1
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Chompunud Na Ayudhya C, Graidist P, Tipmanee V. Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect. Sci Rep 2024; 14:12531. [PMID: 38822100 PMCID: PMC11143223 DOI: 10.1038/s41598-024-63505-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Binding affinity is an important factor in drug design to improve drug-target selectivity and specificity. In this study, in silico techniques based on molecular docking followed by molecular dynamics (MD) simulations were utilized to identify the key residue(s) for CSF1R binding affinity among 14 pan-tyrosine kinase inhibitors and 15 CSF1R-specific inhibitors. We found tryptophan at position 550 (W550) on the CSF1R binding site interacted with the inhibitors' aromatic ring in a π-π way that made the ligands better at binding. Upon W550-Alanine substitution (W550A), the binding affinity of trans-(-)-kusunokinin and imatinib to CSF1R was significantly decreased. However, in terms of structural features, W550 did not significantly affect overall CSF1R structure, but provided destabilizing effect upon mutation. The W550A also did not either cause ligand to change its binding site or conformational changes due to ligand binding. As a result of our findings, the π-π interaction with W550's aromatic ring could be still the choice for increasing binding affinity to CSF1R. Nevertheless, our study showed that the increasing binding to W550 of the design ligand may not ensure CSF1R specificity and inhibition since W550-ligand bound state did not induce significantly conformational change into inactive state.
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Affiliation(s)
- Chompunud Chompunud Na Ayudhya
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
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2
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Sharma KR, Colvis CM, Rodgers GP, Sheeley DM. Illuminating the druggable genome: Pathways to progress. Drug Discov Today 2024; 29:103805. [PMID: 37890715 PMCID: PMC10939933 DOI: 10.1016/j.drudis.2023.103805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
There are ∼4500 genes within the 'druggable genome', the subset of the human genome that expresses proteins able to bind drug-like molecules, yet existing drugs only target a few hundred. A substantial subset of druggable proteins are largely uncharacterized or understudied, with many falling within G protein-coupled receptor (GPCR), ion channel, and kinase protein families. To improve scientific understanding of these three understudied protein families, the US National Institutes of Health launched the Illuminating the Druggable Genome Program. Now, as the program draws to a close, this review will lay out resources developed by the program that are intended to equip the scientific community with the tools necessary to explore previously understudied biology with the potential to rapidly impact human health.
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Affiliation(s)
- Karlie R Sharma
- National Center for Advancing Translational Sciences, National Institutes of Health, 6701 Democracy Blvd, Bethesda, MD 20892, USA.
| | - Christine M Colvis
- National Center for Advancing Translational Sciences, National Institutes of Health, 6701 Democracy Blvd, Bethesda, MD 20892, USA
| | - Griffin P Rodgers
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Douglas M Sheeley
- Office of Strategic Coordination, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
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3
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Paiva ACF, Lemos AR, Busse P, Martins MT, Silva DO, Freitas MC, Santos SP, Freire F, Barrey EJ, Manival X, Koetzner L, Heinrich T, Wegener A, Grädler U, Bandeiras TM, Schwarz D, Sousa PMF. Extract2Chip-Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance. BIOSENSORS 2023; 13:913. [PMID: 37887106 PMCID: PMC10605449 DOI: 10.3390/bios13100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Modern drug discovery relies on combinatorial screening campaigns to find drug molecules targeting specific disease-associated proteins. The success of such campaigns often relies on functional and structural information of the selected therapeutic target, only achievable once its purification is mastered. With the aim of bypassing the protein purification process to gain insights on the druggability, ligand binding, and/or characterization of protein-protein interactions, herein, we describe the Extract2Chip method. This approach builds on the immobilization of site-specific biotinylated proteins of interest, directly from cellular extracts, on avidin-coated sensor chips to allow for the characterization of molecular interactions via surface plasmon resonance (SPR). The developed method was initially validated using Cyclophilin D (CypD) and subsequently applied to other drug discovery projects in which the targets of interest were difficult to express, purify, and crystallize. Extract2Chip was successfully applied to the characterization of Yes-associated protein (YAP): Transcriptional enhancer factor TEF (TEAD1) protein-protein interaction inhibitors, in the validation of a ternary complex assembly composed of Dyskerin pseudouridine synthase 1 (DKC1) and RuvBL1/RuvBL2, and in the establishment of a fast-screening platform to select the most suitable NUAK family SNF1-like kinase 2 (NUAK2) surrogate for binding and structural studies. The described method paves the way for a potential revival of the many drug discovery campaigns that have failed to deliver due to the lack of suitable and sufficient protein supply.
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Affiliation(s)
- Ana C. F. Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana R. Lemos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philipp Busse
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Madalena T. Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
| | - Diana O. Silva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Evelyne J. Barrey
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, F-54000 Nancy, France;
| | - Lisa Koetzner
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ansgar Wegener
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Tiago M. Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Daniel Schwarz
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Pedro M. F. Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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4
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Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Lang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD. Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. eLife 2023; 12:e88206. [PMID: 37490324 PMCID: PMC10406435 DOI: 10.7554/elife.88206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 (CDKL5) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual, and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD has indicated that CDKL5 kinase function is central to disease pathology. CDKL5 encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further, Cdkl5 knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces postsynaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity, and human neuropathology.
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Affiliation(s)
- Anna Castano
- Department of Pharmacology, University of Colorado School of MedicineAuroraUnited States
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Jennifer L Sanderson
- Department of Pharmacology, University of Colorado School of MedicineAuroraUnited States
| | - Carla A Ferrer
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Yi Lang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - William Richardson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Josie A Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State UniversityColumbusUnited States
| | - Frances M Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Isabelle M Genereux
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel HillChapel HillUnited States
| | - Navlot S Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State UniversityColumbusUnited States
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Tim A Benke
- Departments of Pediatrics, Pharmacology, Neurology and Otolaryngology, University of Colorado School of MedicineAuroraUnited States
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
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5
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Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Liang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD. Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538049. [PMID: 37162893 PMCID: PMC10168277 DOI: 10.1101/2023.04.24.538049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 ( CDKL5 ) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD have indicated that CDKL5 kinase function is central to disease pathology. CDKL5 encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further, Cdkl5 knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces post-synaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated, key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity and human neuropathology.
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6
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Bashore FM, Marquez AB, Chaikuad A, Howell S, Dunn AS, Beltran AA, Smith JL, Drewry DH, Beltran AS, Axtman AD. Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. Sci Rep 2023; 13:6118. [PMID: 37059819 PMCID: PMC10104807 DOI: 10.1038/s41598-023-32854-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/03/2023] [Indexed: 04/16/2023] Open
Abstract
Tau tubulin kinase 1 and 2 (TTBK1/2) are highly homologous kinases that are expressed and mediate disease-relevant pathways predominantly in the brain. Distinct roles for TTBK1 and TTBK2 have been delineated. While efforts have been devoted to characterizing the impact of TTBK1 inhibition in diseases like Alzheimer's disease and amyotrophic lateral sclerosis, TTBK2 inhibition has been less explored. TTBK2 serves a critical function during cilia assembly. Given the biological importance of these kinases, we designed a targeted library from which we identified several chemical tools that engage TTBK1 and TTBK2 in cells and inhibit their downstream signaling. Indolyl pyrimidinamine 10 significantly reduced the expression of primary cilia on the surface of human induced pluripotent stem cells (iPSCs). Furthermore, analog 10 phenocopies TTBK2 knockout in iPSCs, confirming a role for TTBK2 in ciliogenesis.
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Affiliation(s)
- Frances M Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ariana B Marquez
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strabe 15, 60438, Frankfurt, Germany
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea S Dunn
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alvaro A Beltran
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adriana S Beltran
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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7
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Davis-Gilbert Z, Krämer A, Dunford JE, Howell S, Senbabaoglu F, Wells CI, Bashore FM, Havener TM, Smith JL, Hossain MA, Oppermann U, Drewry DH, Axtman AD. Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2. ACS Med Chem Lett 2023; 14:432-441. [PMID: 37077385 PMCID: PMC10108397 DOI: 10.1021/acsmedchemlett.2c00530] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/07/2023] [Indexed: 03/15/2023] Open
Abstract
Naphthyridine-based inhibitors were synthesized to yield a potent and cell-active inhibitor of casein kinase 2 (CK2). Compound 2 selectively inhibits CK2α and CK2α' when profiled broadly, thereby making it an exquisitely selective chemical probe for CK2. A negative control that is structurally related but lacks a key hinge-binding nitrogen (7) was designed on the basis of structural studies. Compound 7 does not bind CK2α or CK2α' in cells and demonstrates excellent kinome-wide selectivity. Differential anticancer activity was observed when compound 2 was profiled alongside a structurally distinct CK2 chemical probe: SGC-CK2-1. This naphthyridine-based chemical probe (2) represents one of the best available small molecule tools with which to interrogate biology mediated by CK2.
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Affiliation(s)
- Zachary
W. Davis-Gilbert
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andreas Krämer
- Institute
of Pharmaceutical Chemistry, Goethe University
Frankfurt, Max-von-Laue-Strabe 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strabe 15, Frankfurt 60438, Germany
- Frankfurt
Cancer Institute, Paul-Ehrlich-Straße
42-44, Frankfurt 60596, Germany
| | - James E. Dunford
- Botnar
Research Centre, Nuffield Department of Orthopaedics, Rheumatology
and Musculoskeletal Sciences, University
of Oxford, Oxford OX3 7LD, United Kingdom
| | - Stefanie Howell
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Filiz Senbabaoglu
- Botnar
Research Centre, Nuffield Department of Orthopaedics, Rheumatology
and Musculoskeletal Sciences, University
of Oxford, Oxford OX3 7LD, United Kingdom
| | - Carrow I. Wells
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances M. Bashore
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Tammy M. Havener
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffery L. Smith
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mohammad A. Hossain
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Udo Oppermann
- Botnar
Research Centre, Nuffield Department of Orthopaedics, Rheumatology
and Musculoskeletal Sciences, University
of Oxford, Oxford OX3 7LD, United Kingdom
- Oxford
Translational
Myeloma Centre, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - David H. Drewry
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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8
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Khairnar S, Sonawane A, Cheke RS, Kharkar PS, Gaikwad V, Patil S, Aware V. Hit discovery of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines as potential anti-glioblastoma therapeutics: Design, synthesis, biological evaluation, and computational screening. Drug Dev Res 2023; 84:561-578. [PMID: 36823756 DOI: 10.1002/ddr.22046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/25/2023]
Abstract
Glioblastoma multiforme (GBM) is a highly-aggressive, dreadful disease with poor prognosis and disappointing clinical success. There is an unmet medical need of molecularly-targeted therapeutics for GBM treatment. In the present work, a series of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines was designed, synthesized, purified, characterized, and evaluated for cytotoxicity against glioblastoma cell line U87-MG. The design process (virtual library enumeration around the core, physicochemical and molecular property prediction/calculation of the designs, filtering the undesirable ones, and the diversity analyses of the lead-like designs), was carefully curated so as to obtain a set of structurally-diverse, novel molecules (total 20), with a particular focus on the relatively unexplored core structure, 6,7-dihydro-5H-cyclopenta[d]pyrimidine. The preliminary screening was done using MTT assay at 10 and 100 μM concentrations of the title compounds F1 -F20 and positive control cisplatin, which yielded six hits (% inhibition at 10 μM: ~50%)-F2 , F3 , F5 , F7 , F15 , and F20 , which were taken up for IC50 determination. The top hits F2 and F7 (IC50 < 10 μM) were further used for computational studies such as target prediction, followed by their molecular docking in the binding sites of the top-3 predicted targets (epidermal growth factor receptor kinase domain, cyclin-dependent kinase 2 [CDK2]) /cyclin E, and anaplastic lymphoma kinase [ALK]). The docking pose analyses revealed interesting trends. The relatively planar core structure, presence of favorable hinge-binding substructures, basic groups, all added up, and culminated in appreciable cytotoxicity against GBM cell line.
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Affiliation(s)
- Sanjay Khairnar
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, India.,Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Anjali Sonawane
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Rameshwar S Cheke
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Vishwas Gaikwad
- Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Sambhaji Patil
- Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Valmik Aware
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, India
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9
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Xin X, Wang Y, Zhang L, Zhang D, Sha L, Zhu Z, Huang X, Mao W, Zhang J. Development and therapeutic potential of adaptor-associated kinase 1 inhibitors in human multifaceted diseases. Eur J Med Chem 2023; 248:115102. [PMID: 36640459 DOI: 10.1016/j.ejmech.2023.115102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Adaptor-Associated Kinase 1 (AAK1), a Ser/Thr protein kinase, responsible for regulating clathrin-mediated endocytosis, is ubiquitous in the central nervous system (CNS). AAK1 plays an important role in neuropathic pain and a variety of other human diseases, including viral invasion, Alzheimer's disease, Parkinson's syndrome, etc. Therefore, targeting AAK1 is a promising therapeutic strategy. However, although small molecule AAK1 inhibitors have been vigorously developed, only BMS-986176/LX-9211 has entered clinical trials. Simultaneously, new small molecule inhibitors, including BMS-911172 and LP-935509, exhibited excellent druggability. This review elaborates on the structure, biological function, and disease relevance of AAK1. We emphatically analyze the structure-activity relationships (SARs) of small molecule AAK1 inhibitors based on different binding modalities and discuss prospective strategies to provide insights into novel AAK1 therapeutic agents for clinical practice.
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Affiliation(s)
- Xin Xin
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yue Wang
- Leling Traditional Chinese Medicine Hospital, Leling, 253600, Shandong, China
| | - Lele Zhang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Dan Zhang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Leihao Sha
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ziyu Zhu
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiaoyi Huang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Wuyu Mao
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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10
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Roose TR, Preschel HD, Mayo Tejedor H, Roozee JC, Hamlin TA, Maes BUW, Ruijter E, Orru RVA. Iron-Catalysed Carbene Transfer to Isocyanides as a Platform for Heterocycle Synthesis. Chemistry 2023; 29:e202203074. [PMID: 36305372 PMCID: PMC10108253 DOI: 10.1002/chem.202203074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
An iron-catalysed carbene transfer reaction of diazo compounds to isocyanides has been developed. The resulting ketenimines are trapped in situ with various bisnucleophiles to access a range of densely functionalized heterocycles (pyrimidinones, dihydropyrazolones, 1H-tetrazoles) in a one-pot process. The electron-rich Hieber anion ([Fe(CO)3 NO]- ) facilitates efficient catalytic carbene transfer from acceptor-type α-diazo carbonyl compounds to isocyanides, providing a cost-efficient and benign alternative to similar noble metal-catalysed processes. Based on DFT calculations a plausible reaction mechanism for activation of the α-diazo carbonyl carbene precursor and ketenimine formation is provided.
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Affiliation(s)
- Thomas R. Roose
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - H. Daniel Preschel
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Helena Mayo Tejedor
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Jasper C. Roozee
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Trevor A. Hamlin
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Bert U. W. Maes
- Organic Synthesis Division Department of ChemistryUniversity of AntwerpGroenenborgerlaan 171B-2020AntwerpBelgium
| | - Eelco Ruijter
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Romano V. A. Orru
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life SciencesVrije Universiteit AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
- Department of Organic Chemistry Aachen-Maastricht Institute for Biobased Materials (AMIBM)Maastricht UniversityUrmonderbaan 226167 KDGeleenThe Netherlands
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11
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Zhang Q, Zhang W, Cui R, Zhang Y, Niu D. Synthesis of 2,4-diarylated pyrimidines enabled by Ni-catalyzed C–sulfone bond activation. Org Chem Front 2023. [DOI: 10.1039/d2qo01935c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The readily available pyrimidinyl sulfones, in which the C–S bond is cleaved selectively, could serve as electrophiles in the Ni-catalyzed cross-coupling reactions to prepare 2,4-diarylated pyrimidines under mild conditions with a broad scope.
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Affiliation(s)
- Qian Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
- Sichuan Institute of Edible Fungi, Shizishan Road No. 4, Jinjiang district, Chengdu, China
| | - Wei Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Ruoyan Cui
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Yang Zhang
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Dawen Niu
- Department of Emergency, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and School of Chemical Engineering, Sichuan University, Chengdu, China
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12
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Biological aspects of nitrogen heterocycles for amyotrophic lateral sclerosis. Appl Microbiol Biotechnol 2022; 107:43-56. [DOI: 10.1007/s00253-022-12317-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022]
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13
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Hyland EE, Kelly PQ, McKillop AM, Dherange BD, Levin MD. Unified Access to Pyrimidines and Quinazolines Enabled by N-N Cleaving Carbon Atom Insertion. J Am Chem Soc 2022; 144:19258-19264. [PMID: 36240487 PMCID: PMC9619406 DOI: 10.1021/jacs.2c09616] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Given
the ubiquity of heterocycles in biologically active
molecules,
transformations with the capacity to modify such molecular skeletons
with modularity remain highly desirable. Ring expansions that enable
interconversion of privileged heterocyclic motifs are especially interesting
in this regard. As such, the known mechanisms for ring expansion and
contraction determine the classes of heterocycle amenable to skeletal
editing. Herein, we report a reaction that selectively cleaves the
N–N bond of pyrazole and indazole cores to afford pyrimidines
and quinazolines, respectively. This chlorodiazirine-mediated reaction
provides a unified route to a related pair of heterocycles that are
otherwise typically prepared by divergent approaches. Mechanistic
experiments and DFT calculations support a pathway involving pyrazolium
ylide fragmentation followed by cyclization of the ring-opened diazahexatriene
intermediate to yield the new diazine core. Beyond enabling access
to valuable heteroarenes from easily prepared starting materials,
we demonstrate the synthetic utility of skeletal editing in the synthesis
of a Rosuvastatin analog as well as in an aryl vector-adjusting direct
scaffold hop.
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Affiliation(s)
- Ethan E Hyland
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Patrick Q Kelly
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander M McKillop
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Balu D Dherange
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mark D Levin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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14
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Drewry D, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD. Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. J Med Chem 2022; 65:12860-12882. [PMID: 36111834 PMCID: PMC9574855 DOI: 10.1021/acs.jmedchem.2c00697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 11/29/2022]
Abstract
From a designed library of indolyl pyrimidinamines, we identified a highly potent and cell-active chemical probe (17) that inhibits phosphatidylinositol-3-phosphate 5-kinase (PIKfyve). Comprehensive evaluation of inhibitor selectivity confirmed that this PIKfyve probe demonstrates excellent kinome-wide selectivity. A structurally related indolyl pyrimidinamine (30) was characterized as a negative control that lacks PIKfyve inhibitory activity and exhibits exquisite selectivity when profiled broadly. Chemical probe 17 disrupts multiple phases of the lifecycle of β-coronaviruses: viral replication and viral entry. The diverse antiviral roles of PIKfyve have not been previously probed comprehensively in a single study or using the same compound set. Our scaffold is a distinct chemotype that lacks the canonical morpholine hinge-binder of classical lipid kinase inhibitors and has a non-overlapping kinase off-target profile with known PIKfyve inhibitors. Our chemical probe set can be used by the community to further characterize the role of PIKfyve in virology.
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Affiliation(s)
- David
H. Drewry
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC
Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances M. Potjewyd
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Armin Bayati
- Structural
Genomics Consortium, Department of Neurology and Neurosurgery, Montreal
Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jeffery L. Smith
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rebekah J. Dickmander
- UNC
Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly
Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department
of Microbiology & Immunology, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department
of Chemistry, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefanie Howell
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sharon Taft-Benz
- Rapidly
Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department
of Genetics, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sophia M. Min
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mohammad Anwar Hossain
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark Heise
- Rapidly
Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department
of Genetics, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter S. McPherson
- Structural
Genomics Consortium, Department of Neurology and Neurosurgery, Montreal
Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J. Moorman
- UNC
Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly
Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department
of Microbiology & Immunology, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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15
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SNAr Reactions on 2-Amino-4,6-dichloropyrimidine-5-carbaldehyde. MOLBANK 2022. [DOI: 10.3390/m1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We report the experimental results of unexpected aromatic nucleophilic substitution reaction products on 2-amino-4,6-dichloropyrimidine-5-carbaldehyde. The isolated compounds are products of amination, solvolysis, and condensation processes under mild and environmentally friendly conditions, due to the influence of structural factors of the starting pyrimidine and a high concentration of alkoxide ions. This method allows the building of pyrimidine-based compound precursors of N-heterocyclic systems.
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16
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Multitargeting the Action of 5-HT 6 Serotonin Receptor Ligands by Additional Modulation of Kinases in the Search for a New Therapy for Alzheimer's Disease: Can It Work from a Molecular Point of View? Int J Mol Sci 2022; 23:ijms23158768. [PMID: 35955902 PMCID: PMC9368844 DOI: 10.3390/ijms23158768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022] Open
Abstract
In view of the unsatisfactory treatment of cognitive disorders, in particular Alzheimer’s disease (AD), the aim of this review was to perform a computer-aided analysis of the state of the art that will help in the search for innovative polypharmacology-based therapeutic approaches to fight against AD. Apart from 20-year unrenewed cholinesterase- or NMDA-based AD therapy, the hope of effectively treating Alzheimer’s disease has been placed on serotonin 5-HT6 receptor (5-HT6R), due to its proven, both for agonists and antagonists, beneficial procognitive effects in animal models; however, research into this treatment has so far not been successfully translated to human patients. Recent lines of evidence strongly emphasize the role of kinases, in particular microtubule affinity-regulating kinase 4 (MARK4), Rho-associated coiled-coil-containing protein kinase I/II (ROCKI/II) and cyclin-dependent kinase 5 (CDK5) in the etiology of AD, pointing to the therapeutic potential of their inhibitors not only against the symptoms, but also the causes of this disease. Thus, finding a drug that acts simultaneously on both 5-HT6R and one of those kinases will provide a potential breakthrough in AD treatment. The pharmacophore- and docking-based comprehensive literature analysis performed herein serves to answer the question of whether the design of these kind of dual agents is possible, and the conclusions turned out to be highly promising.
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17
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Potjewyd FM, Annor‐Gyamfi JK, Aubé J, Chu S, Conlon IL, Frankowski KJ, Guduru SKR, Hardy BP, Hopkins MD, Kinoshita C, Kireev DB, Mason ER, Moerk CT, Nwogbo F, Pearce KH, Richardson TI, Rogers DA, Soni DM, Stashko M, Wang X, Wells C, Willson TM, Frye SV, Young JE, Axtman AD. AD Informer Set: Chemical tools to facilitate Alzheimer's disease drug discovery. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2022; 8:e12246. [PMID: 35475262 PMCID: PMC9019904 DOI: 10.1002/trc2.12246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/29/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Introduction The portfolio of novel targets to treat Alzheimer's disease (AD) has been enriched by the Accelerating Medicines Partnership Program for Alzheimer's Disease (AMP AD) program. Methods Publicly available resources, such as literature and databases, enabled a data-driven effort to identify existing small molecule modulators for many protein products expressed by the genes nominated by AMP AD and suitable positive control compounds to be included in the set. Compounds contained within the set were manually selected and annotated with associated published, predicted, and/or experimental data. Results We built an annotated set of 171 small molecule modulators targeting 98 unique proteins that have been nominated by AMP AD consortium members as novel targets for the treatment of AD. The majority of compounds included in the set are inhibitors. These small molecules vary in their quality and should be considered chemical tools that can be used in efforts to validate therapeutic hypotheses, but which will require further optimization. A physical copy of the AD Informer Set can be requested on the Target Enablement to Accelerate Therapy Development for Alzheimer's Disease (TREAT-AD) website. Discussion Small molecules that enable target validation are important tools for the translation of novel hypotheses into viable therapeutic strategies for AD.
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Affiliation(s)
- Frances M. Potjewyd
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Joel K. Annor‐Gyamfi
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Jeffrey Aubé
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Shaoyou Chu
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Ivie L. Conlon
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Kevin J. Frankowski
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Shiva K. R. Guduru
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Brian P. Hardy
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Megan D. Hopkins
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Chizuru Kinoshita
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Dmitri B. Kireev
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Emily R. Mason
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Charles T. Moerk
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Felix Nwogbo
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Kenneth H. Pearce
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Timothy I. Richardson
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - David A. Rogers
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Disha M. Soni
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Michael Stashko
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Xiaodong Wang
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Carrow Wells
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Timothy M. Willson
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Stephen V. Frye
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Jessica E. Young
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Alison D. Axtman
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
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