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Ong HW, de Silva C, Avalani K, Kwarcinski F, Mansfield CR, Chirgwin M, Truong A, Derbyshire ER, Zutshi R, Drewry DH. Characterization of 2,4-Dianilinopyrimidines Against Five P. falciparum Kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. ACS Med Chem Lett 2023; 14:1774-1784. [PMID: 38116430 PMCID: PMC10726455 DOI: 10.1021/acsmedchemlett.3c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Plasmodium kinases are increasingly recognized as potential novel antiplasmodial targets for the treatment of malaria, but only a small subset of these kinases have had structure-activity relationship (SAR) campaigns reported. Herein we report the discovery of CZC-54252 (1) as an inhibitor of five P. falciparum kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. 39 analogues were evaluated against all five kinases to establish SAR at three regions of the kinase active site. Nanomolar inhibitors of each kinase were discovered. We identified common and divergent SAR trends across all five kinases, highlighting substituents in each region that improve potency and selectivity for each kinase. Potent analogues were evaluated against the P. falciparum blood stage. Eight submicromolar inhibitors were discovered, of which 37 demonstrated potent antiplasmodial activity (EC50 = 0.16 μM). Our results provide an understanding of features needed to inhibit each individual kinase and lay groundwork for future optimization efforts toward novel antimalarials.
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Affiliation(s)
- Han Wee Ong
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chandi de Silva
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Krisha Avalani
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Frank Kwarcinski
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Christopher R. Mansfield
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
| | - Michael Chirgwin
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Anna Truong
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Reena Zutshi
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - David H. Drewry
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger
Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Ong HW, Truong A, Kwarcinski F, de Silva C, Avalani K, Havener TM, Chirgwin M, Galal KA, Willis C, Krämer A, Liu S, Knapp S, Derbyshire ER, Zutshi R, Drewry DH. Discovery of potent Plasmodium falciparum protein kinase 6 (PfPK6) inhibitors with a type II inhibitor pharmacophore. Eur J Med Chem 2023; 249:115043. [PMID: 36736152 PMCID: PMC10052868 DOI: 10.1016/j.ejmech.2022.115043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 01/01/2023]
Abstract
Malaria is a devastating disease that causes significant global morbidity and mortality. The rise of drug resistance against artemisinin-based combination therapy demonstrates the necessity to develop alternative antimalarials with novel mechanisms of action. We report the discovery of Ki8751 as an inhibitor of essential kinase PfPK6. 79 derivatives were designed, synthesized and evaluated for PfPK6 inhibition and antiplasmodial activity. Using group efficiency analyses, we established the importance of key groups on the scaffold consistent with a type II inhibitor pharmacophore. We highlight modifications on the tail group that contribute to antiplasmodial activity, cumulating in the discovery of compound 67, a PfPK6 inhibitor (IC50 = 13 nM) active against the P. falciparum blood stage (EC50 = 160 nM), and compound 79, a PfPK6 inhibitor (IC50 < 5 nM) with dual-stage antiplasmodial activity against P. falciparum blood stage (EC50 = 39 nM) and against P. berghei liver stage (EC50 = 220 nM).
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Affiliation(s)
- Han Wee Ong
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna Truong
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Frank Kwarcinski
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Chandi de Silva
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Krisha Avalani
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Tammy M Havener
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael Chirgwin
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Kareem A Galal
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Caleb Willis
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Andreas Krämer
- Structural Genomics Consortium, Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, 27599-3420, USA; Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599-3420, USA
| | - Stefan Knapp
- Structural Genomics Consortium, Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC, 27710, USA.
| | - Reena Zutshi
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA.
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Liu J, Shadpour S, Prévôt ME, Chirgwin M, Nemati A, Hegmann E, Lemieux RP, Hegmann T. Molecular Conformation of Bent-Core Molecules Affected by Chiral Side Chains Dictates Polymorphism and Chirality in Organic Nano- and Microfilaments. ACS Nano 2021; 15:7249-7270. [PMID: 33734664 DOI: 10.1021/acsnano.1c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The coupling between molecular conformation and chirality is a cornerstone in the construction of supramolecular helical structures of small molecules across various length scales. Inspired by biological systems, conformational preselection and control in artificial helical molecules, polymers, and aggregates has guided various applications in optics, photonics, and chiral sorting among others, which are frequently based on an inherent chirality amplification through processes such as templating and self-assembly. The so-called B4 nano- or microfilament phase formed by some bent-shaped molecules is an exemplary case for such chirality amplification across length scales, best illustrated by the formation of distinct nano- or microscopic chiral morphologies controlled by molecular conformation. Introduction of one or more chiral centers in the aliphatic side chains led to the discovery of homochiral helical nanofilament, helical microfilament, and heliconical-layered nanocylinder morphologies. Herein, we demonstrate how a priori calculations of the molecular conformation affected by chiral side chains are used to design bent-shaped molecules that self-assemble into chiral nano- and microfilament as well as nanocylinder conglomerates despite the homochiral nature of the molecules. Furthermore, relocation of the chiral center leads to formation of helical as well as flat nanoribbons. Self-consistent data sets from polarized optical as well as scanning and transmission electron microscopy, thin-film and solution circular dichroism spectropolarimetry, and synchrotron-based X-ray diffraction experiments support the progressive and predictable change in morphology controlled by structural changes in the chiral side chains. The formation of these morphologies is discussed in light of the diminishing effects of molecular chirality as the chain length increases or as the chiral center is moved away from the core-chain juncture. The type of phase (B1-columnar or B4) and morphology of the nano- or microfilaments generated can further be controlled by sample treatment conditions such as by the cooling rate from the isotropic melt or by the presence of an organic solvent in the ensuing colloidal dispersions. We show that these nanoscale morphologies can then organize into a wealth of two- and three-dimensional shapes and structures ranging from flower blossoms to fiber mats formed by intersecting flat nanoribbons.
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Affiliation(s)
- Jiao Liu
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Sasan Shadpour
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Marianne E Prévôt
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Michael Chirgwin
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Ahlam Nemati
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Elda Hegmann
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242-0001, United States
- Brain Health Research Institute, Kent State University, Kent, Ohio 44242-0001, United States
| | - Robert P Lemieux
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Torsten Hegmann
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242-0001, United States
- Brain Health Research Institute, Kent State University, Kent, Ohio 44242-0001, United States
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
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