1
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Shah SKH, Modi U, Patel K, James A, N S, De S, Vasita R, Prabhakaran P. Site-selective post-modification of short α/γ hybrid foldamers: a powerful approach for molecular diversification towards biomedical applications. Biomater Sci 2023; 11:6210-6222. [PMID: 37526301 DOI: 10.1039/d3bm00766a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The extensive research work in the exhilarating area of foldamers (artificial oligomers possessing well-defined conformation in solution) has shown them to be promising candidates in biomedical research and materials science. The post-modification approach is successful in peptides, proteins, and polymers to modulate their functions. To the best of our knowledge, site-selective post-modification of a foldamer affording molecules with different pendant functional groups within a molecular scaffold has not yet been reported. We demonstrate for the first time that late-stage site-selective functionalization of short hybrid oligomers is an efficient approach to afford molecules with diverse functional groups. In this article, we report the design and synthesis of hybrid peptides with repeating units of leucine (Leu) and 5-amino salicylic acid (ASA), regioselective post-modification, conformational analyses (based on solution-state NMR, circular dichroism and computational studies) and morphological studies of the peptide nanostructures. As a proof-of-concept, we demonstrate the applications of differently modified peptides as drug delivery agents, imaging probes, and anticancer agents. The novel feature of the work is that the difference in reactivity of two phenolic OH groups in short biomimetic peptides was utilized to achieve site-selective post-modification. It is challenging to apply the same approach to short α-peptides having a poor folding tendency, and their post-functionalization may considerably affect their conformation.
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Affiliation(s)
| | - Unnati Modi
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Karma Patel
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Anjima James
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi 682022, India
| | - Sreerag N
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut 673635, India
| | - Rajesh Vasita
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Panchami Prabhakaran
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
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2
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Raveendra-Panickar D, Finlay D, Layng FI, Lambert LJ, Celeridad M, Zhao M, Barbosa K, De Backer LJS, Kwong E, Gosalia P, Rodiles S, Holleran J, Ardecky R, Grotegut S, Olson S, Hutchinson JH, Pasquale EB, Vuori K, Deshpande AJ, Cosford NDP, Tautz L. Discovery of novel furanylbenzamide inhibitors that target oncogenic tyrosine phosphatase SHP2 in leukemia cells. J Biol Chem 2021; 298:101477. [PMID: 34896393 PMCID: PMC8760490 DOI: 10.1016/j.jbc.2021.101477] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/11/2022] Open
Abstract
Disturbance of the dynamic balance between tyrosine phosphorylation and dephosphorylation of signaling molecules, controlled by protein tyrosine kinases and protein tyrosine phosphatases (PTPs), is known to lead to the development of cancer. While most approved targeted cancer therapies are tyrosine kinase inhibitors, PTPs have long been stigmatized as undruggable and have only recently gained renewed attention in drug discovery. One PTP target is the Src-homology 2 domain–containing phosphatase 2 (SHP2). SHP2 is implicated in tumor initiation, progression, metastasis, and treatment resistance, primarily because of its role as a signaling nexus of the extracellular signal–regulated kinase pathway, acting upstream of the small GTPase Ras. Efforts to develop small molecules that target SHP2 are ongoing, and several SHP2 allosteric inhibitors are currently in clinical trials for the treatment of solid tumors. However, while the reported allosteric inhibitors are highly effective against cells expressing WT SHP2, none have significant activity against the most frequent oncogenic SHP2 variants that drive leukemogenesis in several juvenile and acute leukemias. Here, we report the discovery of novel furanylbenzamide molecules as inhibitors of both WT and oncogenic SHP2. Importantly, these inhibitors readily cross cell membranes, bind and inhibit SHP2 under physiological conditions, and effectively decrease the growth of cancer cells, including triple-negative breast cancer cells, acute myeloid leukemia cells expressing either WT or oncogenic SHP2, and patient-derived acute myeloid leukemia cells. These novel compounds are effective chemical probes of active SHP2 and may serve as starting points for therapeutics targeting WT or mutant SHP2 in cancer.
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Affiliation(s)
- Dhanya Raveendra-Panickar
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Fabiana Izidro Layng
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Lester J Lambert
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Maria Celeridad
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Ming Zhao
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Karina Barbosa
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Laurent J S De Backer
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Elizabeth Kwong
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Palak Gosalia
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Socorro Rodiles
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - John Holleran
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Robert Ardecky
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Stefan Grotegut
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Steven Olson
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - John H Hutchinson
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Elena B Pasquale
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kristiina Vuori
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Aniruddha J Deshpande
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Nicholas D P Cosford
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA.
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3
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de Souza AC, Mori M, Sens L, Rocha RF, Tizziani T, de Souza LF, Domeneghini Chiaradia-Delatorre L, Botta M, Nunes RJ, Terenzi H, Menegatti AC. A chalcone derivative binds a putative allosteric site of YopH: Inhibition of a virulence factor of Yersinia. Bioorg Med Chem Lett 2020; 30:127350. [DOI: 10.1016/j.bmcl.2020.127350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023]
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4
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Bancet A, Raingeval C, Lomberget T, Le Borgne M, Guichou JF, Krimm I. Fragment Linking Strategies for Structure-Based Drug Design. J Med Chem 2020; 63:11420-11435. [DOI: 10.1021/acs.jmedchem.0c00242] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Bancet
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Claire Raingeval
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Thierry Lomberget
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | - Marc Le Borgne
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | | | - Isabelle Krimm
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, 69008 Lyon, France
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5
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Novel 5-aminosalicylic derivatives as anti-inflammatories and myeloperoxidase inhibitors evaluated in silico, in vitro and ex vivo. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2016.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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6
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Ma YZ, Tang ZB, Sang CY, Qi ZY, Hui L, Chen SW. Synthesis and biological evaluation of nitroxide labeled pyrimidines as Aurora kinase inhibitors. Bioorg Med Chem Lett 2019; 29:694-699. [PMID: 30728112 DOI: 10.1016/j.bmcl.2019.01.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 02/06/2023]
Abstract
To find novel effective Aurora kinases inhibitors, a series of structurally interesting nitroxide labeled pyrimidines were synthesized and evaluated their anti-proliferative and Aurora kinases inhibitory activities. Among them, butyl 2-(3-((5-fluoro-2-((4-((1-oxyl-2,2,6,6-tetramethylpiperidin-4-yl)carbamoyl) phenyl) amino)pyrimidin-4-yl)amino)-1H-pyrazol-5-yl)acetate (22) possessed the most potent anti-proliferative effects against four carcinoma cell lines with IC50 values in range of 0.89-11.41 μM, and kinases inhibition against Aurora A and B with the IC50 values were 9.3 and 2.8 nM, respectively. Furthermore, compound 22 blocked the phosphorylation of Aurora A (T288), Aurora B (Thr232) and HisH3, decreased the expression of proteins TPX2, Eg5 and Bora, as well as disrupted the mitotic spindle formation in HeLa cells. Molecular docking studies indicated that compound 22 well interact with both Aurora A and B. The results showed that compound 22 is a potential anticancer agent as promising pan-Aurora kinase inhibitor.
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Affiliation(s)
- You-Zhen Ma
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Zhen-Bo Tang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Chun-Yan Sang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Zhi-Yuan Qi
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Ling Hui
- Experimental Center of Medicine, General Hospital of Lanzhou Military Command, Lanzhou 730050, China; Key Laboratory of Stem Cells and Gene Drug of Gansu Province, General Hospital of Lanzhou Military Command, Lanzhou 730050, China
| | - Shi-Wu Chen
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
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7
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Sang CY, Qin WW, Zhang XJ, Xu Y, Ma YZ, Wang XR, Hui L, Chen SW. Synthesis and identification of 2,4-bisanilinopyrimidines bearing 2,2,6,6-tetramethylpiperidine-N-oxyl as potential Aurora A inhibitors. Bioorg Med Chem 2019; 27:65-78. [DOI: 10.1016/j.bmc.2018.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/16/2018] [Accepted: 11/05/2018] [Indexed: 12/26/2022]
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8
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Bottini A, Wu B, Barile E, De SK, Leone M, Pellecchia M. High-Throughput Screening (HTS) by NMR Guided Identification of Novel Agents Targeting the Protein Docking Domain of YopH. ChemMedChem 2015; 11:919-27. [PMID: 26592695 DOI: 10.1002/cmdc.201500441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/08/2022]
Abstract
Recently we described a novel approach, named high-throughput screening (HTS) by NMR that allows the identification, from large combinatorial peptide libraries, of potent and selective peptide mimetics against a given target. Here, we deployed the "HTS by NMR" approach for the design of novel peptoid sequences targeting the N-terminal domain of Yersinia outer protein H (YopH-NT), a bacterial toxin essential for the virulence of Yersinia pestis. We aimed at disrupting the protein-protein interactions between YopH-NT and its cellular substrates, with the goal of inhibiting indirectly YopH enzymatic function. These studies resulted in a novel agent of sequence Ac-F-pY-cPG-d-P-NH2 (pY=phosphotyrosine; cPG=cyclopentyl glycine) with a Kd value against YopH-NT of 310 nm. We demonstrated that such a pharmacological inhibitor of YopH-NT results in the inhibition of the dephosphorylation by full-length YopH of a cellular substrate. Hence, potentially this agent represents a valuable stepping stone for the development of novel therapeutics against Yersinia infections. The data reported further demonstrate the utility of the HTS by NMR approach in deriving novel peptide mimetics targeting protein-protein interactions.
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Affiliation(s)
- Angel Bottini
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Sanford Burnham Prebys Graduate School of Biomedical Sciences, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bainan Wu
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Elisa Barile
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Surya K De
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Marilisa Leone
- Institute of Biostructures & Bioimaging, National Research Council (IBB-CNR), Via De Amicis 95, Naples, 80145, Italy
| | - Maurizio Pellecchia
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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9
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Paudyal MP, Wu L, Zhang ZY, Spilling CD, Wong CF. A new class of salicylic acid derivatives for inhibiting YopH of Yersinia pestis. Bioorg Med Chem 2014; 22:6781-8. [PMID: 25468042 DOI: 10.1016/j.bmc.2014.10.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/23/2014] [Accepted: 10/30/2014] [Indexed: 01/26/2023]
Abstract
Previously, we identified a class of salicylic acid derivatives that display inhibitory activity against the protein tyrosine phosphatase YopH from Yersinia pestis. Because docking study suggested that the large phenyl ring attaching to the salicylic acid core might be exposed to the solvent and might not contribute significantly to binding, we have developed a new class of compounds that no longer contain this phenyl ring. We first devised a synthetic scheme for the compounds and then developed an automated computational screening model surrounding this synthetic scheme to help select a small number of compounds for synthesis and experimental testing. Based on this computational screening model and the analysis of the structure-activity relationship of our previous class of compounds, we have synthesized eight compounds and found five that yield micromolar activity. When applying in a larger scale, the synthetic scheme and the computational screening model developed here should help to identify even more potent inhibitors in the future.
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10
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Barile E, Pellecchia M. NMR-based approaches for the identification and optimization of inhibitors of protein-protein interactions. Chem Rev 2014; 114:4749-63. [PMID: 24712885 PMCID: PMC4027952 DOI: 10.1021/cr500043b] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Elisa Barile
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maurizio Pellecchia
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
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Abstract
SIGNIFICANCE Protein tyrosine phosphatases (PTPs) are important enzymes that are involved in the regulation of cellular signaling. Evidence accumulated over the years has indicated that PTPs present exciting opportunities for drug discovery against diseases such as diabetes, cancer, autoimmune diseases, and tuberculosis. However, the highly conserved and partially positive charge of the catalytic sites of PTPs is a major challenge in the development of potent and highly selective PTP inhibitors. RECENT ADVANCES Here, we examine the strategy of developing bidentate inhibitors for selective inhibition of PTPs. Bidentate inhibitors are small-molecular-weight compounds with the ability to bind to both the active site and a non-conserved secondary phosphate binding site. This secondary phosphate binding site was initially discovered in protein tyrosine phosphatase 1B (PTP1B), and, hence, most of the bidentate inhibitors reported in this review are PTP1B inhibitors. CRITICAL ISSUES Although bidentate inhibition is a good strategy for developing potent and selective inhibitors, the cell membrane permeability and pharmacokinetic properties of the inhibitors are also important for successful drug development. In this review, we will also summarize the various efforts made toward the development of phosphotyrosine (pTyr) mimetics for increasing cellular permeability. FUTURE DIRECTIONS Even though the secondary phosphate binding site was initially found in PTP1B, structural data have shown that a secondary binding site can also be found in other PTPs, albeit with varying degrees of accessibility. Along with improvements in pTyr mimetics, we believe that the future will see an increase in the number of orally bioavailable bidentate inhibitors against the various classes of PTPs.
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Affiliation(s)
- Joo-Leng Low
- 1 Institute of Chemical and Engineering Sciences , Agency for Science Technology and Research, Singapore, Singapore
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12
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Harner MJ, Frank AO, Fesik SW. Fragment-based drug discovery using NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2013; 56:65-75. [PMID: 23686385 PMCID: PMC3699969 DOI: 10.1007/s10858-013-9740-z] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/03/2013] [Indexed: 05/04/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience.
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Affiliation(s)
- Mary J Harner
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Ave, 607 Light Hall, Nashville, TN 37232-0146, USA
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Schwardt O, Kelm S, Ernst B. SIGLEC-4 (MAG) Antagonists: From the Natural Carbohydrate Epitope to Glycomimetics. Top Curr Chem (Cham) 2013; 367:151-200. [DOI: 10.1007/128_2013_498] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Small molecule screening for inhibitors of the YopH phosphatase of Yersinia pseudotuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 954:357-63. [PMID: 22782782 DOI: 10.1007/978-1-4614-3561-7_43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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15
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Noberini R, De SK, Zhang Z, Wu B, Raveendra-Panickar D, Chen V, Vazquez J, Qin H, Song J, Cosford NDP, Pellecchia M, Pasquale EB. A disalicylic acid-furanyl derivative inhibits ephrin binding to a subset of Eph receptors. Chem Biol Drug Des 2011; 78:667-78. [PMID: 21791013 DOI: 10.1111/j.1747-0285.2011.01199.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Eph receptor tyrosine kinases and ephrin ligands control many physiological and pathological processes, and molecules interfering with their interaction are useful probes to elucidate their complex biological functions. Moreover, targeting Eph receptors might enable new strategies to inhibit cancer progression and pathological angiogenesis as well as promote nerve regeneration. Because our previous work suggested the importance of the salicylic acid group in antagonistic small molecules targeting Eph receptors, we screened a series of salicylic acid derivatives to identify novel Eph receptor antagonists. This identified a disalicylic acid-furanyl derivative that inhibits ephrin-A5 binding to EphA4 with an IC(50) of 3 μm in ELISAs. This compound, which appears to bind to the ephrin-binding pocket of EphA4, also targets several other Eph receptors. Furthermore, it inhibits EphA2 and EphA4 tyrosine phosphorylation in cells stimulated with ephrin while not affecting phosphorylation of EphB2, which is not a target receptor. In endothelial cells, the disalicylic acid-furanyl derivative inhibits EphA2 phosphorylation in response to TNFα and capillary-like tube formation on Matrigel, two effects that depend on EphA2 interaction with endogenous ephrin-A1. These findings suggest that salicylic acid derivatives could be used as starting points to design new small molecule antagonists of Eph receptors.
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Affiliation(s)
- Roberta Noberini
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.
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Leone M, Barile E, Dahl R, Pellecchia M. Design and NMR studies of cyclic peptides targeting the N-terminal domain of the protein tyrosine phosphatase YopH. Chem Biol Drug Des 2011; 77:12-9. [PMID: 21118379 PMCID: PMC3149900 DOI: 10.1111/j.1747-0285.2010.01058.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report on the design and evaluation of novel cyclic peptides targeting the N-terminal domain of the protein tyrosine phosphatase YopH from Yersinia. Cyclic peptides have been designed based on a short sequence from the protein SKAP-HOM [DE(pY)DDPF (pY=phosphotyrosine)], and they all contain the motif DEZXDPfK (where Z is a phosphotyrosine or a non-hydrolyzable phosphotyrosine mimetic, X is an aspartic acid or a leucine and f is a d-phenylalanine). These peptides present a 'head to tail' architecture, enabling cyclization through formation of an amide bond in between the side chains of the first aspartic acid and the lysine residues. Chemical shift perturbation studies have been carried out to monitor the binding of these peptides to the N-terminal domain of YopH. Peptides containing a phosphotyrosine moiety exhibit binding affinities in the low micromolar range; substitution of the phosphotyrosine with one of its non-hydrolyzable derivatives dramatically reduces the binding affinities. These preliminary studies may pave the way for the discovery of more potent and selective peptide-based ligands of the YopH N-terminal domain which could be further investigated for their ability to inhibit Yersiniae infections.
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Affiliation(s)
- Marilisa Leone
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Elisa Barile
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Russell Dahl
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Maurizio Pellecchia
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
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Shelke S, Cutting B, Jiang X, Koliwer-Brandl H, Strasser D, Schwardt O, Kelm S, Ernst B. A Fragment-Based In Situ Combinatorial Approach To Identify High-Affinity Ligands for Unknown Binding Sites. Angew Chem Int Ed Engl 2010; 49:5721-5. [DOI: 10.1002/anie.200907254] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Shelke S, Cutting B, Jiang X, Koliwer-Brandl H, Strasser D, Schwardt O, Kelm S, Ernst B. A Fragment-Based In Situ Combinatorial Approach To Identify High-Affinity Ligands for Unknown Binding Sites. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Leone M, Barile E, Vazquez J, Mei A, Guiney D, Dahl R, Pellecchia M. NMR-based design and evaluation of novel bidentate inhibitors of the protein tyrosine phosphatase YopH. Chem Biol Drug Des 2010; 76:10-6. [PMID: 20456369 PMCID: PMC2905849 DOI: 10.1111/j.1747-0285.2010.00982.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We describe the use of a furanyl salicyl nitroxide derivative ('spin-labeled' compound), as a paramagnetic phosphotyrosine mimetic, to carry out a second-site screening by NMR against the PTPase YopH from Yersinia pestis. Using such a fragment-based screening approach we identified several small molecules targeting YopH that bind at sites adjacent to the spin-labeled compound. These second-site fragments were subsequently used to design and synthesize bidentate YopH inhibitors with submicromolar in vitro inhibition, selectivity against the human PTPase PTP1B, and cellular activity against Y. pseudotuberculosis. These initial compounds could result useful in elucidating the structural determinants necessary for YopH inhibition and may help in the design of even more active, selective and cell permeable compounds for the development of novel therapies against Yersiniae.
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Affiliation(s)
- Marilisa Leone
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Elisa Barile
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Jesus Vazquez
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Angel Mei
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Donald Guiney
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Russel Dahl
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Maurizio Pellecchia
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
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Le Calvez PB, Scott CJ, Migaud ME. Multisubstrate adduct inhibitors: drug design and biological tools. J Enzyme Inhib Med Chem 2010; 24:1291-318. [PMID: 19912064 DOI: 10.3109/14756360902843809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In drug discovery, different methods exist to create new inhibitors possessing satisfactory biological activity. The multisubstrate adduct inhibitor (MAI) approach is one of these methods, which consists of a covalent combination between analogs of the substrate and the cofactor or of the multiple substrates used by the target enzyme. Adopted as the first line of investigation for many enzymes, this method has brought insights into the enzymatic mechanism, structure, and inhibitory requirements. In this review, the MAI approach, applied to different classes of enzyme, is reported from the point of view of biological activity.
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Vovk AI, Kononets LA, Tanchuk VY, Cherenok SO, Drapailo AB, Kalchenko VI, Kukhar VP. Inhibition of Yersinia protein tyrosine phosphatase by phosphonate derivatives of calixarenes. Bioorg Med Chem Lett 2010; 20:483-7. [DOI: 10.1016/j.bmcl.2009.11.126] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/20/2009] [Accepted: 11/21/2009] [Indexed: 01/22/2023]
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22
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Bertini I, Calderone V, Fragai M, Luchinat C, Talluri E. Structural basis of serine/threonine phosphatase inhibition by the archetypal small molecules cantharidin and norcantharidin. J Med Chem 2009; 52:4838-43. [PMID: 19601647 DOI: 10.1021/jm900610k] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The inhibition of a subgroup of human serine/threonine protein phosphatases is responsible for the cytotoxicity of cantharidin and norcantharidin against tumor cells. It is shown that the anhydride rings of cantharidin and norcantharidin are hydrolyzed when bound to the catalytic domain of the human serine/threonine protein phosphatases 5 (PP5c), and the high-resolution crystal structures of PP5c complexed with the corresponding dicarboxylic acid derivatives of the two molecules are reported. Norcantharidin shows a unique binding conformation with the catalytically active Mn2PP5c, while cantharidin is characterized by a double conformation in its binding mode to the protein. Different binding modes of norcantharidin are observed depending of whether the starting ligand is in the anhydride or in the dicarboxylic acid form. All these structures will provide the basis for the rational design of new cantharidin-based drugs.
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Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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23
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Abstract
In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility.
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Vazquez J, De SK, Chen LH, Riel-Mehan M, Emdadi A, Cellitti J, Stebbins JL, Rega MF, Pellecchia M. Development of paramagnetic probes for molecular recognition studies in protein kinases. J Med Chem 2008; 51:3460-5. [PMID: 18494454 DOI: 10.1021/jm800068w] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We report on the synthesis and evaluation of an indazole-spin-labeled compound that was designed as an effective chemical probe for second site screening against the protein kinase JNK using NMR-based techniques. We demonstrate the utility of the derived compound in detecting and characterizing binding events at the protein kinase docking site. In addition, we report on the NMR-based design and synthesis of a bidentate compound spanning both the ATP site and the docking site. We show that the resulting compound has nanomolar affinity for JNK despite the relatively weak affinities of the individual fragments that constitute it. The approach demonstrates that targeting the docking site of protein kinases represents a valuable yet unexplored avenue to obtain potent kinase inhibitors with increased selectivity.
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Affiliation(s)
- Jesus Vazquez
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA
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25
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Ling Q, Huang Y, Zhou Y, Cai Z, Xiong B, Zhang Y, Ma L, Wang X, Li X, Li J, Shen J. Illudalic acid as a potential LAR inhibitor: synthesis, SAR, and preliminary studies on the mechanism of action. Bioorg Med Chem 2008; 16:7399-409. [PMID: 18579388 DOI: 10.1016/j.bmc.2008.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 06/08/2008] [Accepted: 06/10/2008] [Indexed: 11/30/2022]
Abstract
A novel synthesis of the human leukocyte common antigen-related (LAR) phosphatase inhibitor, illudalic acid, has been achieved by a route more amenable to structure modifications. A series of simpler analogues of illudalic acid was synthesized and evaluated for potency in inhibiting LAR. The structure-activity relationship (SAR) study has shown that the 5-formyl group and the hemi-acetal lactone are crucial for effective inhibition of LAR activity, and are the key pharmacophores of illudalic acid. The fused dimethylcyclopentene ring moiety evidently helps to enhance the potency of illudalic acid against LAR. A preliminary study of the mechanism of action of illudalic acid against LAR was conducted using electrospray ionization mass spectrometry (ESI-MS) and molecular docking techniques. The results are in full agreement with the described mechanism.
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Affiliation(s)
- Qing Ling
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China
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Arendt Y, Bhaumik A, Del Conte R, Luchinat C, Mori M, Porcu M. Fragment Docking to S100 Proteins Reveals a Wide Diversity of Weak Interaction Sites. ChemMedChem 2007; 2:1648-54. [PMID: 17705319 DOI: 10.1002/cmdc.200700096] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The S100 protein family is a highly conserved group of Ca(2+)-binding proteins that belong to the EF-hand type and are considered potential drug targets. In the present study we focused our attention on two members of the family: S100A13 and S100B; the former is involved in the nonclassical protein release of two proangiogenic polypeptides FGF-1 and IL-1alpha that are involved in inflammatory processes, whereas S100B is known to interact with the C-terminal domain of the intracellular tumor suppressor p53 and promote cancer development. We screened, using waterLOGSY NMR experiments, 430 molecules of a generic fragment library and we identified different hits for each protein. The subset of fragments interacting with S100B has very few members in common with the subset interacting with S100A13. From the (15)N-HSQC NMR spectra of the proteins in the presence of those hits the chemical shift differences Deltadelta(HN) were calculated, and the main regions of surface interaction were identified. A relatively large variety of interaction regions for various ligands were identified for the two proteins, including known or suggested protein-protein interaction sites.
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Affiliation(s)
- Yvonne Arendt
- ProtEra S.r.l. University Scientific Campus viale delle Idee, 22, 50019 Sesto Fiorentino FI, Italy
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Jahnke W. Perspectives of biomolecular NMR in drug discovery: the blessing and curse of versatility. JOURNAL OF BIOMOLECULAR NMR 2007; 39:87-90. [PMID: 17701274 DOI: 10.1007/s10858-007-9183-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 07/12/2007] [Indexed: 05/16/2023]
Abstract
The versatility of NMR and its broad applicability to several stages in the drug discovery process is well known and generally considered one of the major strengths of NMR (Pellecchia et al., Nature Rev Drug Discov 1:211-219, 2002; Stockman and Dalvit, Prog Nucl Magn Reson Spectrosc 41:187-231, 2002; Lepre et al., Comb Chem High throughput screen 5:583-590, 2002; Wyss et al., Curr Opin Drug Discov Devel 5:630-647, 2002; Jahnke and Widmer, Cell Mol Life Sci 61:580-599, 2004; Huth et al., Methods Enzymol 394:549-571, 2005b; Klages et al., Mol Biosyst 2:318-332, 2006; Takeuchi and Wagner, Curr Opin Struct Biol 16:109-117, 2006; Zartler and Shapiro, Curr Pharm Des 12:3963-3972, 2006). Indeed, NMR is the only biophysical technique which can detect and quantify molecular interactions, and at the same time provide detailed structural information with atomic level resolution. NMR should therefore be ideally suited and widely requested as a tool for drug discovery research, and numerous examples of drug discovery projects which have substantially benefited from NMR contributions or were even driven by NMR have been described in the literature. However, not all pharmaceutical companies have rigorously implemented NMR as integral tool of their research processes. Some companies invest with limited resources, and others do not use biomolecular NMR at all. This discrepancy in assessing the value of a technology is striking, and calls for clarification--under which circumstances can NMR provide added value to the drug discovery process? What kind of contributions can NMR make, and how is it implemented and integrated for maximum impact? This perspectives article suggests key areas of impact for NMR, and a model of integrating NMR with other technologies to realize synergies and maximize their value for drug discovery.
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Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Discovery Technologies, Basel 4002, Switzerland.
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