1
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Kimura R, Sato Y, Morisaki K, Nishi T. [3 + 2] cycloaddition of 1-(4-Methoxybenzyl)indoles and azaindoles with nitrile oxides. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2
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Yamada K, Mishima N, Saito K, Nishi T. Synthesis and applications of 3-bromo-2-hydroxy-1-tosylazaindolines. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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3
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Raina G, Kannaboina P, Ahmed QN, Mondal K, Das P. Palladium‐Catalyzed Barluenga‐Valdes Type Cross‐Coupling Reaction: Alkenylation of 7‐Azaindole
s. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gaurav Raina
- Medicinal Chemistry Division CSIR-Indian Institute of Integrative Medicine (IIIM) Jammu 180001 India
- Academy of Scientific and Innovative Research (AcSIR) Uttar Pradesh 201002 India
| | - Prakash Kannaboina
- Medicinal Chemistry Division CSIR-Indian Institute of Integrative Medicine (IIIM) Jammu 180001 India
- Academy of Scientific and Innovative Research (AcSIR) Uttar Pradesh 201002 India
| | - Qazi Naveed Ahmed
- Medicinal Chemistry Division CSIR-Indian Institute of Integrative Medicine (IIIM) Jammu 180001 India
- Academy of Scientific and Innovative Research (AcSIR) Uttar Pradesh 201002 India
| | - Krishanu Mondal
- Department of Chemistry Indian Institute of Technology (ISM) Dhanbad 826004 India
| | - Parthasarathi Das
- Department of Chemistry Indian Institute of Technology (ISM) Dhanbad 826004 India
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4
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Zhang M, Fang X, Wang C, Hua Y, Huang C, Wang M, Zhu L, Wang Z, Gao Y, Zhang T, Liu H, Zhang Y, Lu S, Lu T, Chen Y, Li H. Design and synthesis of 1H-indazole-3-carboxamide derivatives as potent and selective PAK1 inhibitors with anti-tumour migration and invasion activities. Eur J Med Chem 2020; 203:112517. [DOI: 10.1016/j.ejmech.2020.112517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/15/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
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5
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Computational insight into the mechanisms of action and selectivity of Afraxis PAK inhibitors. Future Med Chem 2020; 12:367-385. [PMID: 32064922 DOI: 10.4155/fmc-2019-0273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: The p21-activated kinases (PAKs) are involved in many important biological activity regulations. FRAX019, FRAX414, FRAX597, FRAX1036 and G-5555 were identified as PAKs inhibitors. Their detailed inhibitory mechanisms deserve further investigation. Results: Molecular dynamics simulations and further calculations for the PAK1/inhibitor and PAK4/inhibitor complexes indicate that their binding free energies are basically consistent with the trend of experimental activity data. Conclusion: The anchoring of residues Leu347PAK1 and Leu398PAK4 is the structural basis for designing Afraxis PAK inhibitors. This study discloses the inhibitory mechanisms of FRAX019, FRAX414, FRAX597, FRAX1036 and G-5555 toward PAK1 and PAK4 and some clues to enhance kinase activities and selectivities, which will provide valuable information to the development of more potent and selective PAK inhibitors.
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6
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Verdonck S, Pu SY, Sorrell FJ, Elkins JM, Froeyen M, Gao LJ, Prugar LI, Dorosky DE, Brannan JM, Barouch-Bentov R, Knapp S, Dye JM, Herdewijn P, Einav S, De Jonghe S. Synthesis and Structure-Activity Relationships of 3,5-Disubstituted-pyrrolo[2,3- b]pyridines as Inhibitors of Adaptor-Associated Kinase 1 with Antiviral Activity. J Med Chem 2019; 62:5810-5831. [PMID: 31136173 DOI: 10.1021/acs.jmedchem.9b00136] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
There are currently no approved drugs for the treatment of emerging viral infections, such as dengue and Ebola. Adaptor-associated kinase 1 (AAK1) is a cellular serine-threonine protein kinase that functions as a key regulator of the clathrin-associated host adaptor proteins and regulates the intracellular trafficking of multiple unrelated RNA viruses. Moreover, AAK1 is overexpressed specifically in dengue virus-infected but not bystander cells. Because AAK1 is a promising antiviral drug target, we have embarked on an optimization campaign of a previously identified 7-azaindole analogue, yielding novel pyrrolo[2,3- b]pyridines with high AAK1 affinity. The optimized compounds demonstrate improved activity against dengue virus both in vitro and in human primary dendritic cells and the unrelated Ebola virus. These findings demonstrate that targeting cellular AAK1 may represent a promising broad-spectrum antiviral strategy.
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Affiliation(s)
- Sven Verdonck
- Medicinal Chemistry, Rega Institute for Medical Research , KU Leuven , Herestraat 49-bus 1041 , 3000 Leuven , Belgium
| | - Szu-Yuan Pu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Fiona J Sorrell
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC) , University of Oxford , Old Road Campus, Roosevelt Drive , Oxford OX3 7DQ , U.K
| | - Jon M Elkins
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC) , University of Oxford , Old Road Campus, Roosevelt Drive , Oxford OX3 7DQ , U.K.,Structural Genomics Consortium , Universidade Estadual de Campinas , Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550 , Barão Geraldo, Campinas , São Paulo 13083-886 , Brazil
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research , KU Leuven , Herestraat 49-bus 1041 , 3000 Leuven , Belgium
| | - Ling-Jie Gao
- Medicinal Chemistry, Rega Institute for Medical Research , KU Leuven , Herestraat 49-bus 1041 , 3000 Leuven , Belgium
| | - Laura I Prugar
- US Army Medical Research Institute of Infectious Diseases , Viral Immunology Branch , Fort Detrick , Maryland 21702 , United States
| | - Danielle E Dorosky
- US Army Medical Research Institute of Infectious Diseases , Viral Immunology Branch , Fort Detrick , Maryland 21702 , United States
| | - Jennifer M Brannan
- US Army Medical Research Institute of Infectious Diseases , Viral Immunology Branch , Fort Detrick , Maryland 21702 , United States
| | - Rina Barouch-Bentov
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC) , University of Oxford , Old Road Campus, Roosevelt Drive , Oxford OX3 7DQ , U.K.,Institute for Pharmaceutical Chemistry, Buchmann Institute for Life Sciences Campus Riedbeerg , Goethe-University Frankfurt , 60438 Frankfurt am Main , Germany
| | - John M Dye
- US Army Medical Research Institute of Infectious Diseases , Viral Immunology Branch , Fort Detrick , Maryland 21702 , United States
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research , KU Leuven , Herestraat 49-bus 1041 , 3000 Leuven , Belgium
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Steven De Jonghe
- Medicinal Chemistry, Rega Institute for Medical Research , KU Leuven , Herestraat 49-bus 1041 , 3000 Leuven , Belgium
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7
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Biswal J, Jayaprakash P, Suresh Kumar R, Venkatraman G, Poopandi S, Rangasamy R, Jeyaraman J. Identification of Pak1 inhibitors using water thermodynamic analysis. J Biomol Struct Dyn 2019; 38:13-31. [PMID: 30661460 DOI: 10.1080/07391102.2019.1567393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
p21-activated kinases (Paks) play an integral component in various cellular diverse processes. The full activation of Pak is dependent upon several serine residues present in the N-terminal region, a threonine present at the activation loop, and finally the phosphorylation of these residues ensure the complete activation of Pak1. The present study deals with the identification of novel potent candidates of Pak1 using computational methods as anti-cancer compounds. A diverse energy based pharmacophore (e-pharmacophore) was developed using four co-crystal inhibitors of Pak1 having pharmacophore features of 5 (DRDRR), 6 (DRHADR), and 7 (RRARDRP and DRRDADH) hypotheses. These models were used for rigorous screening against e-molecule database. The obtained hits were filtered using ADME/T and molecular docking to identify the high affinity binders. These hits were subjected to hierarchical clustering using dendritic fingerprint inorder to identify structurally diverse molecules. The diverse hits were scored against generated water maps to obtain WM/MM ΔG binding energy. Furthermore, molecular dynamics simulation and density functional theory calculations were performed on the final hits to understand the stability of the complexes. Five structurally diverse novel Pak1 inhibitors (4835785, 32198676, 32407813, 76038049, and 32945545) were obtained from virtual screening, water thermodynamics and WM/MM ΔG binding energy. All hits revealed similar mode of binding pattern with the hinge region residues replacing the unstable water molecules in the binding site. The obtained novel hits could be used as a platform to design potent drugs that could be experimentally tested against cancer patients having increased Pak1 expression.
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Affiliation(s)
- Jayashree Biswal
- Department of Bioinformatics, Science Block Alagappa University, Karaikudi Tamil Nadu, India
| | - Prajisha Jayaprakash
- Department of Bioinformatics, Science Block Alagappa University, Karaikudi Tamil Nadu, India
| | - Rayala Suresh Kumar
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Ganesh Venkatraman
- Department of Human Genetics College of Biomedical Sciences, Sri Ramachandra University, Porur, Chennai, Tamil Nadu, India
| | - Saritha Poopandi
- Department of Bioinformatics, Science Block Alagappa University, Karaikudi Tamil Nadu, India
| | - Raghu Rangasamy
- Department of Bioinformatics, Science Block Alagappa University, Karaikudi Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Department of Bioinformatics, Science Block Alagappa University, Karaikudi Tamil Nadu, India
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8
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Abstract
p21-Activated kinase 1 (PAK1) has attracted much attention as a potential therapeutic target due to its central role in many oncogenic signaling pathways, its frequent dysregulation in cancers and neurological disorders, and its tractability as a target for small-molecule inhibition. To date, several PAK1-targeting compounds have been developed as preclinical agents, including one that has been evaluated in a clinical trial. A series of ATP-competitive inhibitors, allosteric inhibitors and peptide inhibitors with distinct biochemical and pharmacokinetic properties represent useful laboratory tools for studies on the role of PAK1 in biology and in disease contexts, and could lead to promising therapeutic agents. Given the central role of PAK1 in vital signaling pathways, future clinical development of PAK1 inhibitors will require careful investigation of their safety and efficacy.
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9
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McCoull W, Hennessy EJ, Blades K, Chuaqui C, Dowling JE, Ferguson AD, Goldberg FW, Howe N, Jones CR, Kemmitt PD, Lamont G, Varnes JG, Ward RA, Yang B. Optimization of Highly Kinase Selective Bis-anilino Pyrimidine PAK1 Inhibitors. ACS Med Chem Lett 2016; 7:1118-1123. [PMID: 27994749 DOI: 10.1021/acsmedchemlett.6b00322] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/14/2016] [Indexed: 12/26/2022] Open
Abstract
Group I p21-activated kinase (PAK) inhibitors are indicated as important in cancer progression, but achieving high kinase selectivity has been challenging. A bis-anilino pyrimidine PAK1 inhibitor was identified and optimized through structure-based drug design to improve PAK1 potency and achieve high kinase selectivity, giving in vitro probe compound AZ13705339 (18). Reduction of lipophilicity to lower clearance afforded AZ13711265 (14) as an in vivo probe compound with oral exposure in mouse. Such probes will allow further investigation of PAK1 biology.
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Affiliation(s)
- William McCoull
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Edward J. Hennessy
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Kevin Blades
- AstraZeneca, Alderley Park,
Macclesfield, Cheshire, SK10 4TG, U.K
| | - Claudio Chuaqui
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - James E. Dowling
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Andrew D. Ferguson
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | | | - Nicholas Howe
- AstraZeneca, Alderley Park,
Macclesfield, Cheshire, SK10 4TG, U.K
| | | | - Paul D. Kemmitt
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Gillian Lamont
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Jeffrey G. Varnes
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Richard A. Ward
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Bin Yang
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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10
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Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Sci Signal 2015; 8:rs13. [PMID: 26628682 DOI: 10.1126/scisignal.aaa6711] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kimberly L Malecka
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lauren Fink
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - E Joseph Jordan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Duffy
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Samuel Kolander
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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11
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Wilding B, Vidovic C, Klempier N. A convenient synthetic route to substituted pyrrolo[2,3-b]pyridines via a novel ethylene-bridged compound. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Crawford JJ, Lee W, Aliagas I, Mathieu S, Hoeflich KP, Zhou W, Wang W, Rouge L, Murray L, La H, Liu N, Fan PW, Cheong J, Heise CE, Ramaswamy S, Mintzer R, Liu Y, Chao Q, Rudolph J. Structure-Guided Design of Group I Selective p21-Activated Kinase Inhibitors. J Med Chem 2015; 58:5121-36. [PMID: 26030457 DOI: 10.1021/acs.jmedchem.5b00572] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The p21-activated kinases (PAKs) play important roles in cytoskeletal organization, cellular morphogenesis, and survival and have generated significant attention as potential therapeutic targets for cancer. Following a high-throughput screen, we identified an aminopyrazole scaffold-based series that was optimized to yield group I selective PAK inhibitors. A structure-based design effort aimed at targeting the ribose pocket for both potency and selectivity led to much-improved group I vs II selectivity. Early lead compounds contained a basic primary amine, which was found to be a major metabolic soft spot with in vivo clearance proceeding predominantly via N-acetylation. We succeeded in identifying replacements with improved metabolic stability, leading to compounds with lower in vivo rodent clearance and excellent group I PAK selectivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Qi Chao
- #Shanghai Chempartner Inc., 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, People's Republic of China
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13
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Rudolph J, Crawford JJ, Hoeflich KP, Wang W. Inhibitors of p21-activated kinases (PAKs). J Med Chem 2014; 58:111-29. [PMID: 25415869 DOI: 10.1021/jm501613q] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The p21-activated kinase (PAK) family of serine/threonine protein kinases plays important roles in cytoskeletal organization, cellular morphogenesis, and survival, and members of this family have been implicated in many diseases including cancer, infectious diseases, and neurological disorders. Owing to their large and flexible ATP binding cleft, PAKs, particularly group I PAKs (PAK1, -2, and -3), are difficult to drug; hence, few PAK inhibitors with satisfactory kinase selectivity and druglike properties have been reported to date. Examples are a recently discovered group II PAK (PAK4, -5, -6) selective inhibitor series based on a benzimidazole core, a group I PAK selective series based on a pyrido[2,3-d]pyrimidine-7-one core, and an allosteric dibenzodiazepine PAK1 inhibitor series. Only one compound, an aminopyrazole based pan-PAK inhibitor, entered clinical trials but did not progress beyond phase I trials. Clinical proof of concept for pan-group I, pan-group II, or PAK isoform selective inhibition has yet to be demonstrated.
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Affiliation(s)
- Joachim Rudolph
- Discovery Chemistry, and ‡Structural Biology, Genentech , 1 DNA Way, South San Francisco, California 94080, United States
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14
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Mérour JY, Buron F, Plé K, Bonnet P, Routier S. The azaindole framework in the design of kinase inhibitors. Molecules 2014; 19:19935-79. [PMID: 25460315 PMCID: PMC6271083 DOI: 10.3390/molecules191219935] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 11/10/2014] [Accepted: 11/18/2014] [Indexed: 01/05/2023] Open
Abstract
This review article illustrates the growing use of azaindole derivatives as kinase inhibitors and their contribution to drug discovery and innovation. The different protein kinases which have served as targets and the known molecules which have emerged from medicinal chemistry and Fragment-Based Drug Discovery (FBDD) programs are presented. The various synthetic routes used to access these compounds and the chemical pathways leading to their synthesis are also discussed. An analysis of their mode of binding based on X-ray crystallography data gives structural insights for the design of more potent and selective inhibitors.
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Affiliation(s)
- Jean-Yves Mérour
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans F-45067, France.
| | - Frédéric Buron
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans F-45067, France.
| | - Karen Plé
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans F-45067, France.
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans F-45067, France.
| | - Sylvain Routier
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans F-45067, France.
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