New Imadazopyrazines with CDK9 Inhibitory Activity as Anticancer and Antiviral: Synthesis, In Silico, and In Vitro Evaluation Approaches
Abstract
:1. Introduction
2. Results and Discussion
2.1. Chemistry
2.1.1. Synthetic Approach
2.1.2. Rational of Molecule Design
2.2. Anticancer Activity
2.2.1. CDK9 Activity
2.2.2. Cytotoxicity Assay
2.2.3. Molecular Docking Study into CDK9 Active Site
2.3. Antiviral Activity
2.3.1. 229E Inhibitory Assay
2.3.2. Antiviral Target Prediction and Molecular Docking Studies
2.4. In Silico Prediction of Drug-Likeness Properties
2.4.1. Molecular Structured and Physicochemical Properties
2.4.2. ADMET Studies
3. Materials and Methods
3.1. Chemistry
- The N-(Tert-butyl)-2-(furan-3-yl) imidazo[1,2-a] pyrazin-3-amine (1a) Yield: 89.3%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 1.09 (br. s., 9 H), 4.76 (s, 1 H), 7.13 (s, 1 H), 7.76 (br. s., 1 H), 7.84 (br. s., 1 H), 8.32 (s, 1 H), 8.38 (br. s., 1 H), 8.89 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 30.53, 56.85, 110.46, 117.60, 120.40, 125.57, 128.81, 135.55, 137.31, 141.81, 142.52, and 143.76. m/z (ESI-MS) [M]+ 257.13.
- The N-Cyclohexyl-2-(furan-3-yl) imidazo[1,2-a] pyrazin-3-amine (1b) yield: 86.4%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 1.09 (br. s., 9 H), 1.10–1.15 (m, 3 H), 1.28–1.33 (m, 2 H), 1.53 (br. s., 1 H), 1.66 (d, J = 11.83 Hz, 2 H), 1.75 (d, J = 12.69 Hz, 2 H), 2.86–2.90 (m, 1 H), 4.92 (d, J = 7.10 Hz, 1 H), 7.79 (s, 1 H), 7.85 (d, J = 4.52 Hz, 1 H), 7.87 (s, 1 H) 8.25 (s, 1 H), 8.30 (dd, J = 4.52, 1.08 Hz, 1 H), 8.88 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 25.07, 25.81, 34.19, 56.82, 109.78, 116.72, 120.13, 127.17, 120.95, 132.89, 136.65, 141.06, 142.46, and 144.16. m/z (ESI-MS) [M]+ 283.07.
- The N-Benzyl-2-(furan-3-yl) imidazo[1,2-a]pyrazin-3-amine (1c) yield: 91.0%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 4.17 (d, J = 6.24 Hz, 2 H), 5.57 (t, J = 6.35 Hz, 1 H), 7.04 (s, 1 H), 7.23–7.31 (m, 5 H), 7.75 (d, J = 4.52 Hz, 1 H), 7.79 (s, 1 H), 8.12 (d, J = 4.30 Hz, 1 H), 8.20 (s, 1 H), 8.86 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 51.09, 109.79, 116.46, 119.94, 127.63, 126.63, 126.75, 131.98, 132.05, 132.89, 136.47, 140.13, 141.06, 142.45, and 144.20. m/z (ESI-MS) [M]+ 291.14.
- The 2-(Furan-3-yl)-N-(4-methoxyphenyl) imidazo[1,2-a] pyrazin-3-amine (1d) yield: 88.4%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 3.64 (s, 3 H), 6.47 (d, J = 7.31 Hz, 2 H), 6.77 (d, J = 7.74 Hz, 2 H), 6.93 (s, 1 H), 7.75 (br. s., 1 H), 7.89 (br. s., 1 H), 7.99 (br. s., 1 H), 8.03 (br. s., 1 H), 8.04 (br. s., 1 H), 9.04 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 55.69, 109.55, 114.76, 115.47, 132.04, 132.92, 134.91, 137.66, 138.87, 141.47, 142.31, 142.85, 144.41, 153.12, and 156.53. m/z (ESI-MS) [M]+ 291.14.
- The 4-(3-(Tert-butylamino) imidazo[1,2-a]pyrazin-2-yl)benzene-1,3-diol (2a) yield: 96.6%; white solid (MP: 174–176 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 1.00 (s, 9 H), 5.35 (s, 1 H), 6.28 (d, J = 2.75 Hz, 1 H), 6.34 (d, J = 2.06 Hz, 1 H), 7.86 (d, J = 4.81 Hz, 1 H), 7.89 (d, J = 8.94 Hz, 1 H), 8.39 (dd, J = 4.81, 1.37 Hz, 1 H), 8.91 (d, J = 1.37 Hz, 1 H), 9.51 (br. s., 1 H), 11.53 (br. s., 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 29.77, 109.8, 116.7, 119.80, 127.61, 126.67, 126.79, 132.01, 132.70, 132.89, 136.54, 140.15, 141.67, 142.45, and 144.22. m/z (ESI-MS) [M]− 297.04.
- The 4-(3-(Cyclohexylamino) imidazo[1,2-a] pyrazin-2-yl)benzene-1,3-diol (2b) yield: 79.5%; white solid (MP: 245–247 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 1.02–1.11 (m, 4 H), 1.20 (d, J = 11.00 Hz, 2 H), 1.58–1.61 (m, 2 H), 1.66 (d, J = 12.37 Hz, 2 H), 2.81 (tdt, J = 10.35, 10.35, 6.96, 3.69, 3.69 Hz, 1 H), 5.21 (d, J = 6.87 Hz, 1 H), 6.28 (d, J = 2.75 Hz, 1 H), 6.34 (dd, J = 8.59, 2.41 Hz, 1 H), 7.89 (d, J = 4.81 Hz, 1 H), 7.99 (d, J = 8.25 Hz, 1 H), 8.34 (dd, J = 4.12, 1.37 Hz, 1 H), 8.92 (d, J = 1.38 Hz, 1 H), 9.57 (s, 1 H), 12.15 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 51.09, 109.79, 116.46, 119.94, 127.63, 126.63, 126.75, 131.98, 132.05, 132.89, 136.47, 140.13, 141.06, 142.45, and 144.20. m/z (ESI-MS) [M]+ 325.17.
- The 4-(3-(Benzylamino)imidazo[1,2-a]pyrazin-2-yl)benzene-1,3-diol (2c) yield: 91.8%; white solid (MP: 167–169 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 4.06 (d, J = 6.87 Hz, 2 H), 5.65 (t, J = 6.19 Hz, 1 H), 6.31 (d, J = 2.06 Hz, 1 H), 6.33–6.36 (m, 1 H), 7.21–7.23 (m, 4 H), 7.29–7.32 (m, 1 H), 7.79 (d, J = 4.12 Hz, 1 H), 7.98 (d, J = 8.94 Hz, 1 H), 8.14 (dd, J = 4.12, 1.37 Hz, 1 H), 8.89 (d, J = 1.37 Hz, 1 H), 9.60 (s, 1 H), 12.10 (s, 1 H)); 13C NMR (176 MHz, DMSO-d6) δ ppm 51.29, 103.64, 107.74, 109.38, 116.25, 126.32, 127.78, 128.78, 128.83, 129.32, 129.51, 134.65, 136.85, 139.77, 141.63, 158.34, and 159.44. m/z (ESI-MS) [M]+ 331.06.
- The 4-(3-((4-Methoxyphenyl) amino)imidazo[1,2-a]pyrazin-2-yl)benzene-1,3-diol (2d) yield: 79.9%; white solid (MP: 186–188 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 3.60 (s, 3 H), 6.20–6.22 (m, 1 H), 6.29 (d, J = 2.75 Hz, 1 H), 6.44 (m, J = 8.94 Hz, 2 H), 6.72 (m, J = 8.94 Hz, 2 H), 7.75 (d, J = 8.93 Hz, 1 H), 7.93 (d, J = 4.81 Hz, 1 H), 8.00 (s, 1 H) 8.02 (dd, J = 4.12, 1.37 Hz, 1 H), 9.09 (s, 1 H), 9.64 (s, 1 H), 12.49 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 55.74, 103.63, 107.75, 107.96, 114.81, 115.58, 116.44, 119.63, 128.70, 130.62, 135.32, 138.60, 139.75, 141.89, 153.26, 159.15, and 159.81. m/z (ESI-MS) [M]+ 349.12.
- The N-(Tert-butyl)-2-(6-(dimethylamino) pyridin-3-yl)imidazo[1,2-a]pyrazin-3-amine (3a) yield: 98%; white solid (MP: 126–128 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 0.97 (s, 9 H), 3.02 (s, 6 H), 4.72 (s, 1 H), 6.67 (d, J = 8.94 Hz, 1 H), 7.79 (d, J = 4.12 Hz, 1 H), 8.22 (d, J = 8.93 Hz, 1 H), 8.34 (d, J = 4.12 Hz, 1 H), 8.84 (s, 1 H), 8.84 (s, 1H); 13C NMR (176 MHz, DMSO-d6) δ ppm 30.52, 38.16, 56.66, 105.57, 117.54, 118.36, 124.96, 128.85, 136.98, 137.20, 139.86, 142.22, 147.54, and 158.65. m/z (ESI-MS) [M]+ 311.20.
- The N-Cyclohexyl-2-(6-(dimethylamino) pyridin-3-yl)imidazo[1,2-a]pyrazin-3-amine (3b) yield: 85.1%; white solid (MP: 191–193 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 1.04 (br. s., 3 H), 1.19–1.24 (m, 2 H), 1.45 (br. s., 1 H), 1.58 (br. s., 2 H), 1.65 (d, J = 12.37 Hz, 2 H), 2.79 (dd, J = 10.31, 3.44 Hz, 1 H), 3.03 (s, 6 H), 4.91 (d, J = 6.87 Hz, 1 H), 6.70 (d, J = 8.94 Hz, 1 H), 7.78 (d, J = 4.81 Hz, 1 H), 8.23 (dd, J = 8.94, 2.75 Hz, 1 H), 8.26 (d, J = 4.12 Hz, 1 H), 8.81 (s, 1 H), 8.86 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 25.02, 25.84, 34.07, 38.19, 56.84, 106.01, 116.66, 117.90, 118.35, 126.36, 128.99, 136.00, 136.59, 142.14, 146.69, and 158.64. m/z (ESI-MS) [M]+ 336.96.
- The N-Benzyl-2-(6-(dimethylamino) pyridin-3-yl)imidazo[1,2-a]pyrazin-3-amine (3c) yield: 43.3%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 3.05 (s, 6 H), 4.08 (d, J = 6.87 Hz, 2 H), 5.58 (t, J = 6.53 Hz, 1 H), 6.71 (d, J = 8.94 Hz, 1 H), 7.20–7.22 (m, 4 H), 7.68 (d, J = 4.81 Hz, 1 H), 7.76–7.88 (m, 1 H), 8.09 (dd, J = 4.81, 1.37 Hz, 1 H), 8.17 (dd, J = 8.94, 2.75 Hz, 1 H), 8.79 (d, J = 1.37 Hz, 1 H), 8.82 (d, J = 2.06 Hz, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 38.22, 51.22, 106.07, 106.44, 116.36, 117.94, 121.71, 127.67, 128.61, 128.78, 136.12, 136.42, 140.10, 142.22, 146.68, 158.64, and 189.82. m/z (ESI-MS) [M]+ 345.22.
- The 2-(6-(Dimethylamino) pyridin-3-yl)-N-(4-methoxyphenyl) imidazo[1,2-a]pyrazin-3-amine (3d) yield: 47.7%; white solid (MP: 180–182 °C); 1H NMR (700 MHz, DMSO-d6) δ ppm 3.00 (s, 6 H), 3.59 (s, 3 H), 6.40 (m, J = 8.94 Hz, 2 H), 6.67 (d, J = 8.94 Hz, 1 H), 6.72 (m, J = 8.94 Hz, 2 H), 7.82 (d, J = 4.12 Hz, 1 H), 7.96 (dd, J = 4.81, 1.37 Hz, 1 H), 7.97 (s, 1 H), 8.09 (dd, J = 8.94, 2.06 Hz, 1 H), 8.69 (d, J = 2.06 Hz, 1 H), 8.98 (d, J = 1.37 Hz, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 38.14, 55.75, 106.11, 114.59, 115.61, 116.60, 117.11, 120.28, 122.57, 129.61, 135.88, 137.70, 139.10, 142.66, 146.80, 135.11, and 158.87. m/z (ESI-MS) [M]+ 361.31.
- The N-(Tert-butyl)-2-(2-fluoropyridin-4-yl) imidazo[1,2-a] pyrazin-3-amine (4a) yield: 87.7%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 1.00 (s, 9 H), 5.04 (s, 1 H), 7.85 (s, 1 H), 7.87 (d, J = 4.12 Hz, 1 H), 8.11 (d, J = 4.81 Hz, 1 H), 8.27 (d, J = 4.81 Hz, 1 H), 8.43 (d, J = 4.81 Hz, 1 H), 8.98 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 30.40, 57.26, 107.40, 118.13, 120.70, 128.34, 129.30, 136.70, 148.22, 163.34, and 164.89. m/z (ESI-MS) [M]+ 286.04.
- The N-Cyclohexyl-2-(2-fluoropyridin-4-yl) imidazo[1,2-a] pyrazin-3-amine (4b) yield: 81.2%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 1.04–1.10 (m, 3 H), 1.25–1.31 (m, 2 H), 1.47 (br. s., 1 H), 1.59–1.63 (m, 2 H), 1.70 (d, J = 12.37 Hz, 2 H), 2.79–2.86 (m, 1 H), 5.30 (d, J = 7.56 Hz, 1 H), 7.77 (s, 1 H), 7.86 (d, J = 4.81 Hz, 1 H), 8.06 (d, J = 5.50 Hz, 1 H), 8.29 (d, J = 5.50 Hz, 1 H), 8.37 (dd, J = 4.12, 1.37 Hz, 1 H), 8.97 (s, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 25.11, 25.76, 34.17, 57.59, 105.92, 117.29, 119.44, 129.34, 130.71, 134.14, 136.67, 144.22, 148.51, 163.64, and 165.18. m/z (ESI-MS) [M]+ 312.11.
- The N-Benzyl-2-(2-fluoropyridin-4-yl) imidazo[1,2-a] pyrazin-3-amine (4c) yield: 79.2%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 4.14 (d, J = 6.87 Hz, 2 H), 5.94 (t, J = 6.53 Hz, 1 H), 7.16–7.19 (m, 5 H), 7.65 (s, 1 H), 7.77 (d, J = 4.81 Hz, 1 H), 7.96 (d, J = 4.81 Hz, 1 H), 8.20 (dd, J = 4.47, 1.72 Hz, 1 H), 8.25 (d, J = 5.50 Hz, 1 H), 8.94 (d, J = 1.37 Hz, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 51.50, 106.11, 117.07, 119.59, 127.81, 128.70, 128.82, 129.11, 131.01, 134.15, 136.54, 139.65, 144.13, 148.38, 163.57, and 165.12. m/z (ESI-MS) [M]+ 320.11.
- The 2-(2-Fluoropyridin-4-yl)-N-(4-methoxyphenyl) imidazo[1,2-a]pyrazin-3-amine (4d) yield: 97.0%; yellow oil; 1H NMR (700 MHz, DMSO-d6) δ ppm 3.60 (s, 3 H), 6.48 (d, J = 8.94 Hz, 2 H), 6.74 (d, J = 8.94 Hz, 2 H), 6.99 (m, J = 8.94 Hz, 2 H), 7.37 (m, J = 8.94 Hz, 2 H), 7.82 (s, 1 H), 7.89 (d, J = 4.81 Hz, 1 H), 8.02–8.03 (m, 1 H), 8.27 (d, J = 1.37 Hz, 1 H); 13C NMR (176 MHz, DMSO-d6) δ ppm 55.91, 106.22, 115.09, 115.61, 117.30, 119.56, 120.76, 123.68, 130.03, 132.08, 132.94, 137.74, 142.37, 144.52, 149.04, and 155.55. m/z (ESI-MS) [M]+ 336.18.
3.2. In Vitro CDK9 Kinase Assay
3.3. MTT Cytotoxicity Assay
3.4. Antiviral Assay
3.5. Docking Studies
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Bruyère, C.; Meijer, L. Targeting Cyclin-Dependent Kinases in Anti-Neoplastic Therapy. Curr. Opin. Cell Biol. 2013, 25, 772–779. [Google Scholar] [CrossRef] [PubMed]
- McInnes, C. Progress in the Evaluation of CDK Inhibitors as Anti-Tumor Agents. Drug Discov. Today 2008, 13, 875–881. [Google Scholar] [CrossRef] [PubMed]
- Malumbres, M.; Barbacid, M. Cell Cycle, CDKs and Cancer: A Changing Paradigm. Nat. Rev. Cancer 2009, 9, 153–166. [Google Scholar] [CrossRef] [PubMed]
- Morales, F.; Giordano, A. Overview of CDK9 as a Target in Cancer Research. Cell Cycle 2016, 15, 519–527. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Alsfouk, A. Small Molecule Inhibitors of Cyclin-Dependent Kinase 9 for Cancer Therapy. J. Enzym. Inhib. Med. Chem. 2021, 36, 693–706. [Google Scholar] [CrossRef]
- Ma, H.; Seebacher, N.A.; Hornicek, F.J.; Duan, Z. Cyclin-Dependent Kinase 9 (CDK9) Is a Novel Prognostic Marker and Therapeutic Target in Osteosarcoma. EBioMedicine 2019, 39, 182–193. [Google Scholar] [CrossRef] [Green Version]
- Narita, T.; Ishida, T.; Ito, A.; Masaki, A.; Kinoshita, S.; Suzuki, S.; Takino, H.; Yoshida, T.; Ri, M.; Kusumoto, S.; et al. Cyclin-Dependent Kinase 9 Is a Novel Specific Molecular Target in Adult T-Cell Leukemia/Lymphoma. Blood 2017, 130, 1114–1124. [Google Scholar] [CrossRef] [Green Version]
- Sonawane, Y.A.; Taylor, M.A.; Napoleon, J.V.; Rana, S.; Contreras, J.I.; Natarajan, A. Cyclin Dependent Kinase 9 Inhibitors for Cancer Therapy. J. Med. Chem. 2016, 59, 8667–8684. [Google Scholar] [CrossRef]
- Krystof, V.; Baumli, S.; Furst, R. Perspective of Cyclin-Dependent Kinase 9 (CDK9) as a Drug Target. Curr. Pharm. Des. 2012, 18, 2883–2890. [Google Scholar] [CrossRef] [Green Version]
- Wang, J.; Dean, D.C.; Hornicek, F.J.; Shi, H.; Duan, Z. Cyclin-Dependent Kinase 9 (CDK9) Is a Novel Prognostic Marker and Therapeutic Target in Ovarian Cancer. FASEB J. 2019, 33, 5990–6000. [Google Scholar] [CrossRef]
- Kretz, A.L.; Schaum, M.; Richter, J.; Kitzig, E.F.; Engler, C.C.; Leithäuser, F.; Henne-Bruns, D.; Knippschild, U.; Lemke, J. CDK9 Is a Prognostic Marker and Therapeutic Target in Pancreatic Cancer. Tumor Biol. 2017, 39, 1010428317694304. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Franco, L.C.; Morales, F.; Boffo, S.; Giordano, A. CDK9: A Key Player in Cancer and Other Diseases. J. Cell Biochem. 2018, 119, 1273–1284. [Google Scholar] [CrossRef] [PubMed]
- Boffo, S.; Damato, A.; Alfano, L.; Giordano, A. CDK9 Inhibitors in Acute Myeloid Leukemia. J. Exp. Clin. Cancer Res. 2018, 37, 36. [Google Scholar] [CrossRef] [Green Version]
- Alsfouk, A.A.; Alshibl, H.M.; Altwaijry, N.A.; Alsfouk, B.A.; Al-Abdullah, E.S. Synthesis and Biological Evaluation of Seliciclib Derivatives as Potent and Selective CDK9 Inhibitors for Prostate Cancer Therapy. Monatsh. Chem. 2021, 152, 109–120. [Google Scholar] [CrossRef]
- Senderowicz, A.M. Flavopiridol: The First Cyclin-Dependent Kinase Inhibitor in Human Clinical Trials. Investig. New Drugs 1999, 3, 313–320. [Google Scholar] [CrossRef] [PubMed]
- Kumar, S.K.; Fruth, B.; Roy, V.; Erlichman, C.; Stewart, A.K. Dinaciclib, a Novel CDK Inhibitor, Demonstrates Encouraging Single- Agent Activity in Patients with Relapsed Multiple Myeloma. Blood 2015, 125, 443–448. [Google Scholar] [CrossRef]
- Tong, W.; Chen, R.; Plunkett, W.; Siegel, D.; Sinha, R.; Harvey, R.D.; Badros, A.Z.; Popplewell, L.; Coutre, S.; Fox, J.A.; et al. Phase I and Pharmacologic Study of SNS-032, a Potent and Selective Cdk2,7, and 9 Inhibitor, in Patients with Advanced Chronic Lymphocytic Leukemia and Multiple Myeloma. J. Clin. Oncol. 2010, 28, 3015–3022. [Google Scholar] [CrossRef] [Green Version]
- Van der Biessen, D.A.J.; Burger, H.; Bruijn, P.D.; Lamers, C.H.J.; Naus, N.; Loferer, H.; Wiemer, E.A.C.; Mathijssen, R.H.J.; de Jonge, M.J.A. Phase I Study of RGB-286638, a Novel, Multitargeted Cyclin- Dependent Kinase Inhibitor in Patients with Solid Tumors. Clin. Cancer Res. 2014, 20, 4776–4784. [Google Scholar] [CrossRef] [Green Version]
- Walsby, E.; Pratt, G.; Shao, H.; Abbas, A.Y.; Fischer, P.M.; Bradshaw, T.D.; Brennan, P.; Fegan, C.; Wang, S.; Pepper, C. A Novel Cdk9 Inhibitor Preferentially Targets Tumor Cells and Synergizes with Fludarabine. Oncotarget 2014, 5, 375–385. [Google Scholar] [CrossRef] [Green Version]
- Zhai, S.; Senderowicz, A.M.; Sausville, E.A.; Figg, W.D. Flavopiridol, a Novel Cyclin-Dependent Kinase Inhibitor, in Clinical Development. Ann. Pharmacother. 2002, 36, 905–911. [Google Scholar] [CrossRef]
- Lücking, U.; Scholz, A.; Lienau, P.; Siemeister, G.; Kosemund, D.; Bohlmann, R.; Briem, H.; Terebesi, I.; Meyer, K.; Prelle, K.; et al. Identification of Atuveciclib (BAY 1143572), the First Highly Selective, Clinical PTEFb/CDK9 Inhibitor for the Treatment of Cancer. ChemMedChem 2017, 12, 1776–1793. [Google Scholar] [CrossRef]
- Cidado, J.; Boiko, S.; Proia, T.; Ferguson, D.; Criscione, S.W.; Martin, M.S.; Pop-Damkov, P.; Su, N.; Franklin, V.N.R.; Chilamakuri, C.S.R.; et al. AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses Mcl-1 and Induces Apoptosis in Hematologic Cancer Cells. Clin. Cancer Res. 2020, 26, 922–934. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhang, M.; Zhang, L.; Hei, R.; Li, X.; Cai, H.; Wu, X.; Zheng, Q.; Cai, C. CDK Inhibitors in Cancer Therapy, an Overview of Recent Development. Am. J. Cancer Res. 2021, 11, 1913–1935. [Google Scholar]
- Gojo, I.; Sadowska, M.; Walker, A.; Feldman, E.J.; Iyer, S.P.; Baer, M.R.; Sausville, E.A.; Lapidus, R.G.; Zhang, D.; Zhu, Y.; et al. Clinical and Laboratory Studies of the Novel Cyclin-Dependent Kinase Inhibitor Dinaciclib (SCH 727965) in Acute Leukemias. Cancer Chemother. Pharmacol. 2013, 72, 897–908. [Google Scholar] [CrossRef] [Green Version]
- Stephenson, J.J.; Nemunaitis, J.; Joy, A.A.; Martin, J.C.; Jou, Y.M.; Zhang, D.; Statkevich, P.; Yao, S.L.; Zhu, Y.; Zhou, H.; et al. Randomized Phase 2 Study of the Cyclin-Dependent Kinase Inhibitor Dinaciclib (MK-7965) versus Erlotinib in Patients with Non-Small Cell Lung Cancer. Lung Cancer 2014, 83, 219–223. [Google Scholar] [CrossRef] [PubMed]
- Mita, M.M.; Joy, A.A.; Mita, A.; Sankhala, K.; Jou, Y.M.; Zhang, D.; Statkevich, P.; Zhu, Y.; Yao, S.L.; Small, K.; et al. Randomized Phase II Trial of the Cyclin-Dependent Kinase Inhibitor Dinaciclib (MK-7965) versus Capecitabine in Patients with Advanced Breast Cancer. Clin. Breast Cancer 2014, 14, 169–176. [Google Scholar] [CrossRef]
- Conroy, A.; Stockett, D.E.; Walker, D.; Arkin, M.R.; Hoch, U.; Fox, J.A.; Hawtin, R.E. SNS-032 Is a Potent and Selective CDK 2, 7 and 9 Inhibitor That Drives Target Modulation in Patient Samples. Cancer Chemother. Pharmacol. 2009, 64, 723–732. [Google Scholar] [CrossRef]
- Chen, R.; Wierda, W.G.; Chubb, S.; Hawtin, R.E.; Fox, J.A.; Keating, M.J.; Gandhi, V.; Plunkett, W. Mechanism of Action of SNS-032, a Novel Cyclin-Dependent Kinase Inhibitor, in Chronic Lymphocytic Leukemia. Blood 2009, 113, 4637–4645. [Google Scholar] [CrossRef] [Green Version]
- Lin, T.S.; Ruppert, A.S.; Johnson, A.J.; Fischer, B.; Heerema, N.A.; Andritsos, L.A.; Blum, K.A.; Flynn, J.M.; Jones, J.A.; Hu, W.; et al. Phase II Study of Flavopiridol in Relapsed Chronic Lymphocytic Leukemia Demonstrating High Response Rates in Genetically High-Risk Disease. J. Clin. Oncol. 2009, 27, 6012–6018. [Google Scholar] [CrossRef] [PubMed]
- Karp, J.E.; Garrett-Mayer, E.; Estey, E.H.; Rudek, M.A.; Douglas Smith, B.; Greer, J.M.; Michelle Drye, D.; Mackey, K.; Dorcy, K.S.; Gore, S.D.; et al. Randomized Phase II Study of Two Schedules of Flavopiridol given as Timed Sequential Therapy with Cytosine Arabinoside and Mitoxantrone for Adults with Newly Diagnosed, Poor-Risk Acute Myelogenous Leukemia. Haematologica 2012, 97, 1736–1742. [Google Scholar] [CrossRef]
- Luecking, U.T.; Scholz, A.; Kosemund, D.; Bohlmann, R.; Briem, H.; Lienau, P.; Siemeister, G.; Terebesi, I.; Meyer, K.; Prelle, K.; et al. Abstract 984: Identification of Potent and Highly Selective PTEFb Inhibitor BAY 1251152 for the Treatment of Cancer: From p.o. to i.v. Application via Scaffold Hops. Cancer Res. 2017, 77, 984. [Google Scholar] [CrossRef]
- Byrne, M.; Frattini, M.G.; Ottmann, O.G.; Mantzaris, I.; Wermke, M.; Lee, D.J.; Morillo, D.; Scholz, A.; Ince, S.; Valencia, R.; et al. Phase I Study of the PTEFb Inhibitor BAY 1251152 in Patients with Acute Myelogenous Leukemia. Blood 2018, 132, 4055. [Google Scholar] [CrossRef]
- Cidado, J.; Proia, T.; Boiko, S.; Martin, M.S.; Criscione, S.; Ferguson, D.; Shao, W.; Drew, L. Abstract 310: AZD4573, a Novel CDK9 Inhibitor, Rapidly Induces Cell Death in Hematological Tumor Models through Depletion of Mcl1. Cancer Res. 2018, 78, 310. [Google Scholar] [CrossRef]
- Byth, K.F.; Thomas, A.; Hughes, G.; Forder, C.; McGregor, A.; Geh, C.; Oakes, S.; Green, C.; Walker, M.; Newcombe, N.; et al. AZD5438, a Potent Oral Inhibitor of Cyclin-Dependent Kinases 1, 2, and 9, Leads to Pharmacodynamic Changes and Potent Antitumor Effects in Human Tumor Xenografts. Mol. Cancer Ther. 2009, 8, 1856–1866. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mariaule, G.; Belmont, P. Cyclin-Dependent Kinase Inhibitors as Marketed Anticancer Drugs: Where Are We Now? A Short Survey. Molecules 2014, 19, 14366–14382. [Google Scholar] [CrossRef] [Green Version]
- Parry, D.; Guzi, T.; Shanahan, F.; Davis, N.; Prabhavalkar, D.; Wiswell, D.; Seghezzi, W.; Paruch, K.; Dwyer, M.P.; Doll, R.; et al. Dinaciclib (SCH 727965), a Novel and Potent Cyclin-Dependent Kinase Inhibitor. Mol. Cancer Ther. 2010, 9, 2344–2353. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Heath, E.I.; Bible, K.; Martell, R.E.; Adelman, D.C.; LoRusso, P.M. A Phase 1 Study Of SNS-032 (Formerly BMS-387032), A Potent Inhibitor Of Cyclin-Dependent Kinases 2, 7 And 9 Administered As A Single Oral Dose And Weekly Infusion In Patients With Metastatic Refractory Solid Tumors. Investig. New Drugs 2008, 26, 59–65. [Google Scholar] [CrossRef]
- Kim, I.K.; Nam, K.Y.; Kim, S.Y.; Park, S.J. Composition for Prevention and Treatment of Cancer Including CDK9 Inhibitor as Active Ingredient, University of Ulsan Foundation for Industry Cooperation. Patent KR1020180106188, 22 February 2019. [Google Scholar]
- Nandi, S.; Dey, R.; Dey, S.; Samadder, A.; Saxena, A.K. Naturally Sourced CDK Inhibitors and Current Trends in Structure-Based Synthetic Anticancer Drug Design by Crystallography. Anticancer Agents Med. Chem. 2022, 22, 485–498. [Google Scholar] [CrossRef] [PubMed]
- Alsfouk, A.A.; Alshibl, H.M.; Alsfouk, B.A.; Altwaijry, N.A.; Al-Abdullah, E.S. Synthesis and Biological Evaluation of Imadazo[1,2-a]Pyrazines as Anticancer and Antiviral Agents through Inhibition of CDK9 and Human Coronavirus. Pharmaceuticals 2022, 15, 859. [Google Scholar] [CrossRef] [PubMed]
- Cheol-Gyu, H.; Jeong-Hyeok, Y. Novel Imidazole Pyrazine Derivative Compound, a Method for Preparing the Same, and a Pharmaceutical Composition for Antiviral Treatment Containing the Same as an Active Ingredient, Sihwa Industriy. Patent 1020110097448, 31 August 2011. [Google Scholar]
- Nandi, S.; Kumar, M.; Saxena, M.; Saxena, A.K. The Antiviral and Antimalarial Drug Repurposing in Quest of Chemotherapeutics to Combat COVID-19 Utilizing Structure-Based Molecular Docking. Comb. Chem. High Throughput Screen. 2021, 24, 1055–1068. [Google Scholar] [CrossRef]
- Nandi, S.; Roy, H.; Gummadi, A.; Saxena, A.K. Exploring Spike Protein as Potential Target of Novel Coronavirus and to Inhibit the Viability Utilizing Natural Agents. Curr. Drug Targets 2021, 22, 2006–2020. [Google Scholar] [CrossRef] [PubMed]
- Daina, A.; Michielin, O.; Zoete, V. Swiss Target Prediction: Updated Data and New Features for Efficient Prediction of Protein Targets of Small Molecules. Nucleic Acids Res. 2019, 47, 357–364. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Li, Y.C.; Bai, W.Z.; Hashikawa, T. The Neuroinvasive Potential of SARS-CoV2 May Play a Role in the Respiratory Failure of COVID-19 Patients. J. Med. Virol. 2020, 92, 552–555. [Google Scholar] [CrossRef]
- V’kovski, P.; Kratzel, A.; Steiner, S.; Stalder, H.; Thiel, V. Coronavirus Biology and Replication: Implications for SARS-CoV-2. Nat. Rev. Microbiol. 2021, 19, 155–170. [Google Scholar] [CrossRef] [PubMed]
- Daina, A.; Michielin, O.; Zoete, V. SwissADME: A Free Web Tool to Evaluate Pharmacokinetics, Drug-Likeness and Medicinal Chemistry Friendliness of Small Molecules. Sci. Rep. 2017, 7, 42717. [Google Scholar] [CrossRef] [Green Version]
- Dong, J.; Wang, N.N.; Yao, Z.J.; Zhang, L.; Cheng, Y.; Ouyang, D.; Lu, A.P.; Cao, D.S. ADMETlab: A Platform for Systematic ADMET Evaluation Based on a Comprehensively Collected ADMET Database. J. Cheminform. 2018, 10, 29. [Google Scholar] [CrossRef]
- Choi, H.J.; Song, J.H.; Park, K.S.; Kwon, D.H. Inhibitory Effects of Quercetin 3-Rhamnoside on Influenza A Virus Replication. Eur. J. Pharm. Sci. 2009, 37, 329–333. [Google Scholar] [CrossRef]
- Pauwels, R.; Balzarini, J.; Baba, M.; Snoeck, R.; Schols, D.; Herdewijn, P.; Desmyter, J.; De Clercq, E. Rapid and Automated Tetrazolium-Based Colorimetric Assay for the Detection of Anti-HIV Compounds. J. Virol. Methods 1988, 20, 309–321. [Google Scholar] [CrossRef]
CDK9 Inhibitor | Flavopiridol | Dinaciclib | SNS-032 | |
---|---|---|---|---|
Structure | ||||
IC50 (nM) | CDK9 | 11 | 4 | 4 |
CDK2 | 282 | 1 | 48 | |
CDK4 | 132 | - | 925 | |
CDK5 | 110 | 1 | 340 | |
CDK7 | 514 | - | 62 | |
References | [8,34,35] | [8,36] | [8,37] |
CDK9 Inhibitor | Atuveciclib | BAY-1251152 | AZD4573 | |
---|---|---|---|---|
Structure | ||||
IC50 (nM) | CDK9 | 6 | 4 | 3 |
CDK2 | 1000 | 2920 | 10-fold greater than CDK9 IC50 | |
CDK4 | - | 50-fold greater than CDK9 IC50 | ||
CDK5 | 1600 | |||
CDK7 | >10,000 | |||
References | [21] | [32] | [22] |
Compound | CDK9 Inhibitory Activity IC50 (µM) |
---|---|
1a | 0.19 ± 0.003 |
1b | 1.78 ± 0.029 |
1c | 0.46 ± 0.008 |
1d | 0.18 ± 0.003 |
2a | 0.45 ± 0.008 |
2b | 0.30 ± 0.006 |
2c | 0.65 ± 0.011 |
2d | 0.89 ± 0.018 |
3a | 0.30 ± 0.005 |
3b | 0.23 ± 0.005 |
3c | 0.33 ± 0.007 |
3d | 1.66 ± 0.034 |
4a | 0.24 ± 0.004 |
4b | 1.22 ± 0.011 |
4c | 1.11 ± 0.02 |
4d | 0.57 ± 0.011 |
Dinaciclib | 0.08 ± 0.002 |
Compound | IC50 (µM) | |||
---|---|---|---|---|
MCF7 | HCT116 | K652 | Average of the Three Cell Lines | |
1a | 2.85 ± 0.03 | 21.55 ± 0.29 | 13.43 ± 0.19 | 12.61 |
1b | 99.16 ± 3.08 | 163.98 ± 2.1 | 168.23 ± 5.99 | 143.79 |
1c | 17.39 ± 0.34 | 16.39 ± 0.69 | 24.83 ± 0.61 | 19.54 |
1d | 12.35 ± 0.17 | 10.67 ± 0.16 | 11.83 ± 0.19 | 11.62 |
2a | 48.26 ± 0.24 | 136.42 ± 0.25 | 71.05 ± 0.39 | 85.24 |
2b | 45.93 ± 0.67 | 7.61 ± 2.12 | 38.84± 1.16 | 30.79 |
2c | 63.48 ± 0.7 | 56.56 ± 0.13 | 50.24 ± 0.69 | 56.76 |
2d | 71.24 ± 0.99 | 103.99 ± 0.98 | 25.30 ± 0.91 | 66.84 |
3a | 22.81 ± 0.33 | 4.13 ± 0.07 | 78.21 ± 1.32 | 35.05 |
3b | 16.42 ± 0.26 | 11 ± 0.19 | 4.5 ± 0.08 | 10.65 |
3c | 9.52 ± 0.15 | 42.22 ± 0.68 | 26.38 ± 0.43 | 26.04 |
3d | 119.91 ± 2.02 | 147.46 ± 2.75 | 152.74 ± 2.99 | 140.04 |
4a | 4.38 ± 0.06 | 38.2 ± 0.51 | 19.62 ± 0.26 | 20.73 |
4b | 16.21 ± 0.41 | 15.28 ± 0.13 | 23.15 ± 0.81 | 18.22 |
4c | 67.32 ± 1.01 | 97.388 ± 1.46 | 113.67 ± 1.7 | 92.79 |
4d | 25.07 ± 0.39 | 10.22 ± 0.16 | 47.11 ± 0.26 | 27.47 |
Staurosporine | 18.41 ± 0.4 | 10.86 ± 0.26 | 22.08 ± 0.56 | 17.12 |
SI* | ||||
---|---|---|---|---|
Compound | FHC IC50 (µM) | MCF7 | HCT116 | K652 |
1a | 58.64 ± 0.8 | 20.5 | 2.7 | 4.3 |
1c | 61.68 ± 0.96 | 15.16 | 17.55 | 15.8 |
1d | 187.31 ± 2.92 | 3.5 | 3.7 | 2.5 |
3b | 95.80 ± 1.72 | 5.8 | 8.7 | 21.3 |
4b | 74.31 ± 1.26 | 4.5 | 4.8 | 3.2 |
Staurosporine | 38.19 ± 0.97 | 2.07 | 3.5 | 1.7 |
Compound | Docking Score (Kcal/mol) | Interaction Residue (Type of Interaction) | Bond Length (Å) |
---|---|---|---|
1d | −8.3 | Cys106 (HB) | 1.83 |
Val33 (pi–sigma) | 3.63 | ||
Leu156 (pi–sigma) | 3.94 | ||
Ile25(pi–sigma) | 3.63 | ||
Phe103 (pi–pi stacked) | 3.90 | ||
Phe105 (pi–pi stacked) | 5.25 | ||
Al166 (pi–alkyl) | 4.57 | ||
Val79 (pi–alkyl) | 3.93 | ||
3b | −8.4 | Cys106 (HB) | 2.00 |
Asp109 (HB) | 2.53 | ||
Phe105 (pi–pi stacked) | 5.26 | ||
Leu156 (pi–sigma) | 3.99 | ||
Ile25 (pi–sigma) | 3.65 | ||
Ala46 (pi–alkyl) | 3.80 | ||
3c | −8 | Cys106 (HB) | 1.93 |
Asp104 (HB) | 2.79 | ||
Asp109 (HB) | 2.29 | ||
Phe105 (pi–pi stacked) | 5.17 | ||
Leu156 (pi–sigma) | 3.75 and 3.48 | ||
Val33 (pi–sigma) | 3.78 | ||
Ala46 (pi–alkyl) | 4.63 and 3.05 | ||
4a | −8 | Cys106 (HB) | 2.25 |
Asp167 (HB) | 3.14 | ||
Phe103 (pi–pi stacked) | 4.30 | ||
Phe105 (pi–pi stacked) | 5.48 | ||
Leu156 (pi–sigma) | 4.67 | ||
Ile25 (pi–sigma) | 3.76 | ||
Val33 (pi–alkyl) | 5.46 | ||
Al46 (pi–alkyl) | 5.43 and 4.69 |
Compound | CC50 (µM) | IC50 (µM) | SI |
---|---|---|---|
1a | 1319.90 | 1057.79 | 1.25 |
1c | 652.80 | 516.45 | 2.1 |
1d | 845.57 | 404.72 | 1.27 |
3a | 186.14 | 392.83 | 0.48 |
3b | 212.98 | 590.07 | 0.37 |
4a | 303.15 | 63.28 | 4.8 |
4b | 174.36 | 617.75 | 0.29 |
4c | 270.64 | 330.56 | 0.9 |
Ribavirin | 160.47 | 113.81 | 1.4 |
Docking Score (Kcal/mol) | Interaction Residue (Type of Interaction) | Bond Length (Å) |
---|---|---|
−8.7 | Glu166 (HB) | 2.15 |
Phe140 (HB) | 2.16 | |
Cys145 (pi–sulfur, pi–anion) | 4.57, 5.21 | |
His41 (pi–pi stacked) | 5.02 | |
Met165 (pi–Alkyl) | 5.12 | |
Asn142 (fluorine) | 3.51 |
Compound | M. wt | Clog P | tPSA (Å2) | Log S | HBA | HBD | Lipinski |
---|---|---|---|---|---|---|---|
1a | 286.37 | 4.02 | 55.36 | −4.44 | 3 | 1 | Yes; with 0 violations |
1d | 306.32 | 2.79 | 64.59 | −4.18 | 4 | 1 | Yes; with 0 violations |
2c | 332.36 | 2.42 | 82.68 | −4.44 | 4 | 3 | Yes; with 0 violations |
3b | 336.43 | 3.15 | 58.35 | −4.54 | 3 | 1 | Yes; with 0 violations |
4a | 285.32 | 2.55 | 55.11 | −3.84 | 4 | 1 | Yes; with 0 violations |
4b | 313.37 | 2.90 | 55.10 | −3.08 | 5 | 1 | Yes; with 0 violations |
Compound | 1d | 3b | 4a | ||
---|---|---|---|---|---|
Property | Test | Recommended | |||
Absorption | Papp (Caco-2 permeability) (cm/s) | >−5.15 | −4.871 | −4.677 | −4.525 |
Pg protein inhibitor | Inhibitor | Noninhibitor | Noninhibitor | ||
Pg protein substrate | Nonsubstrate | Nonsubstrate | Nonsubstrate | ||
HIA (human intestinal absorption) | HIA+ | HIA+ | HIA+ | ||
Bioavailability score | 0.55 | 0.55 | 0.55 | 0.55 | |
Distribution | PPB (Plasma protein binding) % | <90 | 81.421 | 82.13 | 78.804 |
BBB (Blood–brain barrier) | BBB+ | BBB+ | BBB+ | ||
VD (volume of distribution) L/kg | 0.04–20 | 0.125 | 0.725 | 0.121 | |
Metabolism | CYP3A4 inhibitor | Inhibitor | Inhibitor | Inhibitor | |
CYP3A4 substrate | Nonsubstrate | Substrate | Substrate | ||
Excretion | T1/2 (Half live) h | >0.5 | 1.812 | 1.827 | 1.807 |
Clearance mL/min/kg | <15 | 1.979 | 2.028 | 1.95 | |
Toxicity | hERG blocker | Blocker | Blocker | Blocker | |
Ames mutagenicity | Ames+ | Ames+ | Ames− | ||
Skin sensitivity | Nonsensitizer | Nonsensitizer | Nonsensitizer | ||
LD50 of acute toxicity | >500 mg/kg | 2.527 | 2.598 | 2.701 | |
DILI (drug-induced liver injury) | DILI+ | DILI+ | DILI+ | ||
FDAMDD (maximum recommended daily dose) | FDAMDD+ | FDAMDD− | FDAMDD+ |
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Alsfouk, A.A.; Alshibl, H.M.; Altwaijry, N.A.; Alanazi, A.; AlKamaly, O.; Sultan, A.; Alsfouk, B.A. New Imadazopyrazines with CDK9 Inhibitory Activity as Anticancer and Antiviral: Synthesis, In Silico, and In Vitro Evaluation Approaches. Pharmaceuticals 2023, 16, 1018. https://doi.org/10.3390/ph16071018
Alsfouk AA, Alshibl HM, Altwaijry NA, Alanazi A, AlKamaly O, Sultan A, Alsfouk BA. New Imadazopyrazines with CDK9 Inhibitory Activity as Anticancer and Antiviral: Synthesis, In Silico, and In Vitro Evaluation Approaches. Pharmaceuticals. 2023; 16(7):1018. https://doi.org/10.3390/ph16071018
Chicago/Turabian StyleAlsfouk, Aisha A., Hanan M. Alshibl, Najla A. Altwaijry, Ashwag Alanazi, Omkulthom AlKamaly, Ahlam Sultan, and Bshra A. Alsfouk. 2023. "New Imadazopyrazines with CDK9 Inhibitory Activity as Anticancer and Antiviral: Synthesis, In Silico, and In Vitro Evaluation Approaches" Pharmaceuticals 16, no. 7: 1018. https://doi.org/10.3390/ph16071018