1
|
Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
Collapse
Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| |
Collapse
|
2
|
Góral I, Wichur T, Sługocka E, Godyń J, Szałaj N, Zaręba P, Głuch-Lutwin M, Mordyl B, Panek D, Więckowska A. Connecting GSK-3β Inhibitory Activity with IKK-β or ROCK-1 Inhibition to Target Tau Aggregation and Neuroinflammation in Alzheimer's Disease-Discovery, In Vitro and In Cellulo Activity of Thiazole-Based Inhibitors. Molecules 2024; 29:2616. [PMID: 38893493 PMCID: PMC11173485 DOI: 10.3390/molecules29112616] [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: 04/29/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
GSK-3β, IKK-β, and ROCK-1 kinases are implicated in the pathomechanism of Alzheimer's disease due to their involvement in the misfolding and accumulation of amyloid β (Aβ) and tau proteins, as well as inflammatory processes. Among these kinases, GSK-3β plays the most crucial role. In this study, we present compound 62, a novel, remarkably potent, competitive GSK-3β inhibitor (IC50 = 8 nM, Ki = 2 nM) that also exhibits additional ROCK-1 inhibitory activity (IC50 = 2.3 µM) and demonstrates anti-inflammatory and neuroprotective properties. Compound 62 effectively suppresses the production of nitric oxide (NO) and pro-inflammatory cytokines in the lipopolysaccharide-induced model of inflammation in the microglial BV-2 cell line. Furthermore, it shows neuroprotective effects in an okadaic-acid-induced tau hyperphosphorylation cell model of neurodegeneration. The compound also demonstrates the potential for further development, characterized by its chemical and metabolic stability in mouse microsomes and fair solubility.
Collapse
Affiliation(s)
- Izabella Góral
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, 16 Lazarza St., 31-530 Krakow, Poland
| | - Tomasz Wichur
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
| | - Emilia Sługocka
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, 16 Lazarza St., 31-530 Krakow, Poland
| | - Justyna Godyń
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
| | - Natalia Szałaj
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
| | - Paula Zaręba
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
| | - Monika Głuch-Lutwin
- Department of Pharmacobiology, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (M.G.-L.); (B.M.)
| | - Barbara Mordyl
- Department of Pharmacobiology, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (M.G.-L.); (B.M.)
| | - Dawid Panek
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
| | - Anna Więckowska
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (I.G.); (T.W.); (E.S.); (J.G.); (N.S.); (P.Z.); (D.P.)
| |
Collapse
|
3
|
Drakontaeidi A, Pontiki E. Multi-Target-Directed Cinnamic Acid Hybrids Targeting Alzheimer's Disease. Int J Mol Sci 2024; 25:582. [PMID: 38203753 PMCID: PMC10778916 DOI: 10.3390/ijms25010582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Progressive cognitive decline in Alzheimer's disease (AD) is a growing challenge. Present therapies are based on acetylcholinesterase inhibition providing only temporary relief. Promising alternatives include butyrylcholinesterase (BuChE) inhibitors, multi-target ligands (MTDLs) that address the multi-factorial nature of AD, and compounds that target oxidative stress and inflammation. Cinnamate derivatives, known for their neuroprotective properties, show potential when combined with established AD agents, demonstrating improved efficacy. They are being positioned as potential AD therapeutic leads due to their ability to inhibit Aβ accumulation and provide neuroprotection. This article highlights the remarkable potential of cinnamic acid as a basic structure that is easily adaptable and combinable to different active groups in the struggle against Alzheimer's disease. Compounds with a methoxy substitution at the para-position of cinnamic acid display increased efficacy, whereas electron-withdrawing groups are generally more effective. The effect of the molecular volume is worthy of further investigation.
Collapse
Affiliation(s)
| | - Eleni Pontiki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| |
Collapse
|
4
|
Wu L, Liu W, Huang Y, Zhu C, Ma Q, Wu Q, Tian L, Feng X, Liu M, Wang N, Xu X, Liu X, Xu C, Qiu J, Xu Z, Liu W, Zhao Q. Development and structure-activity relationship of tacrine derivatives as highly potent CDK2/9 inhibitors for the treatment of cancer. Eur J Med Chem 2022; 242:114701. [DOI: 10.1016/j.ejmech.2022.114701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022]
|
5
|
Liu W, Huang Y, Wu L, Liu W, Jiang X, Xu Z, Zhao Q. Novel tacrine derivatives as potential CDK9 inhibitors with low cholinesterase inhibitory properties: design, synthesis, and biological evaluation. NEW J CHEM 2022. [DOI: 10.1039/d2nj03667c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel tacrine derivative ZLWT-48 possessed potent CDK9 inhibition activity (8.639 nM) and good selectivity over CDK2 (SI > 57).
Collapse
Affiliation(s)
- Wenwu Liu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Limeng Wu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Wenjie Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiaowen Jiang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Zihua Xu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Qingchun Zhao
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People's Republic of China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| |
Collapse
|
6
|
Babu A, Joy MN, Sunil K, Sajith AM, Santra S, Zyryanov GV, Konovalova OA, Butorin II, Muniraju K. Towards novel tacrine analogues: Pd(dppf)Cl 2·CH 2Cl 2 catalyzed improved synthesis, in silico docking and hepatotoxicity studies. RSC Adv 2022; 12:22476-22491. [PMID: 36105950 PMCID: PMC9366599 DOI: 10.1039/d2ra03225b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 01/23/2023] Open
Abstract
A plethora of 6-(hetero)aryl C–C and C–N bonded tacrine analogues has been made accessible by employing palladium mediated (Suzuki–Miyaura, Heck, Sonogashira, Stille and Buchwald) cross-coupling reactions, starting from either halogenated or borylated residues. The successful use of Pd(dppf)Cl2·CH2Cl2 as a common catalytic system in realizing all these otherwise challenging transformations is the highlight of our optimized protocols. The analogues thus synthesized allow the available chemical space around the C-6 of this biologically relevant tacrine core to be explored. The in silico docking studies of the synthesized compounds were carried out against the acetylcholinesterase (AChE) enzyme. The hepatotoxicity studies of these compounds were done against complexes of CYP1A2 and CYP3A4 proteins with known inhibitors like 7,8-benzoflavone and ketoconazole, respectively. 24 synthesized compounds by various cross-coupling reactions on 6-bromo tacrine. Molecular docking and toxicity prediction studies were also performed.![]()
Collapse
Affiliation(s)
- Aravinda Babu
- Department of Chemistry, SSIT, Sri Siddhartha Academy of Higher Education, Tumkur, Karnataka, India-572107
| | - Muthipeedika Nibin Joy
- Institute of Chemical Technology, Ural Federal University, 19 Mira Street, Yekaterinburg, Russia-620002
| | - K. Sunil
- Department of Chemistry, SSIT, Sri Siddhartha Academy of Higher Education, Tumkur, Karnataka, India-572107
| | | | - Sougata Santra
- Institute of Chemical Technology, Ural Federal University, 19 Mira Street, Yekaterinburg, Russia-620002
| | - Grigory V. Zyryanov
- Institute of Chemical Technology, Ural Federal University, 19 Mira Street, Yekaterinburg, Russia-620002
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, Yekaterinburg, Russia-620219
| | - Olga A. Konovalova
- Institute of Chemical Technology, Ural Federal University, 19 Mira Street, Yekaterinburg, Russia-620002
| | - Ilya I. Butorin
- Institute of Chemical Technology, Ural Federal University, 19 Mira Street, Yekaterinburg, Russia-620002
| | - Keesaram Muniraju
- Government Degree College-Puttur (Affiliated to S. V. University, Tirupati), Narayanavanam Road, Puttur, Chittoor (Dt), Andhra Pradesh, India-517583
| |
Collapse
|
7
|
Huang Y, Li D, Xu C, Zhu C, Wu L, Shen M, Li Y, Jiang X, Liu W, Zhao Q, Ren T. Discovery of novel and potent tacrine derivatives as CDK2 inhibitors. NEW J CHEM 2022. [DOI: 10.1039/d2nj03591j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
After optimization of the lead compound, ZLHT-7, a compound with 10-fold higher selectivity for CDK2 over CDK9, was discovered.
Collapse
Affiliation(s)
- Yaoguang Huang
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| | - Deping Li
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| | - Chang Xu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| | - Chengze Zhu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang, 110016, People's Republic of China
| | - Limeng Wu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| | - Meiling Shen
- School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China
| | - Yue Li
- School of Chemical Engineering, Sichuan University of Science & Engineering, 180 Xueyuan Street, Huixing Road, Zigong, Sichuan, 643000, People's Republic of China
| | - Xiaowen Jiang
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| | - Wenwu Liu
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| | - Qingchun Zhao
- Teaching Hospital of Shenyang Pharmaceutical University, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang, 110016, People's Republic of China
| | - Tianshu Ren
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, People’s Republic of China
| |
Collapse
|