang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies , Fuzhou University , Fujian 350116 , China
| | - Zhihong Xu
- Pancreatic Research Group, South Western Sydney Clinical School , University of New South Wales, and Ingham Institute for Applied Medical Research , Liverpool , NSW 2170 , Australia
| | - Umar Ali
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Karen Fildes
- Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia.,Graduate School of Medicine , University of Wollongong , Wollongong , NSW 2522 , Australia
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology , University of Otago , Otago 9016 , New Zealand
| | - Simon M Cook
- Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Darren C Johnson
- Tri-Institutional PhD Program in Chemical Biology , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Daniel A Bachovchin
- Tri-Institutional PhD Program in Chemical Biology , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Gregory M Cook
- Department of Microbiology and Immunology , University of Otago , Otago 9016 , New Zealand
| | - Minoti Apte
- Pancreatic Research Group, South Western Sydney Clinical School , University of New South Wales, and Ingham Institute for Applied Medical Research , Liverpool , NSW 2170 , Australia
| | - Mingdong Huang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies , Fuzhou University , Fujian 350116 , China
| | - Marie Ranson
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
| | - Michael J Kelso
- Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.,Illawarra Health & Medical Research Institute , Wollongong , NSW 2522 , Australia
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Islam I, Yuan S, West CW, Adler M, Bothe U, Bryant J, Chang Z, Chu K, Emayan K, Gualtieri G, Ho E, Light D, Mallari C, Morser J, Phillips G, Schaefer C, Sukovich D, Whitlow M, Chen D, Buckman BO. Discovery of selective urokinase plasminogen activator (uPA) inhibitors as a potential treatment for multiple sclerosis. Bioorg Med Chem Lett 2018; 28:3372-3375. [PMID: 30201291 DOI: 10.1016/j.bmcl.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 11/28/2022]
Abstract
We report here the design and synthesis of a novel series of benzylamines that are potent and selective inhibitors of uPA with promising oral availability in rat. Further evaluation of one representative (ZK824859) of the new structural class showed that this compound lowered clinical scores when dosed in either acute or chronic mouse EAE models, suggesting that uPA inhibitors of this type could be useful for the treatment of multiple sclerosis.
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Affiliation(s)
- Imadul Islam
- Medical Core Facility and Research Platforms, King Abdullah International Medical Research Center/King Saud Bin, Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia; Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States.
| | - Shendong Yuan
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Christopher W West
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Marc Adler
- Department of Biophysics, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Ulrich Bothe
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States; Research and Development Pharmaceutical, Bayer AG, 13342 Berlin, Germany
| | - Judi Bryant
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Zheng Chang
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Kieu Chu
- Department of Molecular Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Kumar Emayan
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Giovanna Gualtieri
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Elena Ho
- Department of Animal Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - David Light
- Department of Antibody Technology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Cornell Mallari
- Department of Animal Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - John Morser
- Cardiovascular Department, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Gary Phillips
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Caralee Schaefer
- Department of Animal Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Drew Sukovich
- Department of Molecular Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Marc Whitlow
- Department of Biophysics, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Deborah Chen
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
| | - Brad O Buckman
- Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States
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10
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Jiang L, Zhang X, Zhou Y, Chen Y, Luo Z, Li J, Yuan C, Huang M. Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases. RSC Adv 2018; 8:28189-28197. [PMID: 35542712 PMCID: PMC9083945 DOI: 10.1039/c8ra03145b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinase-type plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the high-resolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases. These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.
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Affiliation(s)
| | - Xu Zhang
- Center for Life Science, School of Life Sciences, Yunnan University Kunming 650021 China
| | - Yang Zhou
- College of Chemistry, Fuzhou University Fuzhou 350116 China
| | - Yayu Chen
- College of Chemistry, Fuzhou University Fuzhou 350116 China
| | - Zhipu Luo
- Synchrotron Radiation Research Section, NCI, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Jinyu Li
- College of Chemistry, Fuzhou University Fuzhou 350116 China
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University Fuzhou 350116 China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University Fuzhou 350116 China
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11
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uPA/uPAR and SERPINE1 in head and neck cancer: role in tumor resistance, metastasis, prognosis and therapy. Oncotarget 2018; 7:57351-57366. [PMID: 27385000 PMCID: PMC5302994 DOI: 10.18632/oncotarget.10344] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/13/2016] [Indexed: 12/25/2022] Open
Abstract
There is strong evidence supporting the role of the plasminogen activator system in head and neck squamous cell carcinoma (HNSCC), particularly of its uPA (urokinase plasminogen activator) / uPAR (urokinase plasminogen activator receptor) and SERPINE1 components. Overexpression of uPA/uPAR and SERPINE1 enhances tumor cell migration and invasion and plays a key role in metastasis development, conferring poor prognosis. The apparent paradox of uPA/uPAR and its inhibitor SERPINE1 producing similar effects is solved by the identification of SERPINE1 activated signaling pathways independent of uPA inhibition. Both uPA/uPAR and SERPINE1 are directly linked to the induction of epithelial-to-mesenchymal transition, the acquisition of stem cell properties and resistance to antitumor agents. The aim of this review is to provide insight on the deregulation of these proteins in all these processes. We also summarize their potential value as prognostic biomarkers or potential drug targets in HNSCC patients. Concomitant overexpression of uPA/uPAR and SERPINE1 is associated with a higher risk of metastasis and could be used to identify patients that would benefit from an adjuvant treatment. In the future, the specific inhibitors of uPA/uPAR and SERPINE1, which are still under development, could be used to design new therapeutic strategies in HNSCCs.
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12
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Lee JE, Kwon YJ, Baek HS, Ye DJ, Cho E, Choi HK, Oh KS, Chun YJ. Synergistic induction of apoptosis by combination treatment with mesupron and auranofin in human breast cancer cells. Arch Pharm Res 2017; 40:746-759. [DOI: 10.1007/s12272-017-0923-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 05/26/2017] [Indexed: 12/14/2022]
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13
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Gladysz R, Adriaenssens Y, De Winter H, Joossens J, Lambeir AM, Augustyns K, Van der Veken P. Discovery and SAR of Novel and Selective Inhibitors of Urokinase Plasminogen Activator (uPA) with an Imidazo[1,2-a]pyridine Scaffold. J Med Chem 2015; 58:9238-57. [DOI: 10.1021/acs.jmedchem.5b01171] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Rafaela Gladysz
- Laboratory
of Medicinal Chemistry (UAMC), Department of Pharmaceutical Sciences, University of Antwerp (UA), Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
| | - Yves Adriaenssens
- Laboratory
of Medicinal Chemistry (UAMC), Department of Pharmaceutical Sciences, University of Antwerp (UA), Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
| | - Hans De Winter
- Laboratory
of Medicinal Chemistry (UAMC), Department of Pharmaceutical Sciences, University of Antwerp (UA), Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
| | - Jurgen Joossens
- Laboratory
of Medicinal Chemistry (UAMC), Department of Pharmaceutical Sciences, University of Antwerp (UA), Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
| | - Anne-Marie Lambeir
- Medical Biochemistry, Department
of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein
1, B-2610 Wilrijk, Antwerp, Belgium
| | - Koen Augustyns
- Laboratory
of Medicinal Chemistry (UAMC), Department of Pharmaceutical Sciences, University of Antwerp (UA), Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
| | - Pieter Van der Veken
- Laboratory
of Medicinal Chemistry (UAMC), Department of Pharmaceutical Sciences, University of Antwerp (UA), Universiteitsplein 1, B-2610 Wilrijk, Antwerp, Belgium
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14
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Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends Pharmacol Sci 2015; 36:724-736. [PMID: 26538314 DOI: 10.1016/j.tips.2015.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/01/2023]
Abstract
Analysis of binding energy hot spots at protein surfaces can provide crucial insights into the prospects for successful application of fragment-based drug discovery (FBDD), and whether a fragment hit can be advanced into a high-affinity, drug-like ligand. The key factor is the strength of the top ranking hot spot, and how well a given fragment complements it. We show that published data are sufficient to provide a sophisticated and quantitative understanding of how hot spots derive from a protein 3D structure, and how their strength, number, and spatial arrangement govern the potential for a surface site to bind to fragment-sized and larger ligands. This improved understanding provides important guidance for the effective application of FBDD in drug discovery.
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Affiliation(s)
- David R Hall
- Acpharis Inc., 160 North Mill Street, Holliston, MA 01746, USA
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA, 02215, USA.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA; Department of Chemistry, Boston University, Boston, MA, 02215, USA.
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15
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Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-Protein Interactions: Structures and Druggability. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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16
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Biased and unbiased strategies to identify biologically active small molecules. Bioorg Med Chem 2014; 22:4474-89. [DOI: 10.1016/j.bmc.2014.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 12/20/2022]
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17
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Application of molecular modeling to urokinase inhibitors development. BIOMED RESEARCH INTERNATIONAL 2014; 2014:625176. [PMID: 24967388 PMCID: PMC4055159 DOI: 10.1155/2014/625176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/22/2014] [Indexed: 01/01/2023]
Abstract
Urokinase-type plasminogen activator (uPA) plays an important role in the regulation of diverse physiologic and pathologic processes. Experimental research has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients, whereas suppression of proteolytic activity of uPA leads to evident decrease of metastasis. Therefore, uPA has been considered as a promising molecular target for development of anticancer drugs. The present study sets out to develop the new selective uPA inhibitors using computer-aided structural based drug design methods. Investigation involves the following stages: computer modeling of the protein active site, development and validation of computer molecular modeling methods: docking (SOL program), postprocessing (DISCORE program), direct generalized docking (FLM program), and the application of the quantum chemical calculations (MOPAC package), search of uPA inhibitors among molecules from databases of ready-made compounds to find new uPA inhibitors, and design of new chemical structures and their optimization and experimental examination. On the basis of known uPA inhibitors and modeling results, 18 new compounds have been designed, calculated using programs mentioned above, synthesized, and tested in vitro. Eight of them display inhibitory activity and two of them display activity about 10 μM.
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18
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Abstract
Crystallography is a major tool for structure-driven drug design, as it allows knowledge of the 3D structure of protein targets and protein-ligand complexes. However, the route for crystal structure determination involves many steps, some of which may hamper its high-throughput use. Recent efforts have produced significant advances in experimental and computational tools and protocols. They include automatic crystallization tools, faster data collection devices, more efficient phasing methods and improved ligand-fitting procedures. The timescales of drug-discovery processes have been also reduced by using a fragment-based screening approach. Herein, the achievements in protein crystallography over the last 5 years are reviewed, and advantages and disadvantages of the fragment-based approaches to drug discovery that make use of x-ray crystallography as a primary screening method are examined. In particular, in some detail, five recent case studies pertaining to the development of new hits or leads in relevant therapeutic areas, such as cancer, immune response, inflammation, metabolic syndrome and neurology are described.
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19
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Brear P, Telford J, Taylor GL, Westwood NJ. Synthesis and Structural Characterisation of Selective Non-Carbohydrate-Based Inhibitors of Bacterial Sialidases. Chembiochem 2012; 13:2374-83. [DOI: 10.1002/cbic.201200433] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Indexed: 11/08/2022]
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20
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Hain AUP, Weltzer RR, Hammond H, Jayabalasingham B, Dinglasan RR, Graham DRM, Colquhoun DR, Coppens I, Bosch J. Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction. J Struct Biol 2012; 180:551-62. [PMID: 22982544 DOI: 10.1016/j.jsb.2012.09.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/26/2012] [Accepted: 09/03/2012] [Indexed: 12/22/2022]
Abstract
The autophagy-related proteins are thought to serve multiple functions in Plasmodium and are considered essential to parasite survival and development. We have studied two key interacting proteins, Atg8 and Atg3, of the autophagy pathway in Plasmodium falciparum. These proteins are vital for the formation and elongation of the autophagosome and essential to the process of macroautophagy. Autophagy may be required for conversion of the sporozoite into erythrocytic-infective merozoites and may be crucial for other functions during asexual blood stages. Here we describe the identification of an Atg8 family interacting motif (AIM) in Plasmodium Atg3, which binds Plasmodium Atg8. We determined the co-crystal structure of PfAtg8 with a short Atg3¹⁰³⁻¹¹⁰ peptide, corresponding to this motif, to 2.2 Å resolution. Our in vitro interaction studies are in agreement with our X-ray crystal structure. Furthermore they suggest an important role for a unique Apicomplexan loop absent from human Atg8 homologues. Prevention of the protein-protein interaction of full length PfAtg8 with PfAtg3 was achieved at low micromolar concentrations with a small molecule, 1,2,3-trihydroxybenzene. Together our structural and interaction studies represent a starting point for future antimalarial drug discovery and design for this novel protein-protein interaction.
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Affiliation(s)
- Adelaide U P Hain
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
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21
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Murray CW, Verdonk ML, Rees DC. Experiences in fragment-based drug discovery. Trends Pharmacol Sci 2012; 33:224-32. [PMID: 22459076 DOI: 10.1016/j.tips.2012.02.006] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022]
Abstract
Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches.
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Affiliation(s)
- Christopher W Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.
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22
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Venkatraj M, Messagie J, Joossens J, Lambeir AM, Haemers A, Van der Veken P, Augustyns K. Synthesis and evaluation of non-basic inhibitors of urokinase-type plasminogen activator (uPA). Bioorg Med Chem 2012; 20:1557-68. [DOI: 10.1016/j.bmc.2011.12.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/15/2011] [Accepted: 12/17/2011] [Indexed: 11/16/2022]
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23
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Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies. J Mol Model 2011; 18:2553-66. [DOI: 10.1007/s00894-011-1280-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 10/12/2011] [Indexed: 11/25/2022]
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24
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Köster H, Craan T, Brass S, Herhaus C, Zentgraf M, Neumann L, Heine A, Klebe G. A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes. J Med Chem 2011; 54:7784-96. [PMID: 21972967 DOI: 10.1021/jm200642w] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.
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Affiliation(s)
- Helene Köster
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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25
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Nowicki TS, Moscatello AL, Shin E, Schantz S, Tiwari RK, Geliebter J. The urokinase plasminogen activator system in metastatic papillary thyroid carcinoma: a potential therapeutic target. J Clin Endocrinol Metab 2011; 96:3062-4. [PMID: 21832115 PMCID: PMC3417282 DOI: 10.1210/jc.2011-1123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Theodore S Nowicki
- Department of Microbiology, New York Medical College, Valhalla, New York 10595, USA
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26
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Böttcher J, Jestel A, Kiefersauer R, Krapp S, Nagel S, Steinbacher S, Steuber H. Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology. Methods Enzymol 2011; 493:61-89. [PMID: 21371587 DOI: 10.1016/b978-0-12-381274-2.00003-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
In the past two decades, fragment-based approaches have evolved as a predominant strategy in lead discovery. The availability of structural information on the interaction geometries of binding fragments is key to successful structure-guided fragment-to-lead evolution. In this chapter, we illustrate methodological advances for protein-fragment crystal structure generation in order to offer general lessons on the importance of fragment properties and the most appropriate crystallographic setup to evaluate them. We analyze elaborate protocols, methods, and clues applied to challenging complex formation projects. The results should assist medicinal chemists to select the most promising targets and strategies for fragment-based crystallography as well as provide a tutorial to structural biologists who attempt to determine protein-fragment structures.
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Affiliation(s)
- Jark Böttcher
- Proteros biostructures GmbH, Am Klopferspitz 19, Martinsried, Germany
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27
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Abstract
The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.
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28
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Bienstock RJ. Overview: Fragment-Based Drug Design. LIBRARY DESIGN, SEARCH METHODS, AND APPLICATIONS OF FRAGMENT-BASED DRUG DESIGN 2011. [DOI: 10.1021/bk-2011-1076.ch001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rachelle J. Bienstock
- National Institute of Environmental Health Sciences, P.O. Box 12233, MD F0-011, Research Triangle Park, North Carolina 27709
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29
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Barelier S, Pons J, Gehring K, Lancelin JM, Krimm I. Ligand specificity in fragment-based drug design. J Med Chem 2010; 53:5256-66. [PMID: 20575554 DOI: 10.1021/jm100496j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fragment-based drug design consists of identifying low-molecular weight compounds that weakly bind to a target macromolecule and will then be modified or linked to yield potent inhibitors. The specificity of these low-complexity and low-affinity molecules has rarely been discussed in the literature. To address this question, NMR spectroscopy was used to investigate the interactions of 150 fragments with five proteins: three proteins from the Bcl-2 family (Bcl-x(L), Bcl-w, and Mcl-1), human peroxiredoxin 5, for which very few ligands have been reported, and human serum albumin, which is known to bind a large number of ligands. Our results show that the fragments are rather versatile binders and able to identify binding hot spots in very different targets. Despite the different hit rates observed related to the druggability of the proteins, two scaffolds appear as preferred binders for all proteins. Low specificity was observed between homologous proteins or unrelated poorly druggable proteins, while higher specificity could be achieved with highly druggable targets.
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Affiliation(s)
- Sarah Barelier
- Laboratoire des Sciences Analytiques, UMR CNRS 5180, Universite de Lyon, Universite Claude Bernard, Lyon 1, Bat. ESCPE Lyon, Domaine Scientifique de la Doua, 69100 Villeurbanne, France
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30
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Murray CW, Blundell TL. Structural biology in fragment-based drug design. Curr Opin Struct Biol 2010; 20:497-507. [DOI: 10.1016/j.sbi.2010.04.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/26/2010] [Accepted: 04/14/2010] [Indexed: 10/19/2022]
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31
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Hildenbrand R, Allgayer H, Marx A, Stroebel P. Modulators of the urokinase-type plasminogen activation system for cancer. Expert Opin Investig Drugs 2010; 19:641-52. [PMID: 20402599 DOI: 10.1517/13543781003767400] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
IMPORTANCE OF THE FIELD The serine protease urokinase-type plasminogen activator (uPA) and its receptor uPAR as well as two specific inhibitors, the plasminogen activator inhibitor type-1 (PAI-1) and type-2 (PAI-2), are involved in the control of extracellular matrix turnover and tumor growth. Data accumulating over the past 20 years have made increasingly clear that the uPA system has a multifunctional role in neoplastic evolution, affecting cancer cell proliferation, tumor angiogenesis, adhesion and migration. AREAS COVERED IN THIS REVIEW Several therapeutic strategies inhibiting the uPA system have been or are currently being developed for suppression of tumor growth. This review examines the role of the uPA system in tumor progression and assesses the various therapeutic strategies developed to selectively exploit this system. WHAT WILL THE READER GAIN We focus on the therapeutic developments of the last 15 years. In addition to antibodies and recombinant uPA- or uPAR-derived proteins, various antagonistic peptides as well as small molecules have been designed and synthesized that inhibit the uPA system, leading to reduced tumor progression. TAKE HOME MESSAGE The multifunctional potential of the uPA system in cancer has rendered this system an attractive novel target for anticancer therapy. A few novel tumor biology-based therapeutic strategies reported here, opening new ways for patient-optimized and individualized cancer therapy. It may be the right time to evaluate the hypothesis that the uPA system plays a pivotal role in cancer progression and that targeting this system will lead to clinical benefit in cancer patients.
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32
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Lu SY, Jiang YJ, Zhou P, Zou JW, Wu TX. Geometric characteristics and energy landscapes of halogen–water–hydrogen bridges at protein–ligand interfaces. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Lima LMT, Silva VDA, Palmieri LDC, Oliveira MCB, Foguel D, Polikarpov I. Identification of a novel ligand binding motif in the transthyretin channel. Bioorg Med Chem 2010; 18:100-10. [DOI: 10.1016/j.bmc.2009.11.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 11/05/2009] [Accepted: 11/06/2009] [Indexed: 10/20/2022]
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34
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Identification of orally bioavailable, non-amidine inhibitors of Urokinase Plasminogen Activator (uPA). Bioorg Med Chem Lett 2009; 19:5712-5. [DOI: 10.1016/j.bmcl.2009.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 08/01/2009] [Accepted: 08/04/2009] [Indexed: 11/20/2022]
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35
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de Kloe GE, Bailey D, Leurs R, de Esch IJP. Transforming fragments into candidates: small becomes big in medicinal chemistry. Drug Discov Today 2009; 14:630-46. [PMID: 19443265 DOI: 10.1016/j.drudis.2009.03.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 03/12/2009] [Accepted: 03/16/2009] [Indexed: 11/15/2022]
Abstract
Fragment-based drug discovery (FBDD) represents a logical and efficient approach to lead discovery and optimisation. It can draw on structural, biophysical and biochemical data, incorporating a wide range of inputs, from precise mode-of-binding information on specific fragments to wider ranging pharmacophoric screening surveys using traditional HTS approaches. It is truly an enabling technology for the imaginative medicinal chemist. In this review, we analyse a representative set of 23 published FBDD studies that describe how low molecular weight fragments are being identified and efficiently transformed into higher molecular weight drug candidates. FBDD is now becoming warmly endorsed by industry as well as academia and the focus on small interacting molecules is making a big scientific impact.
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Affiliation(s)
- Gerdien E de Kloe
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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