1
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Wang H, Ba J, Kang Y, Gong Z, Liang T, Zhang Y, Qi J, Wang J. Recent Progress in CDK4/6 Inhibitors and PROTACs. Molecules 2023; 28:8060. [PMID: 38138549 PMCID: PMC10745860 DOI: 10.3390/molecules28248060] [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: 10/31/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cell division in eukaryotes is a highly regulated process that is critical to the life of a cell. Dysregulated cell proliferation, often driven by anomalies in cell Cyclin-dependent kinase (CDK) activation, is a key pathological mechanism in cancer. Recently, selective CDK4/6 inhibitors have shown clinical success, particularly in treating advanced-stage estrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer. This review provides an in-depth analysis of the action mechanism and recent advancements in CDK4/6 inhibitors, categorizing them based on their structural characteristics and origins. Furthermore, it explores proteolysis targeting chimers (PROTACs) targeting CDK4/6. We hope that this review could be of benefit for further research on CDK4/6 inhibitors and PROTACs.
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Affiliation(s)
| | | | | | | | | | | | - Jianguo Qi
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University Jinming Campus, Kaifeng 475004, China
| | - Jianhong Wang
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University Jinming Campus, Kaifeng 475004, China
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2
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Cheng SS, Qu YQ, Wu J, Yang GJ, Liu H, Wang W, Huang Q, Chen F, Li G, Wong CY, Wong VKW, Ma DL, Leung CH. Inhibition of the CDK9-cyclin T1 protein-protein interaction as a new approach against triple-negative breast cancer. Acta Pharm Sin B 2022; 12:1390-1405. [PMID: 35530158 PMCID: PMC9069406 DOI: 10.1016/j.apsb.2021.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/10/2021] [Accepted: 10/25/2021] [Indexed: 12/22/2022] Open
Abstract
Cyclin-dependent kinase 9 (CDK9) activity is correlated with worse outcomes of triple-negative breast cancer (TNBC) patients. The heterodimer between CDK9 with cyclin T1 is essential for maintaining the active state of the kinase and targeting this protein–protein interaction (PPI) may offer promising avenues for selective CDK9 inhibition. Herein, we designed and generated a library of metal complexes bearing the 7-chloro-2-phenylquinoline CˆN ligand and tested their activity against the CDK9–cyclin T1 PPI. Complex 1 bound to CDK9 via an enthalpically-driven binding mode, leading to disruption of the CDK9–cyclin T1 interaction in vitro and in cellulo. Importantly, complex 1 showed promising anti-metastatic activity against TNBC allografts in mice and was comparably active compared to cisplatin. To our knowledge, 1 is the first CDK9–cyclin T1 PPI inhibitor with anti-metastatic activity against TNBC. Complex 1 could serve as a new platform for the future design of more efficacious kinase inhibitors against cancer, including TNBC.
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Affiliation(s)
- Sha-Sha Cheng
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao 999078, China
| | - Yuan-Qing Qu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Jia Wu
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao 999078, China
| | - Guan-Jun Yang
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao 999078, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Hao Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qi Huang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
| | - Feng Chen
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao 999078, China
| | - Guodong Li
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao 999078, China
| | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao 999078, China
- Corresponding authors. Tel.: +853 8897 2408 (Vincent Kam Wai Wong), +852 3411 7075 (Dik-Lung Ma), +853 8822 4688 (Chung-Hang Leung).
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China
- Corresponding authors. Tel.: +853 8897 2408 (Vincent Kam Wai Wong), +852 3411 7075 (Dik-Lung Ma), +853 8822 4688 (Chung-Hang Leung).
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao 999078, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao 999078, China
- Corresponding authors. Tel.: +853 8897 2408 (Vincent Kam Wai Wong), +852 3411 7075 (Dik-Lung Ma), +853 8822 4688 (Chung-Hang Leung).
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3
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Patel B, Dahiya A, Das B, SAHOO ASHISHKUMAR. Visible‐Light‐Driven Isocyanide Insertion to o‐Alkenylanilines: A Route to Isoindolinone Synthesis. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202101431] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Bubul Das
- Indian Institute of Technology Guwahati INDIA
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4
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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5
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Biswas S, Porashar B, Arandhara PJ, Saikia AK. Synthesis of pyrimido[2,1- a]isoindolone and isoindolo[2,1- a]quinazolinone via intramolecular aza-Prins type reaction. Chem Commun (Camb) 2021; 57:11701-11704. [PMID: 34693411 DOI: 10.1039/d1cc04554g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel aza-Prins type cyclization reaction involving N-acyliminium ions and amides is reported for the synthesis of tetrahydropyrimido[2,1-a]isoindole-2,6-dione and 6,6a-dihydroisoindolo[2,1-a]quinazoline-5,11-dione derivatives in excellent yields. The strategy features inexpensive reagents, mild reaction conditions, and metal-free synthesis of N-heterocyclic frameworks. Further, post-synthetic modification results in the unprecedented formation of its triazole, tetracyclic diazacyclopenta[def]phenanthrene-1,4(9a1H)-dione and carbonyl derivatives.
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Affiliation(s)
- Subhamoy Biswas
- Department of Chemistry, Indian Institute of Technology, Guwahati, 781039, Assam, India.
| | - Bikoshita Porashar
- Department of Chemistry, Indian Institute of Technology, Guwahati, 781039, Assam, India.
| | - Pallav Jyoti Arandhara
- Department of Chemistry, Indian Institute of Technology, Guwahati, 781039, Assam, India.
| | - Anil K Saikia
- Department of Chemistry, Indian Institute of Technology, Guwahati, 781039, Assam, India.
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6
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Divya V, Pushpa VL. High-throughput virtual screening followed by in vitro investigation to identify new lead inhibitors of Cyclin Dependent Kinase 4. J Mol Graph Model 2021; 109:108020. [PMID: 34592583 DOI: 10.1016/j.jmgm.2021.108020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/11/2021] [Accepted: 09/02/2021] [Indexed: 11/15/2022]
Abstract
In the family of serine/threonine kinases, Cyclin Dependent Kinase 4 (CDK4), is an important regulator in numerous signal transduction pathways. The cell cycle is dysregulated in human breast adenocarcinoma (MCF-7). A set of various categorical QSAR models were generated and validated in the current examination. A recursive partition model, with predictive ability shown by an accuracy of greater than 0.90, was used for virtual screening of 500,000 molecules. Following a consecutive series of molecular docking procedures, followed by pharmacokinetic analysis of 49759 molecules predicted to have pIC50 greater than 7.39, 25 molecules displayed properties that could be described as drug-like. We selected the lead molecules in the MCF-7 cell line based on its ability to promote cell cycle progression.
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Affiliation(s)
- V Divya
- Department of Chemistry, Milad-E-Sherief Memorial College, Kayamkulam, Affiliated to University of Kerala, Kerala, PIN: 690502, India.
| | - V L Pushpa
- Research Department of Chemistry, DST-FIST Supported Department Sree Narayana College, Kollam, Affiliated to University of Kerala, Kerala, PIN: 691001, India.
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7
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Pharmacological relevance of CDK inhibitors in Alzheimer's disease. Neurochem Int 2021; 148:105115. [PMID: 34182065 DOI: 10.1016/j.neuint.2021.105115] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022]
Abstract
Evidence suggests that cell cycle activation plays a role in the pathophysiology of neurodegenerative diseases. Alzheimer's disease is a progressive, terminal neurodegenerative disease that affects memory and other important mental functions. Intracellular deposition of Tau protein, a hyperphosphorylated form of a microtubule-associated protein, and extracellular aggregation of Amyloid β protein, which manifests as neurofibrillary tangles (NFT) and senile plaques, respectively, characterize this condition. In recent years, however, several studies have concluded that cell cycle re-entry is one of the key causes of neuronal death in the pathogenesis of Alzheimer's disease. The eukaryotic cell cycle is well-coordinated machinery that performs critical functions in cell replenishment, such as DNA replication, cell creation, repair, and the birth of new daughter cells from the mother cell. The complex interplay between the levels of various cyclins and cyclin-dependent kinases (CDKs) at different checkpoints is needed for cell cycle synchronization. CDKIs (cyclin-dependent kinase inhibitors) prevent cyclin degradation and CDK inactivation. Different external and internal factors regulate them differently, and they have different tissue expression and developmental functions. The checkpoints ensure that the previous step is completed correctly before starting the new cell cycle phase, and they protect against the transfer of defects to the daughter cells. Due to the development of more selective and potent ATP-competitive CDK inhibitors, CDK inhibitors appear to be on the verge of having a clinical impact. This avenue is likely to yield new and effective medicines for the treatment of cancer and other neurodegenerative diseases. These new methods for recognizing CDK inhibitors may be used to create non-ATP-competitive agents that target CDK4, CDK5, and other CDKs that have been recognized as important therapeutic targets in Alzheimer's disease treatment.
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8
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Shawky AM, Ibrahim NA, Abourehab MAS, Abdalla AN, Gouda AM. Pharmacophore-based virtual screening, synthesis, biological evaluation, and molecular docking study of novel pyrrolizines bearing urea/thiourea moieties with potential cytotoxicity and CDK inhibitory activities. J Enzyme Inhib Med Chem 2021; 36:15-33. [PMID: 33103497 PMCID: PMC7594867 DOI: 10.1080/14756366.2020.1837124] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In the current study, virtual screening of a small library of 1302 pyrrolizines bearing urea/thiourea moieties was performed. The top-scoring hits were synthesised and evaluated for their cytotoxicity against three cancer (MCF-7, A2780, and HT29) and one normal (MRC-5) cell lines. The results of the MTT assay revealed potent cytotoxic activities for most of the new compounds (IC50 = 0.16–34.13 μM). The drug-likeness study revealed that all the new compounds conform to Lipinski’s rule. Mechanistic studies of compounds 18 b, 19a, and 20a revealed the induction of apoptosis and cell cycle arrest at the G1 phase in MCF-7 cells. The three compounds also displayed potent inhibitory activity against CDK-2 (IC50 = 25.53–115.30 nM). Moreover, the docking study revealed a nice fitting of compound 19a into the active sites of CDK-2/6/9. These preliminary results suggested that compound 19a could serve as a promising scaffold in the discovery of new potent anticancer agents.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Nashwa A Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmed M Gouda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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9
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Widyan K. An Improved Synthesis of Polyfunctional Acyl Azides in PEG 400. ORG PREP PROCED INT 2021. [DOI: 10.1080/00304948.2020.1862029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Khalid Widyan
- Department of Chemistry, Tafila Technical University, Tafila, Jordan
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10
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He Y, Yan Y, Ren Z, Wang Y, Yu Q, Xiong J, Wang M. Regioselective Synthesis of 2,3‐Dihydrobenzo[
f
]isoindolones via Ag‐Catalyzed Sequential Ugi 4CR/Cascade Radical Cyclization Reaction. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ying‐Chun He
- Institute of Applied Chemistry Shanxi University Taiyuan 030006 People's Republic of China
| | - Yan‐Mei Yan
- Department of Chemistry Taiyuan Normal University Jinzhong 030619 People's Republic of China
| | - Zhen‐Xing Ren
- Institute of Applied Chemistry Shanxi University Taiyuan 030006 People's Republic of China
| | - Yong‐Zhao Wang
- Engineering Research Center of Ministry of Education for Fine Chemicals Shanxi University Taiyuan 030006 People's Republic of China
| | - Qiang Yu
- Department of medical imaging Shanxi Medical University Taiyuan 030006 People's Republic of China
| | - Jun Xiong
- School of Pharmacy Hubei University of Science and Technology Xianning 437100 People's Republic of China
| | - Meng‐Liang Wang
- Institute of Applied Chemistry Shanxi University Taiyuan 030006 People's Republic of China
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11
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Yuan K, Wang X, Dong H, Min W, Hao H, Yang P. Selective inhibition of CDK4/6: A safe and effective strategy for developing anticancer drugs. Acta Pharm Sin B 2021; 11:30-54. [PMID: 33532179 PMCID: PMC7838032 DOI: 10.1016/j.apsb.2020.05.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 01/02/2023] Open
Abstract
The sustained cell proliferation resulting from dysregulation of the cell cycle and activation of cyclin-dependent kinases (CDKs) is a hallmark of cancer. The inhibition of CDKs is a highly promising and attractive strategy for the development of anticancer drugs. In particular, third-generation CDK inhibitors can selectively inhibit CDK4/6 and regulate the cell cycle by suppressing the G1 to S phase transition, exhibiting a perfect balance between anticancer efficacy and general toxicity. To date, three selective CDK4/6 inhibitors have received approval from the U.S. Food and Drug Administration (FDA), and 15 CDK4/6 inhibitors are in clinical trials for the treatment of cancers. In this perspective, we discuss the crucial roles of CDK4/6 in regulating the cell cycle and cancer cells, analyze the rationale for selectively inhibiting CDK4/6 for cancer treatment, review the latest advances in highly selective CDK4/6 inhibitors with different chemical scaffolds, explain the mechanisms associated with CDK4/6 inhibitor resistance and describe solutions to overcome this issue, and briefly introduce proteolysis targeting chimera (PROTAC), a new and revolutionary technique used to degrade CDK4/6.
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Key Words
- AKT, protein kinase B
- AML, acute myeloid leukemia
- CDK4/6
- CDKs, cyclin-dependent kinases
- CIP/KIP, cyclin-dependent kinase inhibitor 1/kinase inhibitory protein
- CKIs, cyclin-dependent kinase inhibitors
- CPU, China Pharmaceutical University
- CRPC, castration-resistant prostate cancer
- Cancer
- Cell cycle
- Drug resistance
- ER, estrogen receptor
- ERK, extracellular regulated protein kinases
- FDA, U.S. Food and Drug Administration
- FLT, fms-like tyrosine kinase
- HER2, human epidermal growth factor receptor 2
- INK4, inhibitors of CDK4
- JAK, janus kinase
- MCL, mantle cell lymphoma
- MM, multiple myeloma
- NSCLC, non-small cell lung cancer
- ORR, overall response rates
- PDK1, 3-phosphoinositide-dependent protein kinase 1
- PFS, progression-free survival
- PI3K, phosphatidylinositol 3-hydroxy kinase
- PR, progesterone receptor
- PROTAC
- PROTAC, proteolysis targeting chimera
- RB, retinoblastoma protein
- SPH, Shanghai Pharmaceuticals Holding Co., Ltd.
- STATs, signal transducers and activators of transcription
- Selectivity
- UNISA, University of South Australia
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Affiliation(s)
- Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haojie Dong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding authors. Tel.: +86 13681986682.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding authors. Tel.: +86 13681986682.
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12
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Konar D, Maru S, Kar S, Kumar K. Synthesis and Clinical Development of Palbociclib: An overview. Med Chem 2020; 18:2-25. [PMID: 33280599 DOI: 10.2174/1573406417666201204161243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 09/29/2020] [Accepted: 10/12/2020] [Indexed: 11/22/2022]
Abstract
Breast cancer is the second most commonly identified cancer in women in the United States after skin cancer. The past few years have seen a substantial increase in breast cancer awareness campaigns and active research in fields of diagnosis and targeted therapy. These factors have led to a better mechanistic understanding of the disease, detection at earlier stages and more personalized approach to treatment, ultimately causing a crucial increase in the survival rates after detection. However, with the advances in treatment, cases of patients developing primary resistance and acquired resistance are increasing. Most of the breast cancers which develop resistance to therapy are ER+ and are typically treated with tamoxifen and fulvestrant. These drugs either lower the levels of estrogen or inhibit the receptors for estrogen and prevent the tumor from spreading. Around one third of women treated with these drugs develop resistance to them, lowering their chances of survival. This has directed to the search of newer drug therapies to target advanced breast cancer and resistance. One of these efforts has resulted in the development of Palbociclib, a first in class inhibitor of cyclin dependent kinases 4 and 6 (CDK4 and CDK6), which was granted accelerated approval from FDA for combination therapy in postmenopausal women with ER+, HER2- metastatic breast cancer. This review is focused on the various aspects of "Palbociclib" including its synthesis, molecular modeling studies and efficacy and safety profile with clinical trials data.
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Affiliation(s)
- Debabrata Konar
- National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar, Mohali, Punjab-160062. India
| | - Saurabh Maru
- School of Pharmacy and Technology Management, SVKM's NMIMS, Shirpur, Maharashtra-425405. India
| | - Subhabrata Kar
- Schoolof Biosciences, ApeejayStya University, Sohna-Palwal Road, Sohna, Gurgaon, Haryana-122103. India
| | - Kapil Kumar
- National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar, Mohali, Punjab-160062. India
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Shaaban S, Davies C, Merten C, Flegel J, Otte F, Strohmann C, Waldmann H. Rh III -Catalyzed C-H Activation of Aryl Hydroxamates for the Synthesis of Isoindolinones. Chemistry 2020; 26:10729-10734. [PMID: 32428319 PMCID: PMC7496876 DOI: 10.1002/chem.202002384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 01/20/2023]
Abstract
RhIII -catalyzed C-H functionalization reaction yielding isoindolinones from aryl hydroxamates and ortho-substituted styrenes is reported. The reaction proceeds smoothly under mild conditions at room temperature, and tolerates a range of functional groups. Experimental and computational investigations support that the high regioselectivity observed for these substrates results from the presence of an ortho-substituent embedded in the styrene. The resulting isoindolinones are valuable building blocks for the synthesis of bioactive compounds. They provide easy access to the natural-product-like compounds, isoindolobenzazepines, in a one-pot two-step reaction. Selected isoindolinones inhibited Hedgehog (Hh)-dependent differentiation of multipotent murine mesenchymal progenitor stem cells into osteoblasts.
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Affiliation(s)
- Saad Shaaban
- Max-Planck-Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Caitlin Davies
- Max-Planck-Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Technical University DortmundFaculty of Chemical BiologyOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Christian Merten
- Ruhr University BochumOrganic Chemistry IIUniversitätsstrasse 15044801BochumGermany
| | - Jana Flegel
- Max-Planck-Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Technical University DortmundFaculty of Chemical BiologyOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Felix Otte
- Technical University DortmundDepartment of Inorganic ChemistryOtto-Hahn-Strasse 644227DortmundGermany
| | - Carsten Strohmann
- Technical University DortmundDepartment of Inorganic ChemistryOtto-Hahn-Strasse 644227DortmundGermany
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Technical University DortmundFaculty of Chemical BiologyOtto-Hahn-Strasse 4a44227DortmundGermany
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14
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Kumar M, Verma S, Verma AK. Ru(II)-Catalyzed Oxidative Olefination of Benzamides: Switchable Aza-Michael and Aza-Wacker Reaction for Synthesis of Isoindolinones. Org Lett 2020; 22:4620-4626. [DOI: 10.1021/acs.orglett.0c01237] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Shalini Verma
- Department of Chemistry, University of Delhi, Delhi 110007, India
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15
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Maryam A, Khalid RR, Siddiqi AR, Ece A. E-pharmacophore based virtual screening for identification of dual specific PDE5A and PDE3A inhibitors as potential leads against cardiovascular diseases. J Biomol Struct Dyn 2020; 39:2302-2317. [DOI: 10.1080/07391102.2020.1748718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul, Turkey
| | | | | | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul, Turkey
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Abstract
Aim: CDK4/6 have critical roles in the early stage of the cell cycle. CDK2 acts later in the cell cycle and has a considerably broader range of protein substrates, some of which are essential for normal cell proliferation. Therefore, increasing the selectivity of cyclin-dependent kinase (CDK) inhibitors is critical. Methodology: In this study, we construct a versatile, specific CDK4 pharmacophore model that not only matches well with 8119 of the reported 9349 CDK4/6 inhibitors but also differentiates from the CDK2 pharmacophore. Results & Conclusion: we demonstrate the activity and selectivity determinants of CDK4/6 selective inhibitors based on the CDK4 pharmacophore model. Finally, we propose the future optimization strategy for CDK4/6 selective inhibitors, providing a theoretical basis for further research and development of CDK4/6 selective inhibitors.
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17
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Synthesis of novel isoindolone derivatives via cascade reactions. Contrasting diastereoselectivity under solution-phase vis-a-vis solvent-free ball-milling reaction conditions. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.130594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Sroor FM, Abdelmoniem AM, Abdelhamid IA. Facile Synthesis, Structural Activity Relationship, Molecular Modeling and In Vitro Biological Evaluation of New Urea Derivatives with Incorporated Isoxazole and Thiazole Moieties as Anticancer Agents. ChemistrySelect 2019. [DOI: 10.1002/slct.201901415] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Farid M. Sroor
- Organometallic and Organometalloid Chemistry DepartmentNational Research Centre 12622 Cairo Egypt
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19
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Xu M, Yuan Y, Wang Y, Tao Q, Wang C, Li Y. Controllable α- or β-Functionalization of α-Diazoketones with Aromatic Amides via Cobalt-Catalyzed C–H Activation: A Regioselective Approach to Isoindolinones. Org Lett 2019; 21:6264-6269. [DOI: 10.1021/acs.orglett.9b02145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Murong Xu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road 200241, Shanghai, China
| | - Yang Yuan
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road 200241, Shanghai, China
| | - Ye Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road 200241, Shanghai, China
| | - Qihai Tao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road 200241, Shanghai, China
| | - Chengyu Wang
- School of Chemistry and Chemical Engineering, Linyi University, Shuangling Road, Linyi, Shandong 276000, China
| | - Yanzhong Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road 200241, Shanghai, China
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20
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Abstract
Introduction: The development of drug candidates with a defined selectivity profile and a unique molecular structure is of fundamental interest for drug discovery. In contrast to the costly screening of large substance libraries, the targeted de novo design of a drug by using structural information of either the biological target and/or structure-activity relationship data of active modulators offers an efficient and intellectually appealing alternative. Areas covered: This review provides an overview on the different techniques of de novo drug design (ligand-based drug design, structure-based drug design, and fragment-based drug design) and highlights successful examples of this targeted approach toward selective modulators of therapeutically relevant targets. Expert opinion: De novo drug design has established itself as a very efficient method for the development of potent and selective modulators for a variety of different biological target classes. The ever-growing wealth of structural data on therapeutic targets will certainly further enhance the importance of de novo design for the drug discovery process in the future. However, a consistent use of the terminology of de novo drug design in the scientific literature should be sought.
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Affiliation(s)
- Thomas Fischer
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
| | - Silvia Gazzola
- b Dipartimento di Scienza e Alta Tecnologia , Università degli Studi dell'Insubria , Como , Italy
| | - Rainer Riedl
- a Center of Organic and Medicinal Chemistry, Institute of Chemistry and Biotechnology , Zurich University of Applied Sciences ZHAW , Wädenswil , Switzerland
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21
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Schneider G, Clark DE. Automated De Novo Drug Design: Are We Nearly There Yet? Angew Chem Int Ed Engl 2019; 58:10792-10803. [PMID: 30730601 DOI: 10.1002/anie.201814681] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Indexed: 11/09/2022]
Abstract
Medicinal chemistry and, in particular, drug design have often been perceived as more of an art than a science. The many unknowns of human disease and the sheer complexity of chemical space render decision making in medicinal chemistry exceptionally demanding. Computational models can assist the medicinal chemist in this endeavour. Provided here is an overview of recent examples of automated de novo molecular design, a discussion of the concepts and computational approaches involved, and the daring prediction of some of the possibilities and limitations of drug design using machine intelligence.
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Affiliation(s)
- Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - David E Clark
- Charles River, 6-9 Spire Green Centre, Harlow, Essex, CM19 5TR, UK
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22
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Schneider G, Clark DE. Automated De Novo Drug Design: Are We Nearly There Yet? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gisbert Schneider
- ETH ZurichDepartment of Chemistry and Applied Biosciences, RETHINK Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - David E. Clark
- Charles River 6–9 Spire Green Centre Harlow Essex CM19 5TR UK
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23
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Miura H, Kimura Y, Terajima S, Shishido T. Ruthenium-Catalyzed Synthesis of Isoindolinones via Amide-Directed Addition of Aromatic C-H Bonds to Aldimines. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Hiroki Miura
- Department of Applied Chemistry for Environment; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
- Research Center for Hydrogen Energy-based Society; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
- Elements Strategy Initiative for Catalysts & Batteries; Kyoto University; 1-30 Goryo-Ohara, Nishikyo-ku Kyoto 615-8245 Japan
| | - Yuriko Kimura
- Department of Applied Chemistry for Environment; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
| | - Sachie Terajima
- Department of Applied Chemistry for Environment; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
| | - Tetsuya Shishido
- Department of Applied Chemistry for Environment; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
- Research Center for Hydrogen Energy-based Society; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
- Research Center for Gold Chemistry; Minami-Osawa, Hachioji Tokyo 192-0397 Japan
- Elements Strategy Initiative for Catalysts & Batteries; Kyoto University; 1-30 Goryo-Ohara, Nishikyo-ku Kyoto 615-8245 Japan
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24
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Vasanthakumari D, Vadakkethil Lalithabhai P, Kanthimathi Bahuleyan M. An in silico approach to discover the best molecular modeling strategy for designing novelCDK4 inhibitors. Chem Biol Drug Des 2019; 93:556-569. [DOI: 10.1111/cbdd.13452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/23/2018] [Accepted: 11/17/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Divya Vasanthakumari
- Department of ChemistrySree Narayana College Kollam Kerala India
- Department of ChemistryMilad‐E‐Sherief Memorial College Kayamkulam Kerala India
| | | | - Manoj Kanthimathi Bahuleyan
- Department of ChemistrySree Narayana College Kollam Kerala India
- Department of ChemistrySree Narayana College Cherthala Kerala India
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25
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Fang YM, Lin DQ, Yao SJ. Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification. J Chromatogr A 2018; 1571:1-15. [DOI: 10.1016/j.chroma.2018.07.082] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/12/2018] [Accepted: 07/29/2018] [Indexed: 10/28/2022]
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26
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Li J, Jiao A, Chen S, Wu Z, Xu E, Jin Z. RETRACTED: Application of the small-angle X-ray scattering technique for structural analysis studies: A review. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Abstract
Fragment-based drug design strategies have been used in drug discovery since it was first demonstrated using experimental structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. The underlying idea is that existing or new chemical entities with known desirable properties may serve both as tool compounds and as starting points for hit-to-lead expansion. Despite the recent advancements, there remain challenges to overcome, such as assembly of the synthetically feasible structures, development of scoring functions to correlate structure and their activities, and fine tuning of the promising molecules. This chapter first covers the theoretical background needed to understand the concepts and the challenges related to the field of study, followed by the description of important protocols and related software. Case studies are presented to demonstrate practical applications.
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28
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Miura H, Terajima S, Tsutsui K, Shishido T. Ruthenium-Catalyzed Addition of Aromatic Amides to Internal Alkynes and Subsequent Intramolecular Cyclization for the Atom-Economical Synthesis of Isoindolinones. J Org Chem 2017; 82:1231-1239. [DOI: 10.1021/acs.joc.6b02552] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hiroki Miura
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8520, Japan
| | | | | | - Tetsuya Shishido
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8520, Japan
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29
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Huang Z, Chen Q, Yang X, Liu Y, Zhang L, Lu T, Zhou Q. Phosphine-mediated domino reactions of phthalimidomalonates with allenoates or but-2-ynoate: facile entry into highly functionalized pyrroloisoindolinone derivatives. Org Chem Front 2017. [DOI: 10.1039/c6qo00775a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A phosphine-mediated γ-umpolung/Wittig/γ-umpolung reaction between phthalimidomalonates and allenoates/but-2-ynoate furnishes highly functionalized pyrroloisoindolinone derivatives in synthetically useful yields.
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Affiliation(s)
- Zhusheng Huang
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Qingqing Chen
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Xiuqin Yang
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Yang Liu
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Li Zhang
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Tao Lu
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Qingfa Zhou
- State Key Laboratory of Natural Medicines
- Department of Organic Chemistry
- China Pharmaceutical University
- Nanjing
- P. R. China
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30
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Zhang X, Tang Z, Niu X, Li Z, Fan X, Zhang G. Selenium-catalyzed carbonylation of 2-aminothiazole with nitro aromatics to N-aryl-N′-2-thiazolylureas. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.10.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Mushtaq G, Greig NH, Anwar F, Al-Abbasi FA, Zamzami MA, Al-Talhi HA, Kamal MA. Neuroprotective Mechanisms Mediated by CDK5 Inhibition. Curr Pharm Des 2016; 22:527-34. [PMID: 26601962 DOI: 10.2174/1381612822666151124235028] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 11/24/2015] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) is a proline-directed serine/threonine kinase belonging to the family of cyclin-dependent kinases. In addition to maintaining the neuronal architecture, CDK5 plays an important role in the regulation of synaptic plasticity, neurotransmitter release, neuron migration and neurite outgrowth. Although various reports have shown links between neurodegeneration and deregulation of cyclin-dependent kinases, the specific role of CDK5 inhibition in causing neuroprotection in cases of neuronal insult or in neurodegenerative diseases is not wellunderstood. This article discusses current evidence for the involvement of CDK5 deregulation in neurodegenerative disorders and neurodegeneration associated with stroke through various mechanisms. These include upregulation of cyclin D1 and overactivation of CDK5 mediated neuronal cell death pathways, aberrant hyperphosphorylation of human tau proteins and/or neurofilament proteins, formation of neurofibrillary lesions, excitotoxicity, cytoskeletal disruption, motor neuron death (due to abnormally high levels of CDK5/p25) and colchicine- induced apoptosis in cerebellar granule neurons. A better understanding of the role of CDK5 inhibition in neuroprotective mechanisms will help scientists and researchers to develop selective, safe and efficacious pharmacological inhibitors of CDK5 for therapeutic use against human neurodegenerative disorders, such as Alzheimer's disease, amyotrophic lateral sclerosis and neuronal loss associated with stroke.
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Affiliation(s)
- Gohar Mushtaq
- Department of Biochemistry, College of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National, Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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32
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Abstract
Cyclin-dependent kinases (CDKs) are core components of the cell cycle machinery that govern the transition between phases during cell cycle progression. Abnormalities in CDKs activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. One of the main bottlenecks hampering the development of drugs for kinase is the difficulty to attain selectivity. A huge variety of small molecules have been reported as CDK inhibitors, as potential anticancer agents, but none of these has been approved for commercial use. Computer-based molecular design supports drug discovery by suggesting novel new chemotypes and compound modifications for lead candidate optimization. One of the methods known as de novo ligand design technique has emerged as a complementary approach to high-throughput screening. Several automated de novo software programs have been written, which automatically design novel structures to perfectly fit in known binding site. The de novo design supports drug discovery assignments by generating novel pharmaceutically active agents with desired properties in a cost as well as time efficient approach. This chapter describes procedure and an overview of computer-based molecular de novo design methods on a conceptual level with successful examples of CDKs inhibitors.
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33
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El Newahie AMS, Ismail NSM, Abou El Ella DA, Abouzid KAM. Quinoxaline-Based Scaffolds Targeting Tyrosine Kinases and Their Potential Anticancer Activity. Arch Pharm (Weinheim) 2016; 349:309-26. [PMID: 27062086 DOI: 10.1002/ardp.201500468] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/06/2016] [Accepted: 03/11/2016] [Indexed: 12/31/2022]
Abstract
Quinoxaline derivatives, also called benzopyrazines, are an important class of heterocyclic compounds. Quinoxalines have drawn great attention due to their wide spectrum of biological activities. They are considered as an important basis for anticancer drugs due to their potential activity as protein kinase inhibitors. In this review, we focus on the chemistry of the quinoxaline derivatives, the strategies for their synthesis, their potential activities against various tyrosine kinases, and on the structure-activity relationship studies reported to date.
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Affiliation(s)
- Aliya M S El Newahie
- Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry, October University for Modern Science and Arts (MSA), Cairo, Egypt
| | - Nasser S M Ismail
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries, Department of Pharmaceutical Chemistry, Future University, Cairo, Egypt
| | - Dalal A Abou El Ella
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ain Shams University, Abbassia, Cairo, Egypt
| | - Khaled A M Abouzid
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ain Shams University, Abbassia, Cairo, Egypt
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34
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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35
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Abstract
Computational medicinal chemistry offers viable strategies for finding, characterizing, and optimizing innovative pharmacologically active compounds. Technological advances in both computer hardware and software as well as biological chemistry have enabled a renaissance of computer-assisted "de novo" design of molecules with desired pharmacological properties. Here, we present our current perspective on the concept of automated molecule generation by highlighting chemocentric methods that may capture druglike chemical space, consider ligand promiscuity for hit and lead finding, and provide fresh ideas for the rational design of customized screening of compound libraries.
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Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.,inSili.com LLC , Segantinisteig 3, 8049 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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36
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Zhou QF, Ge FF, Chen QQ, Lu T. Construction of pyrazolo[5,1-a]isoindol-8(3aH)-one derivatives via phosphine-catalyzed cyclization of electron-deficient alkynes and N-amino substituted phthalimide. RSC Adv 2016. [DOI: 10.1039/c5ra17267e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel method for the synthesis of diversely functionalized pyrazolo[5,1-a]isoindol-8(3aH)-ones is developed via phosphine-catalyzed reaction of electron-deficient alkynes and N-amino substituted phthalimide.
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Affiliation(s)
- Qing-Fa Zhou
- School of Basic Sciences
- China Pharmaceutical University
- Nanjing
- P. R. China
- State Key Laboratory of Natural Medicines
| | - Fei-Fei Ge
- School of Basic Sciences
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Qing-Qing Chen
- School of Basic Sciences
- China Pharmaceutical University
- Nanjing
- P. R. China
| | - Tao Lu
- School of Basic Sciences
- China Pharmaceutical University
- Nanjing
- P. R. China
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37
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Hagui W, Yuan K, Besbes N, Srasra E, Soulé JF, Doucet H. Palladium-Catalyzed Iterative C−H Bond Arylations: Synthesis of Medium-Size Heterocycles with a Bridgehead Nitrogen Atom. ChemCatChem 2015. [DOI: 10.1002/cctc.201500652] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wided Hagui
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes 1; Organométalliques Matériaux et Catalyse; Campus de Beaulieu 35042 Rennes France
- Université de Tunis El Manar; Falculté des Sciences de Tunis; Campus Universitaire El-Manar 2092 El Manar Tunis Tunisia
- Laboratoire Physicochimie des Matériaux Minéraux et leurs Applications; Centre National des Recherches en Sciences des Matériaux; Technopole de Bordj Cedria; Soliman 8027 Tunisia
| | - Kedong Yuan
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes 1; Organométalliques Matériaux et Catalyse; Campus de Beaulieu 35042 Rennes France
| | - Néji Besbes
- Laboratoire Physicochimie des Matériaux Minéraux et leurs Applications; Centre National des Recherches en Sciences des Matériaux; Technopole de Bordj Cedria; Soliman 8027 Tunisia
| | - Ezzeddine Srasra
- Laboratoire Physicochimie des Matériaux Minéraux et leurs Applications; Centre National des Recherches en Sciences des Matériaux; Technopole de Bordj Cedria; Soliman 8027 Tunisia
| | - Jean-François Soulé
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes 1; Organométalliques Matériaux et Catalyse; Campus de Beaulieu 35042 Rennes France
| | - Henri Doucet
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes 1; Organométalliques Matériaux et Catalyse; Campus de Beaulieu 35042 Rennes France
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38
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Nozawa-Kumada K, Kadokawa J, Kameyama T, Kondo Y. Copper-Catalyzed sp3 C–H Aminative Cyclization of 2-Alkyl-N-arylbenzamides: An Approach for the Synthesis of N-Aryl-isoindolinones. Org Lett 2015; 17:4479-81. [DOI: 10.1021/acs.orglett.5b02235] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kanako Nozawa-Kumada
- Graduate
School of Pharmaceutical
Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Jun Kadokawa
- Graduate
School of Pharmaceutical
Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takehiro Kameyama
- Graduate
School of Pharmaceutical
Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yoshinori Kondo
- Graduate
School of Pharmaceutical
Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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39
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N N, Zhu H, Liu J, V K, C GPD, Chakraborty C, Chen L. Analysing the Effect of Mutation on Protein Function and Discovering Potential Inhibitors of CDK4: Molecular Modelling and Dynamics Studies. PLoS One 2015; 10:e0133969. [PMID: 26252490 PMCID: PMC4529227 DOI: 10.1371/journal.pone.0133969] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/03/2015] [Indexed: 11/18/2022] Open
Abstract
The cyclin-dependent kinase 4 (CDK4)-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1) and protein-ligand (CDK4-flavopiridol) interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL) _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment.
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Affiliation(s)
- Nagasundaram N
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Hailong Zhu
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- * E-mail:
| | - Jiming Liu
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Karthick V
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - George Priya Doss C
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Chiranjib Chakraborty
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- Department of Bioinformatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, Uttra Pradesh, India
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Wróbel TM, Kiełbus M, Kaczor AA, Kryštof V, Karczmarzyk Z, Wysocki W, Fruziński A, Król SK, Grabarska A, Stepulak A, Matosiuk D. Discovery of nitroaryl urea derivatives with antiproliferative properties. J Enzyme Inhib Med Chem 2015; 31:608-18. [PMID: 26114307 DOI: 10.3109/14756366.2015.1057716] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A series of urea derivatives bearing nitroaryl moiety has been synthesized and assayed for their potential antiproliferative activities. Some of the tested compounds displayed activity in RK33 laryngeal cancer cells and TE671 rhabdomyosarcoma cells while being generally less toxic to healthy HSF human fibroblasts cells. One compound was demonstrated to be a moderate CDK2 inhibitor with IC50 = 14.3 µM. Its structure was solved by an X-ray crystallography and molecular modelling was performed to determine structure-activity relationship. Obtained compounds constitute novel structures and generally demonstrated greater cytotoxicity in comparison to cisplatin. This study offers new structural motifs with potential for further development.
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Affiliation(s)
- Tomasz M Wróbel
- a Department of Synthesis and Chemical Technology of Pharmaceutical Substances and
| | - Michał Kiełbus
- b Department of Biochemistry and Molecular Biology , Medical University of Lublin , Lublin , Poland
| | - Agnieszka A Kaczor
- a Department of Synthesis and Chemical Technology of Pharmaceutical Substances and.,c School of Pharmacy, University of Eastern Finland , Kuopio , Finland
| | - Vladimír Kryštof
- d Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University , Olomouc , Czech Republic
| | - Zbigniew Karczmarzyk
- e Department of Chemistry , Siedlce University of Natural Sciences and Humanities , Siedlce , Poland , and
| | - Waldemar Wysocki
- e Department of Chemistry , Siedlce University of Natural Sciences and Humanities , Siedlce , Poland , and
| | - Andrzej Fruziński
- f Institute of General and Ecological Chemistry, Technical University of Lodz , Lodz , Poland
| | - Sylwia K Król
- b Department of Biochemistry and Molecular Biology , Medical University of Lublin , Lublin , Poland
| | - Aneta Grabarska
- b Department of Biochemistry and Molecular Biology , Medical University of Lublin , Lublin , Poland
| | - Andrzej Stepulak
- b Department of Biochemistry and Molecular Biology , Medical University of Lublin , Lublin , Poland
| | - Dariusz Matosiuk
- a Department of Synthesis and Chemical Technology of Pharmaceutical Substances and
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Mahale S, Bharate SB, Manda S, Joshi P, Jenkins PR, Vishwakarma RA, Chaudhuri B. Antitumour potential of BPT: a dual inhibitor of cdk4 and tubulin polymerization. Cell Death Dis 2015; 6:e1743. [PMID: 25950473 PMCID: PMC4669722 DOI: 10.1038/cddis.2015.96] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 11/09/2022]
Abstract
The marine natural product fascaplysin (1) is a potent Cdk4 (cyclin-dependent kinase 4)-specific inhibitor, but is toxic to all cell types possibly because of its DNA-intercalating properties. Through the design and synthesis of numerous fascaplysin analogues, we intended to identify inhibitors of cancer cell growth with good therapeutic window with respect to normal cells. Among various non-planar tryptoline analogues prepared, N-(biphenyl-2-yl) tryptoline (BPT, 6) was identified as a potent inhibitor of cancer cell growth and free from DNA-binding properties owing to its non-planar structure. This compound was tested in over 60 protein kinase assays. It displayed inhibition of Cdk4-cyclin D1 enzyme in vitro far more potently than many other kinases including Cdk family members. Although it blocks growth of cancer cells deficient in the mitotic-spindle checkpoint at the G0/G1 phase of the cell cycle, the block occurs primarily at the G2/M phase. BPT inhibits tubulin polymerization in vitro and acts as an enhancer of tubulin depolymerization of paclitaxel-stabilized tubulin in live cells. Western blot analyses indicated that, in p53-positive cells, BPT upregulates the expression of p53, p21 and p27 proteins, whereas it downregulates the expression of cyclin B1 and Cdk1. BPT selectively kills SV40-transformed mouse embryonic hepatic cells and human fibroblasts rather than untransformed cells. BPT inhibited the growth of several human cancer cells with an IC50<1 μM. The pharmacokinetic study in BALB/c mice indicated good plasma exposure after intravenous administration. It was found to be efficacious at 1/10th the maximum-tolerated dose (1000 mg/kg) against human tumours derived from HCT-116 (colon) and NCI-H460 (lung) cells in SCID (severe-combined immunodeficient) mice models. BPT is a relatively better anticancer agent than fascaplysin with an unusual ability to block two overlapping yet crucial phases of the cell cycle, mitosis and G0/G1. Its ability to effectively halt tumour growth in human tumour-bearing mice would suggest that BPT has the potential to be a candidate for further clinical development.
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Affiliation(s)
- S Mahale
- School of Pharmacy, De Montfort University, Leicester LE1 9BH, UK
| | - S B Bharate
- 1] Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India [2] Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - S Manda
- 1] Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India [2] Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - P Joshi
- 1] Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India [2] Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - P R Jenkins
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - R A Vishwakarma
- 1] Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India [2] Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - B Chaudhuri
- School of Pharmacy, De Montfort University, Leicester LE1 9BH, UK
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Oukoloff K, Buron F, Routier S, Jean L, Renard PY. Synthetic Route to Rare Isoindolones Derivatives. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403649] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kaur N. Palladium Catalysts: Synthesis of Five-MemberedN-Heterocycles Fused with Other Heterocycles. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2014. [DOI: 10.1080/01614940.2014.976118] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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44
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Coya E, Sotomayor N, Lete E. Intramolecular Direct Arylation and Heck Reactions in the Formation of Medium-Sized Rings: Selective Synthesis of Fused Indolizine, Pyrroloazepine and Pyrroloazocine Systems. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400075] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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45
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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Reddy MVR, Akula B, Cosenza SC, Athuluridivakar S, Mallireddigari MR, Pallela VR, Billa VK, Subbaiah DRCV, Bharathi EV, Vasquez-Del Carpio R, Padgaonkar A, Baker SJ, Reddy EP. Discovery of 8-cyclopentyl-2-[4-(4-methyl-piperazin-1-yl)-phenylamino]-7-oxo-7,8-dihydro-pyrido[2,3-d]pyrimidine-6-carbonitrile (7x) as a potent inhibitor of cyclin-dependent kinase 4 (CDK4) and AMPK-related kinase 5 (ARK5). J Med Chem 2014; 57:578-99. [PMID: 24417566 PMCID: PMC3983396 DOI: 10.1021/jm401073p] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The success of imatinib, a BCR-ABL inhibitor for the treatment of chronic myelogenous leukemia, has created a great impetus for the development of additional kinase inhibitors as therapeutic agents. However, the complexity of cancer has led to recent interest in polypharmacological approaches for developing multikinase inhibitors with low toxicity profiles. With this goal in mind, we analyzed more than 150 novel cyano pyridopyrimidine compounds and identified structure-activity relationship trends that can be exploited in the design of potent kinase inhibitors. One compound, 8-cyclopentyl-2-[4-(4-methyl-piperazin-1-yl)-phenylamino]-7-oxo-7,8-dihydro-pyrido[2,3-d]pyrimidine-6-carbonitrile (7x), was found to be the most active, inducing apoptosis of tumor cells at a concentration of approximately 30-100 nM. In vitro kinase profiling revealed that 7x is a multikinase inhibitor with potent inhibitory activity against the CDK4/CYCLIN D1 and ARK5 kinases. Here, we report the synthesis, structure-activity relationship, kinase inhibitory profile, in vitro cytotoxicity, and in vivo tumor regression studies by this lead compound.
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Affiliation(s)
- M V Ramana Reddy
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029-6514, United States
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47
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Synthesis of novel 3-aryl isoindolinone derivatives. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2294-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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48
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Beccari AR, Cavazzoni C, Beato C, Costantino G. LiGen: a high performance workflow for chemistry driven de novo design. J Chem Inf Model 2013; 53:1518-27. [PMID: 23617275 DOI: 10.1021/ci400078g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented.
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Affiliation(s)
- Andrea R Beccari
- Dompé R&D Centre, Dompé SpA, Via Campo di Pile, 67100 L'Aquila, Italy.
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49
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Alvarez-Mico X, Jensen PR, Fenical W, Hughes CC. Chlorizidine, a cytotoxic 5H-pyrrolo[2,1-a]isoindol-5-one-containing alkaloid from a marine Streptomyces sp. Org Lett 2013; 15:988-91. [PMID: 23405849 PMCID: PMC3702164 DOI: 10.1021/ol303374e] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cultivation of an obligate marine Streptomyces strain has provided the cytotoxic natural product chlorizidine A. X-ray crystallographic analysis revealed that the metabolite is composed of a chlorinated 2,3-dihydropyrrolizine ring attached to a chlorinated 5H-pyrrolo[2,1-a]isoindol-5-one. The carbon stereocenter in the dihydropyrrolizine is S-configured. Remarkably, the 5H-pyrrolo[2,1-a]isoindol-5-one moiety has no precedence in the field of natural products. The presence of this ring system, which was demonstrated to undergo facile nucleophilic substitution reactions at the activated carbonyl group, is essential to the molecule's cytotoxicity against HCT-116 human colon cancer cells.
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Affiliation(s)
- Xavier Alvarez-Mico
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California 92093-0204, USA
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50
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Zhao L, Bruneau C, Doucet H. Palladium-Catalysed Direct Polyarylation of Pyrrole Derivatives. ChemCatChem 2012. [DOI: 10.1002/cctc.201200521] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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