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A Malik A, Dangroo NA, Kaur P, Attery S, A Rather M, Khan A, Ara T, Nandanwar H. Discovery of novel dihydronaphthalene-imidazole ligands as potential inhibitors of Staphylococcus aureus multidrug resistant NorA efflux pump: A combination of experimental and in silico molecular docking studies. Microb Pathog 2024; 190:106627. [PMID: 38521473 DOI: 10.1016/j.micpath.2024.106627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Overexpression of the efflux pump is a predominant mechanism by which bacteria show antimicrobial resistance (AMR) and leads to the global emergence of multidrug resistance (MDR). In this work, the inhibitory potential of library of dihydronapthyl scaffold-based imidazole derivatives having structural resemblances with some known efflux pump inhibitors (EPI) were designed, synthesized and evaluated against efflux pump inhibitor against overexpressing bacterial strains to study the synergistic effect of compounds and antibiotics. Out of 15 compounds, four compounds (Dz-1, Dz-3, Dz-7, and Dz-8) were found to be highly active. DZ-3 modulated the MIC of ciprofloxacin, erythromycin, and tetracycline by 128-fold each against 1199B, XU212 and RN4220 strains of S. aureus respectively. DZ-3 also potentiated tetracycline by 64-fold in E. coli AG100 strain. DZ-7 modulated the MIC of both tetracycline and erythromycin 128-fold each in S. aureus XU212 and S. aureus RN4220 strains. DZ-1 and DZ-8 showed the moderate reduction in MIC of tetracycline in E. coli AG100 only by 16-fold and 8-fold, respectively. DZ-3 was found to be the potential inhibitor of NorA as determined by ethidium bromide efflux inhibition and accumulation studies employing NorA overexpressing strain SA-1199B. DZ-3 displayed EPI activity at non-cytotoxic concentration to human cells and did not possess any antibacterial activity. Furthermore, molecular docking studies of DZ-3 was carried out in order to understand the possible binding sites of DZ-3 with the active site of the protein. These studies indicate that dihydronaphthalene scaffolds could serve as valuable cores for the development of promising EPIs.
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Affiliation(s)
- Asif A Malik
- Department of Chemistry, National Institute of Technology, Srinagar, J&K, 190006, India
| | - Nisar A Dangroo
- Department of Chemistry, Islamic University of Science and Technology, Awantipora, J &K, 192122, India.
| | - Parminder Kaur
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Shobit Attery
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Manzoor A Rather
- Department of Chemistry, Islamic University of Science and Technology, Awantipora, J &K, 192122, India.
| | - Abrar Khan
- Department of Chemistry, National Institute of Technology, Srinagar, J&K, 190006, India
| | - Tabassum Ara
- Department of Chemistry, National Institute of Technology, Srinagar, J&K, 190006, India.
| | - Hemraj Nandanwar
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India.
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2
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Conrad J, Paras NA, Vaz RJ. Model of P-Glycoprotein Ligand Binding and Validation with Efflux Substrate Matched Pairs. J Med Chem 2024; 67:5854-5865. [PMID: 38544305 PMCID: PMC11017244 DOI: 10.1021/acs.jmedchem.4c00139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The blood-brain barrier (BBB) poses a significant obstacle in developing therapeutics for neurodegenerative diseases and central nervous system (CNS) disorders. P-glycoprotein (P-gp), a multidrug resistance protein, is a critical gatekeeper in the BBB and plays a role in cancer chemoresistance. This paper uses cryo-EM P-gp structures as starting points with an induced fit docking (IFD) model to evaluate 19 pairs of compounds with known P-gp efflux data. The study reveals significant differences in binding energy and sheds light on structural modifications' impact on efflux properties. In the cases examined, fluorine incorporation influences the efflux by altering the molecular conformation rather than proximal heteroatom basicity. Although there are limitations in addressing covalent interactions or when binding extends into the more flexible vestibule region of the protein, the results provide valuable insights and potential strategies to overcome P-gp efflux, contributing to the advancement of drug development for both CNS disorders and cancer therapies.
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Affiliation(s)
- Jay Conrad
- Institute
for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Nick A. Paras
- Institute
for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Roy J. Vaz
- Institute
for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158, United States
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3
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Peytam F, Emamgholipour Z, Mousavi A, Moradi M, Foroumadi R, Firoozpour L, Divsalar F, Safavi M, Foroumadi A. Imidazopyridine-based kinase inhibitors as potential anticancer agents: A review. Bioorg Chem 2023; 140:106831. [PMID: 37683538 DOI: 10.1016/j.bioorg.2023.106831] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Considering the fundamental role of protein kinases in the mechanism of protein phosphorylation in critical cellular processes, their dysregulation, especially in cancers, has underscored their therapeutic relevance. Imidazopyridines represent versatile scaffolds found in abundant bioactive compounds. Given their structural features, imidazopyridines have possessed pivotal potency to interact with different protein kinases, inspiring researchers to carry out numerous structural variations. In this comprehensive review, we encompass an extensive survey of the design and biological evaluations of imidazopyridine-based small molecules as potential agents targeting diverse kinases for anticancer applications. We describe the structural elements critical to inhibitory potency, elucidating their key structure-activity relationships (SAR) and mode of actions, where available. We classify these compounds into two groups: Serine/threonine and Tyrosine inhibitors. By highlighting the promising role of imidazopyridines in kinase inhibition, we aim to facilitate the design and development of more effective, targeted compounds for cancer treatment.
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Affiliation(s)
- Fariba Peytam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Emamgholipour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mousavi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahfam Moradi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Roham Foroumadi
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Loghman Firoozpour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Divsalar
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran; Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
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4
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Emadi R, Bahrami Nekoo A, Molaverdi F, Khorsandi Z, Sheibani R, Sadeghi-Aliabadi H. Applications of palladium-catalyzed C-N cross-coupling reactions in pharmaceutical compounds. RSC Adv 2023; 13:18715-18733. [PMID: 37346956 PMCID: PMC10280806 DOI: 10.1039/d2ra07412e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
C-N cross-coupling bond formation reactions have become valuable approaches to synthesizing anilines and their derivatives, known as important chemical compounds. Recent developments in this field have focused on versatile catalysts, simple operation methods, and green reaction conditions. This review article presents an overview of C-N cross-coupling reactions in pharmaceutical compound synthesis reports. Selected examples of N-arylation reactions of various nitrogen-based compounds and aryl halides are defined for preparing pharmaceutical molecules.
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Affiliation(s)
- Reza Emadi
- Department of Biochemistry, Institute of Biochemistry & Biophysics (IBB), University of Tehran Tehran Iran
| | - Abbas Bahrami Nekoo
- Nanoalvand Pharmaceutical Company, Department of Quality Control, Unit of Raw Materials Simindasht Alborz Iran
| | - Fatemeh Molaverdi
- Department of Organic Chemistry, School of Chemistry, College of Science, Tehran University Tehran Islamic Republic of Iran
| | - Zahra Khorsandi
- Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences Isfahan 81746-73461 Iran
| | - Reza Sheibani
- Amirkabir University of Technology-Mahshahr Campus University St., Nahiyeh san'ati Mahshahr Khouzestan Iran
| | - Hojjat Sadeghi-Aliabadi
- Pharmaceutical Sciences Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences Isfahan 81746-73461 Iran
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5
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Application of Chiral Piperidine Scaffolds in Drug Design. PHARMACEUTICAL FRONTS 2023. [DOI: 10.1055/s-0043-1764218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Chiral piperidine scaffolds are prevalent as the common cores of a large number of active pharmaceuticals in medical chemistry. This review outlined the diversity of chiral piperidine scaffolds in recently approved drugs, and also covers the scaffolds in leads and drug candidates. The significance of chiral piperidine scaffolds in drug design is also discussed in this article. With the introduction of chiral piperidine scaffolds into small molecules, the exploration of drug-like molecules can be benefitted from the following aspect: (1) modulating the physicochemical properties; (2) enhancing the biological activities and selectivity; (3) improving pharmacokinetic properties; and (4) reducing the cardiac hERG toxicity. Given above, chiral piperidine-based discovery of small molecules will be a promising strategy to enrich our molecules' library to fight against diseases.
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6
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Tetramethylammonium Fluoride: Fundamental Properties and Applications in C-F Bond-Forming Reactions and as a Base. Catalysts 2022. [DOI: 10.3390/catal12020233] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nucleophilic ionic sources of fluoride are essential reagents in the synthetic toolbox to access high added-value fluorinated building blocks unattainable by other means. In this review, we provide a concise description and rationale of the outstanding features of one of these reagents, tetramethylammonium fluoride (TMAF), as well as disclosing the different methods for its preparation, and how its physicochemical properties and solvation effects in different solvents are intimately associated with its reactivity. Furthermore, herein we also comprehensively describe its historic and recent utilization, up to December 2021, in C-F bond-forming reactions with special emphasis on nucleophilic aromatic substitution fluorinations with a potential sustainable application in industrial settings, as well as its use as a base capable of rendering unprecedented transformations.
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7
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Gilbert A, Langowski P, Paquin JF. Synthesis of N-(2-SF5-ethyl)amines and impact of the SF5 substituent on their basicity and lipophilicity. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Qami AE, Jismy B, El Hakmaoui A, Akssira M, Abarbri M. Cu/Pd‐Catalyzed One‐Pot Synthesis of 2‐(1,2,3‐Triazolyl)methyl‐3‐alkynylImidazo[1,2‐
a
]pyridines Involving Sequential SN Reaction/[3+2] Cycloaddition/Sonogashira Coupling Reactions. ChemistrySelect 2021. [DOI: 10.1002/slct.202102228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Abdelkarim El Qami
- Department of chemistry Université de Tours. Laboratoire de Physico-Chimie des Matériaux et des Electrolytes pour l'Energie (PCM2E) EA 6299 Avenue Monge, Faculté des Sciences, Parc de Grandmont 37200 Tours France
- Department of chemistry Université Hassan II de Casablanca Laboratoire de Chimie Physique et de Chimie Bioorganique, URAC 22 BP Casablanca, 146 28800 Mohammedia Morocco
| | - Badr Jismy
- Department of chemistry Université de Tours. Laboratoire de Physico-Chimie des Matériaux et des Electrolytes pour l'Energie (PCM2E) EA 6299 Avenue Monge, Faculté des Sciences, Parc de Grandmont 37200 Tours France
| | - Ahmed El Hakmaoui
- Department of chemistry Université Hassan II de Casablanca Laboratoire de Chimie Physique et de Chimie Bioorganique, URAC 22 BP Casablanca, 146 28800 Mohammedia Morocco
| | - Mohamed Akssira
- Department of chemistry Université Hassan II de Casablanca Laboratoire de Chimie Physique et de Chimie Bioorganique, URAC 22 BP Casablanca, 146 28800 Mohammedia Morocco
| | - Mohamed Abarbri
- Department of chemistry Université de Tours. Laboratoire de Physico-Chimie des Matériaux et des Electrolytes pour l'Energie (PCM2E) EA 6299 Avenue Monge, Faculté des Sciences, Parc de Grandmont 37200 Tours France
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9
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Almeida AF, Ataíde FAP, Loureiro RMS, Moreira R, Rodrigues T. Augmenting Adaptive Machine Learning with Kinetic Modeling for Reaction Optimization. J Org Chem 2021; 86:14192-14198. [PMID: 34235919 DOI: 10.1021/acs.joc.1c01038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We combine random sampling and active machine learning (ML) to optimize the synthesis of isomacroin, executing only 3% of all possible Friedländer reactions. Employing kinetic modeling, we augment machine intuition by extracting mechanistic knowledge and verify that a global optimum was obtained with ML. Our study contributes evidence on the potential of multiscale approaches to expedite the access to chemical matter, further democratizing organic chemistry in a data-motivated fashion.
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Affiliation(s)
- A Filipa Almeida
- R&D, Process Chemistry Development, Hovione FarmaCiência S.A, Campus do Lumiar, Building S 1649-038 Lisboa, Portugal.,Research Institute for Medicines (iMed.Ulisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Filipe A P Ataíde
- R&D, Process Chemistry Development, Hovione FarmaCiência S.A, Campus do Lumiar, Building S 1649-038 Lisboa, Portugal
| | - Rui M S Loureiro
- R&D, Process Chemistry Development, Hovione FarmaCiência S.A, Campus do Lumiar, Building S 1649-038 Lisboa, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.Ulisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Tiago Rodrigues
- Research Institute for Medicines (iMed.Ulisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
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10
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Trost BM, Tracy JS, Yusoontorn T, Hung CJ. Acyclic Branched α‐Fluoro Ketones for the Direct Asymmetric Mannich Reaction Leading to the Synthesis of β‐Tetrasubstituted β‐Fluoro Amines. Angew Chem Int Ed Engl 2020; 59:2370-2374. [DOI: 10.1002/anie.201913927] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Barry M. Trost
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
| | - Jacob S. Tracy
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
| | - Tas Yusoontorn
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
| | - Chao‐I Joey Hung
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
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11
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Trost BM, Tracy JS, Yusoontorn T, Hung CJ. Acyclic Branched α‐Fluoro Ketones for the Direct Asymmetric Mannich Reaction Leading to the Synthesis of β‐Tetrasubstituted β‐Fluoro Amines. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Barry M. Trost
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
| | - Jacob S. Tracy
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
| | - Tas Yusoontorn
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
| | - Chao‐I Joey Hung
- Department of ChemistryStanford University 333 Campus Dr Stanford CA 94305 USA
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12
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A Toolbox for the Identification of Modes of Action of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 110 2019; 110:73-97. [DOI: 10.1007/978-3-030-14632-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Fjelbye K, Marigo M, Clausen RP, Jørgensen EB, Christoffersen CT, Juhl K. Elucidation of fluorine's impact on p Ka and in vitro Pgp-mediated efflux for a series of PDE9 inhibitors. MEDCHEMCOMM 2018; 9:893-896. [PMID: 30108979 DOI: 10.1039/c8md00114f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/15/2018] [Indexed: 01/04/2023]
Abstract
P-Glycoprotein (Pgp)-mediated cellular efflux is recognized as a common challenge in CNS drug discovery. In this study, the influence of replacing a hydrogen atom with fluorine on the pKa and Pgp-mediated efflux is elucidated for a series of PDE9 inhibitors. The PDE9 inhibitors with and without fluorine were synthesized using a novel condensation-oxidation approach, providing access to several analogues, all from the same stereoenriched aldehyde building block. The incorporation of fluorine was found to influence two acid-base functionalities concomitantly, both of which were involved in Pgp-recognition. By methylating the acidic functionality, it was possible to isolate the effect responsible for lowering the Pgp-mediated efflux.
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Affiliation(s)
- Kasper Fjelbye
- H. Lundbeck A/S , Ottiliavej 9 , 2500 Valby , Denmark . .,Department of Drug Design and Pharmacology , Faculty of Health and Medical Sciences , University of Copenhagen , 2 Universitetsparken , 2100 , Copenhagen , Denmark
| | - Mauro Marigo
- H. Lundbeck A/S , Ottiliavej 9 , 2500 Valby , Denmark .
| | - Rasmus P Clausen
- Department of Drug Design and Pharmacology , Faculty of Health and Medical Sciences , University of Copenhagen , 2 Universitetsparken , 2100 , Copenhagen , Denmark
| | | | | | - Karsten Juhl
- H. Lundbeck A/S , Ottiliavej 9 , 2500 Valby , Denmark .
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14
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Rutaganira FU, Barks J, Dhason MS, Wang Q, Lopez MS, Long S, Radke JB, Jones NG, Maddirala AR, Janetka JW, El Bakkouri M, Hui R, Shokat KM, Sibley LD. Inhibition of Calcium Dependent Protein Kinase 1 (CDPK1) by Pyrazolopyrimidine Analogs Decreases Establishment and Reoccurrence of Central Nervous System Disease by Toxoplasma gondii. J Med Chem 2017; 60:9976-9989. [PMID: 28933846 DOI: 10.1021/acs.jmedchem.7b01192] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Calcium dependent protein kinase 1 (CDPK1) is an essential enzyme in the opportunistic pathogen Toxoplasma gondii. CDPK1 controls multiple processes that are critical to the intracellular replicative cycle of T. gondii including secretion of adhesins, motility, invasion, and egress. Remarkably, CDPK1 contains a small glycine gatekeeper residue in the ATP binding pocket making it sensitive to ATP-competitive inhibitors with bulky substituents that complement this expanded binding pocket. Here we explored structure-activity relationships of a series of pyrazolopyrimidine inhibitors of CDPK1 with the goal of increasing selectivity over host enzymes, improving antiparasite potency, and improving metabolic stability. The resulting lead compound 24 exhibited excellent enzyme inhibition and selectivity for CDPK1 and potently inhibited parasite growth in vitro. Compound 24 was also effective at treating acute toxoplasmosis in the mouse, reducing dissemination to the central nervous system, and decreasing reactivation of chronic infection in severely immunocompromised mice. These findings provide proof of concept for the development of small molecule inhibitors of CDPK1 for treatment of CNS toxoplasmosis.
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Affiliation(s)
- Florentine U Rutaganira
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco , San Francisco, California 94158, United States
| | - Jennifer Barks
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Mary Savari Dhason
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Qiuling Wang
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Michael S Lopez
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco , San Francisco, California 94158, United States
| | - Shaojun Long
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Joshua B Radke
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Nathaniel G Jones
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Amarendar R Maddirala
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63130, United States
| | - Majida El Bakkouri
- Structural Genomics Consortium, University of Toronto , MaRS South Tower, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Raymond Hui
- Structural Genomics Consortium, University of Toronto , MaRS South Tower, 101 College St, Toronto, ON M5G 1L7, Canada.,Toronto General Hospital Research Institute , 200 Elizabeth St., Toronto, ON M5G 2C4, Canada
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco , San Francisco, California 94158, United States
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine , St. Louis, Missouri 63130, United States
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15
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Abstract
![]()
Pd-catalyzed
cross-coupling reactions that form C–N bonds
have become useful methods to synthesize anilines and aniline derivatives,
an important class of compounds throughout chemical research. A key
factor in the widespread adoption of these methods has been the continued
development of reliable and versatile catalysts that function under
operationally simple, user-friendly conditions. This review provides
an overview of Pd-catalyzed N-arylation reactions found in both basic
and applied chemical research from 2008 to the present. Selected examples
of C–N cross-coupling reactions between nine classes of nitrogen-based
coupling partners and (pseudo)aryl halides are described for the synthesis
of heterocycles, medicinally relevant compounds, natural products,
organic materials, and catalysts.
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Affiliation(s)
- Paula Ruiz-Castillo
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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16
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Abstract
Fluorination reactions of medicinal and biologically-active compounds will be discussed. Late stage fluorination strategies of medicinal targets have recently attracted considerable attention on account of the influence that a fluorine atom can impart to targets of medicinal importance, such as modulation of lipophilicity, electronegativity, basicity and bioavailability, the latter as a consequence of membrane permeability. Therefore, the recourse to late-stage fluorine substitution on compounds with already known and relevant biological activity can provide the pharmaceutical industry with new leads with improved medicinal properties. The fluorination strategies will take into account different fluorinating reagents, either of nucleophilic or electrophilic, and of radical nature. Diverse families of organic compounds such as (hetero)aromatic rings, and aliphatic substrates (sp(3), sp(2), and sp carbon atoms) will be studied in late-stage fluorination reaction strategies.
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Affiliation(s)
- Damian E Yerien
- Departamento de Química Orgánica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires-CONICET, Junín 954 CP, 1113-Buenos Aires, Argentina.
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17
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Yan N, Fang Z, Liu QQ, Guo XH, Hu XG. Conformation-induced regioselective and divergent opening of epoxides by fluoride: facile access to hydroxylated fluoro-piperidines. Org Biomol Chem 2016; 14:3469-75. [PMID: 26971837 DOI: 10.1039/c6ob00063k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Utilizing molecular conformation as a controlling factor, epoxide-containing 2-aryl-piperidines can be ring-opened with the reagent combination of tetrabutylammonium fluoride (TBAF) and potassium bifluoride (KHF2) in a regioselective and divergent fashion. Four different types of hydroxylated fluoro-piperidines, valuable building blocks in drug development, were readily synthesized using this method. The basic nature of the reagent combination allowed a one-pot deprotection/ring opening process, which increased the efficacy of this transformation.
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Affiliation(s)
- Nan Yan
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, China.
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18
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Chen JF, Liu ZQ. Synthesis of imidazo[1,2-a]quinoxalines by double Groebke reactions and inhibitory effects on radicals and DNA oxidation. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.02.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sloman DL, Noucti N, Altman MD, Chen D, Mislak AC, Szewczak A, Hayashi M, Warren L, Dellovade T, Wu Z, Marcus J, Walker D, Su HP, Edavettal SC, Munshi S, Hutton M, Nuthall H, Stanton MG. Optimization of microtubule affinity regulating kinase (MARK) inhibitors with improved physical properties. Bioorg Med Chem Lett 2016; 26:4362-6. [PMID: 27491711 DOI: 10.1016/j.bmcl.2016.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/02/2016] [Indexed: 12/13/2022]
Abstract
Inhibition of microtubule affinity regulating kinase (MARK) represents a potentially attractive means of arresting neurofibrillary tangle pathology in Alzheimer's disease. This manuscript outlines efforts to optimize a pyrazolopyrimidine series of MARK inhibitors by focusing on improvements in potency, physical properties and attributes amenable to CNS penetration. A unique cylcyclohexyldiamine scaffold was identified that led to remarkable improvements in potency, opening up opportunities to reduce MW, Pgp efflux and improve pharmacokinetic properties while also conferring improved solubility.
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Affiliation(s)
- David L Sloman
- Discovery Chemistry, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Njamkou Noucti
- Discovery Chemistry, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Michael D Altman
- Chemistry Modeling and Informatics, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Dapeng Chen
- Drug Metabolism and Pharmacokinetics, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Andrea C Mislak
- Drug Metabolism and Pharmacokinetics, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Alexander Szewczak
- CNS Pharmacology, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Mansuo Hayashi
- CNS Pharmacology, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Lee Warren
- CNS Pharmacology, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Tammy Dellovade
- Core Pharmacology, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Zhenhua Wu
- Core Pharmacology, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Jacob Marcus
- Neuroscience Drug Discovery, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Deborah Walker
- Pharmaceutical Research and Development, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Hua-Poo Su
- Structural Biology, 770 Sumneytown Pike, West Point, PA 19486, United States
| | - Suzanne C Edavettal
- Structural Biology, 770 Sumneytown Pike, West Point, PA 19486, United States
| | - Sanjeev Munshi
- Structural Biology, 770 Sumneytown Pike, West Point, PA 19486, United States
| | - Michael Hutton
- Neuroscience Drug Discovery, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Hugh Nuthall
- Neuroscience Drug Discovery, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
| | - Matthew G Stanton
- Discovery Chemistry, Merck and Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02215, United States
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20
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Schimler SD, Ryan SJ, Bland DC, Anderson JE, Sanford MS. Anhydrous Tetramethylammonium Fluoride for Room-Temperature SNAr Fluorination. J Org Chem 2015; 80:12137-45. [DOI: 10.1021/acs.joc.5b02075] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Sydonie D. Schimler
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sarah J. Ryan
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Douglas C. Bland
- Process Science, Dow Chemical Company, 1710 Building, Midland, Michigan 48674, United States
| | - John E. Anderson
- Process Science, Dow Chemical Company, 1710 Building, Midland, Michigan 48674, United States
| | - Melanie S. Sanford
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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21
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Abstract
The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, (18)F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in positron emission tomography.
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Affiliation(s)
- Eric P Gillis
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kyle J Eastman
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Matthew D Hill
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - David J Donnelly
- Discovery Chemistry Platforms, PET Radiochemical Synthesis, Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development , 5 Research Parkway, Wallingford, Connecticut 06492, United States
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22
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Rodrigues T, Reker D, Kunze J, Schneider P, Schneider G. Revealing the Macromolecular Targets of Fragment-Like Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201504241] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Rodrigues T, Reker D, Kunze J, Schneider P, Schneider G. Revealing the Macromolecular Targets of Fragment-Like Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504241] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Liu S, Xi H, Zhang J, Wu X, Gao Q, Wu A. Organopromoted direct synthesis of 6-iodo-3-methylthioimidazo[1,2-a]pyridines via convergent integration of three self-sorting domino sequences. Org Biomol Chem 2015. [DOI: 10.1039/c5ob01313e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An NH2CN-promoted convergent integration of three self-sorting domino sequences is described for the construction of 6-iodo-3-methylthioimidazo[1,2-a]pyridines from aryl methyl ketones and 2-aminopyridines.
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Affiliation(s)
- Shan Liu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan
| | - Hailing Xi
- State Key Laboratory of NBC Protection for Civilian
- Beijing 102205
- China
| | - Jingjing Zhang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan
| | - Xia Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan
| | - Qinghe Gao
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan
| | - Anxin Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan
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25
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Horbert R, Pinchuk B, Johannes E, Schlosser J, Schmidt D, Cappel D, Totzke F, Schächtele C, Peifer C. Optimization of potent DFG-in inhibitors of platelet derived growth factor receptorβ (PDGF-Rβ) guided by water thermodynamics. J Med Chem 2014; 58:170-82. [PMID: 25007344 DOI: 10.1021/jm500373x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this study we report on the hit optimization of substituted 3,5-diaryl-pyrazin-2(1H)-ones toward potent and effective platelet-derived growth factor receptor (PDGF-R) β-inhibitors. Originally, the 3,5-diaryl-pyrazin-2-one core was derived from the marine sponge alkaloid family of hamacanthins. In our first series compound 2 was discovered as a promising hit showing strong activity against PDGF-Rβ in the kinase assay (IC50 = 0.5 μM). Furthermore, 2 was shown to be selective for PDGF-Rβ in a panel of 24 therapeutically relevant protein kinases. Molecular modeling studies on a PDGF-Rβ homology model using prediction of water thermodynamics suggested an optimization strategy for the 3,5-diaryl-pyrazin-2-ones as DFG-in binders by using a phenolic OH function to replace a structural water molecule in the ATP binding site. Indeed, we identified compound 38 as a highly potent inhibitor with an IC50 value of 0.02 μM in a PDGF-Rβ enzymatic assay also showing activity against PDGF-R dependent cancer cells.
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Affiliation(s)
- Rebecca Horbert
- Institute of Pharmacy, Christian-Albrechts-University of Kiel , Gutenbergstraße 76, D-24116 Kiel, Germany
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26
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Seerden JPG, Leusink-Ionescu G, Woudenberg-Vrenken T, Dros B, Molema G, Kamps JAAM, Kellogg RM. Synthesis and structure-activity relationships of 4-fluorophenyl-imidazole p38α MAPK, CK1δ and JAK2 kinase inhibitors. Bioorg Med Chem Lett 2014; 24:3412-8. [PMID: 24930833 DOI: 10.1016/j.bmcl.2014.05.080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 01/11/2023]
Abstract
The synthesis and structure-activity relationships of novel 4-(4'-fluorophenyl)imidazoles as selective p38α MAPK, CK1δ and JAK2 inhibitors with improved water solubility are described. Microwave-assisted multicomponent reactions afforded 4-fluorophenyl-2,5-disubstituted imidazoles. Carboxylate and phosphonate groups were introduced via 'click' reactions. The kinase selectivity was influenced by the heteroaryl group at imidazole C-5 and the position of a carboxylic acid or tetrazole at imidazole C-2. For example, pyrimidines 15 and 34 inhibited p38α MAPK with IC50=250 nM and 96 nM, respectively. Pyridine 3 gave CK1δ inhibition with IC50=89 nM and pyridin-2-one 31 gave JAK2 inhibition with IC50=62 nM.
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Affiliation(s)
| | | | - Titia Woudenberg-Vrenken
- Laboratory for Endothelial Biomedicine & Vascular Drug Targeting Research, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Bas Dros
- Syncom B.V., Kadijk 3, Groningen 9747 AT, The Netherlands
| | - Grietje Molema
- Laboratory for Endothelial Biomedicine & Vascular Drug Targeting Research, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Jan A A M Kamps
- Laboratory for Endothelial Biomedicine & Vascular Drug Targeting Research, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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