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de Azevedo WF, Quiroga R, Villarreal MA, da Silveira NJF, Bitencourt-Ferreira G, da Silva AD, Veit-Acosta M, Oliveira PR, Tutone M, Biziukova N, Poroikov V, Tarasova O, Baud S. SAnDReS 2.0: Development of machine-learning models to explore the scoring function space. J Comput Chem 2024; 45:2333-2346. [PMID: 38900052 DOI: 10.1002/jcc.27449] [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: 02/14/2024] [Revised: 05/04/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
Classical scoring functions may exhibit low accuracy in determining ligand binding affinity for proteins. The availability of both protein-ligand structures and affinity data make it possible to develop machine-learning models focused on specific protein systems with superior predictive performance. Here, we report a new methodology named SAnDReS that combines AutoDock Vina 1.2 with 54 regression methods available in Scikit-Learn to calculate binding affinity based on protein-ligand structures. This approach allows exploration of the scoring function space. SAnDReS generates machine-learning models based on crystal, docked, and AlphaFold-generated structures. As a proof of concept, we examine the performance of SAnDReS-generated models in three case studies. For all three cases, our models outperformed classical scoring functions. Also, SAnDReS-generated models showed predictive performance close to or better than other machine-learning models such as KDEEP, CSM-lig, and ΔVinaRF20. SAnDReS 2.0 is available to download at https://github.com/azevedolab/sandres.
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Affiliation(s)
| | - Rodrigo Quiroga
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET-Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Marcos Ariel Villarreal
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET-Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | | | | | - Amauri Duarte da Silva
- Programa de Pós-Graduação em Tecnologias da Informação e Gestão em Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | | | | | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Palermo, Italy
| | | | | | | | - Stéphaine Baud
- Laboratoire SiRMa, UMR CNRS/URCA 7369, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
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2
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El-Bayaa MN, Kotb ER, Messaoudi S, Awad HM, Saleh MG, Soliman HA. Synthesis, anticancer activity, docking and computational studies of new pyridyl-glycosyl hybrids and acyclic analogs. Future Med Chem 2024:1-15. [PMID: 39263964 DOI: 10.1080/17568919.2024.2389768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/30/2024] [Indexed: 09/13/2024] Open
Abstract
New pyridine-O-glycosides and their acyclic nucleoside analogues were prepared by heterocyclization and glycosylation. The anticancer activity against HCT-116, HepG2 and MCF-7 human cancer cells and BJ-1 cell revealed that the galacto- and xylopyranosyl glycosides possessing 4-bromophenyl have superior cytotoxic activities against HepG2 cell while glycosides 7-9 resulted in superior cytotoxic activities regarding MCF-7 breast cell. In case of HCT-116 colorectal carcinoma cells, two products and the derived glycosides and acyclic analogues showed potent activities. The most potent compounds were investigated for their possible binding affinities to the active site of CDK2 enzyme via in silico molecular docking simulation in addition to computational studies. The results support the antiproliferative effect and elucidate the interactions of 3a and 8 with catalytic sites.
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Affiliation(s)
- Mohamed N El-Bayaa
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Eman R Kotb
- Photochemistry Department, National Research Centre, Dokki, P.O. Box 12622, Cairo, Egypt
| | - Sabri Messaoudi
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Hanem M Awad
- Tanning Materials & Leather Technology Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Mahmoud G Saleh
- Department of Chemistry, College of Science, Northern Border University, Arar, Saudi Arabia
| | - Hanan A Soliman
- Photochemistry Department, National Research Centre, Dokki, P.O. Box 12622, Cairo, Egypt
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3
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Huang X, Xu S, Duan L, Xu S, Zhu W. A patent review of small molecule CDK4/6 inhibitors in the treatment of cancer: 2020-present. Expert Opin Ther Pat 2024; 34:825-842. [PMID: 39011556 DOI: 10.1080/13543776.2024.2379926] [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: 12/15/2023] [Accepted: 07/04/2024] [Indexed: 07/17/2024]
Abstract
INTRODUCTION Cyclin-dependent protein kinase 4/6 (CDK4/6) is a class of serine/threonine protein kinases that plays a key role in the regulation of the cell cycle. CDK4/6 is highly expressed in cancers such as breast cancer, melanoma, and non-small cell lung cancer (NSCLC). Currently, a variety of CDK4/6 inhibitors have been developed, aiming to develop effective inhibitors to solve CDK4/6 resistance and toxicity. AREAS COVERED This article searches patents through Espacenet and reviews the development of widely studied CDK inhibitors and FDA-approved CDK4/6 inhibitors, as well as the latest progress of patented inhibitors with good inhibitory activity against CDK4/6 from 2020 to now. EXPERT OPINION CDK4/6 is highly expressed in many tumors and has become an important anti-tumor target. Among the patents from 2020 to the present, many inhibitors have good kinase inhibitory effects on CDK4/6 and also show great development potential in anti-tumor. However, there is still an urgent need to develop novel CDK4/6 inhibitors that address challenges such as drug resistance, toxicity, and selectivity.
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Affiliation(s)
- Xiaoling Huang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Shidi Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Lei Duan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
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4
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Elsbaey M, Igarashi Y, Alnajjar R, Darwish KM, Miyamoto T. Nuciferol C, a new sesquineolignan dimer from Cocos nucifera L.: bioactivity and theoretical investigation. RSC Adv 2024; 14:25900-25907. [PMID: 39157580 PMCID: PMC11328675 DOI: 10.1039/d4ra02940b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024] Open
Abstract
Nuciferol C (NC), an undescribed dimer of nuciferol B (NB), was isolated from the endocarp of Cocos nucifera L. The planar structure of NC was determined using 1D- and 2D-NMR spectroscopy as well as high resolution MS spectrometry. The absolute configuration was concluded based on analysis of NOESY spectra. NC showed cytotoxic activity against colon cancer cells (CaCo-2) with an IC50 value of 76 μM, and significantly decreased the expression of human epidermal growth factor receptor (EGFR) and tumor necrosis factor alpha (TNF-α) in CaCo-2 as compared with untreated cells by 39% and 33%, respectively (p < 0.05). In addition, NC exhibited anti-herpes simplex virus (HSV-I) activity with an IC50 value of 23 μM. In silico study of NC was implemented at three levels: density functional theory (DFT) was used to study its electronic properties, molecular mechanics was used to estimate the docking results, and finally, molecular dynamic simulation was used to study the behavior and stability of NC inside the active site of the target protein of HSV-1.
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Affiliation(s)
- Marwa Elsbaey
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University 5180 Kurokawa, Imizu Toyama 939-0398 Japan
| | - Radwan Alnajjar
- CADD Unit, Faculty of Pharmacy, Libyan International Medical University Benghazi 16063 Libya
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia 41522 Egypt
| | - Tomofumi Miyamoto
- School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
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Islam MS, Al-Jassas RM, Al-Majid AM, Haukka M, Nafie MS, Abu-Serie MM, Teleb M, El-Yazbi A, Alayyaf AMA, Barakat A, Shaaban MM. Exploiting spirooxindoles for dual DNA targeting/CDK2 inhibition and simultaneous mitigation of oxidative stress towards selective NSCLC therapy; synthesis, evaluation, and molecular modelling studies. RSC Med Chem 2024; 15:2937-2958. [PMID: 39149093 PMCID: PMC11324055 DOI: 10.1039/d4md00337c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/10/2024] [Indexed: 08/17/2024] Open
Abstract
The unique structure of spirooxindoles and their ability to feature various pharmacophoric motifs render them privileged scaffolds for tailoring new multitarget anticancer agents. Herein, a stereoselective multicomponent reaction was utilized to generate a small combinatorial library of pyrazole-tethered spirooxindoles targeting DNA and CDK2 with free radical scavenging potential as an extra bonus. The designed spirooxindoles were directed to combat NSCLC via inducing apoptosis and alleviating oxidative stress. The series' absolute configuration was assigned by X-ray diffraction analysis. Cytotoxicity screening of the developed spirooxindoles against NSCLC A549 and H460 cells compared to normal lung fibroblasts Wi-38 revealed the sensitivity of A549 cells to the compounds and raised 6e and 6h as the study hits (IC50 ∼ 0.09 μM and SI > 3). They damaged DNA at 24.6 and 35.3 nM, and surpassed roscovitine as CDK2 inhibitors (IC50 = 75.6 and 80.2 nM). Docking and MDs simulations postulated their receptors binding modes. The most potent derivative, 6e, induced A549 apoptosis by 40.85% arresting cell cycle at G2/M phase, and exhibited antioxidant activity in a dose-dependent manner compared to Trolox as indicated by DPPH scavenging assay. Finally, in silico ADMET analysis predicted the drug-likeness properties of 6e.
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Affiliation(s)
- Mohammad Shahidul Islam
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Refaah M Al-Jassas
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Abdullah Mohammed Al-Majid
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Matti Haukka
- Department of Chemistry, University of Jyväskylä P.O. Box 35 FI-40014 Jyväskylä Finland
| | - Mohamed S Nafie
- Department of Chemistry, College of Sciences, University of Sharjah Sharjah (P.O. Box 27272) United Arab Emirates
- Chemistry Department, Faculty of Science, Suez Canal University Ismailia 41522 Egypt
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City) Egypt
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University Alexandria 21521 Egypt
| | - Amira El-Yazbi
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University Alexandria Egypt
| | | | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Marwa M Shaaban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University Alexandria 21521 Egypt
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Giugliano G, Gajo M, Marforio TD, Zerbetto F, Mattioli EJ, Calvaresi M. Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking. Chemistry 2024; 30:e202400871. [PMID: 38777795 DOI: 10.1002/chem.202400871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5 %), isoleucine (11.3 %), phenylalanines (11.3 %) and valine (9.5 %) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator-activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer-related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well-defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.
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Affiliation(s)
- Giulia Giugliano
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Margherita Gajo
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
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7
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Abdjan MI, Shafiq M, Nerukh D, Nur-E-Alam M, Ul-Haq Z. Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach. Phys Chem Chem Phys 2024; 26:16139-16152. [PMID: 38787638 DOI: 10.1039/d4cp00844h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Cyclin-dependent kinase 2 (CDK2) regulates cell cycle checkpoints in the synthesis and mitosis phases and plays a pivotal role in cancerous cell proliferation. The activation of CDK2, influenced by various protein signaling pathways, initiates the phosphorylation process. Due to its crucial role in carcinogenesis, CDK2 is a druggable hotspot target to suppress cancer cell proliferation. In this context, several studies have identified spirooxindoles as an effective class of CDK2 inhibitors. In the present study, three spirooxindoles (SOI1, SOI2, and SOI3) were studied to understand their inhibitory mechanism against CDK2 through a structure-based approach. Molecular docking and molecular dynamics (MD) simulations were performed to explore their interactions with CDK2 at the molecular level. The calculated binding free energy for the spirooxindole-based CDK2 inhibitors aligned well with experimental results regarding CDK2 inhibition. Energy decomposition (ED) analysis identified key binding residues, including I10, G11, T14, R36, F82, K89, L134, P155, T158, Y159, and T160, in the CDK2 active site and T-loop phosphorylation. Molecular mechanics (MM) energy was identified as the primary contributor to stabilizing inhibitor binding in the CDK2 protein structure. Furthermore, the analysis of binding affinity revealed that the inhibitor SOI1 binds more strongly to CDK2 compared to the other inhibitors under investigation. It demonstrated a robust interaction with the crucial residue T160 in the T-loop phosphorylation site, responsible for kinase activation. These insights into the inhibitory mechanism are anticipated to contribute to the development of potential CDK2 inhibitors using the spirooxindole scaffold.
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Affiliation(s)
- Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
| | - Muhammad Shafiq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, B4 7ET, UK
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Kingdom of Saudi Arabia.
| | - Zaheer Ul-Haq
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
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8
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Kazansky Y, Cameron D, Mueller HS, Demarest P, Zaffaroni N, Arrighetti N, Zuco V, Kuwahara Y, Somwar R, Ladanyi M, Qu R, de Stanchina E, Dela Cruz FS, Kung AL, Gounder MM, Kentsis A. Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy. Cancer Discov 2024; 14:965-981. [PMID: 38315003 PMCID: PMC11147720 DOI: 10.1158/2159-8290.cd-23-0110] [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: 02/06/2023] [Revised: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024]
Abstract
Epigenetic dependencies have become evident in many cancers. On the basis of antagonism between BAF/SWI-SNF and PRC2 in SMARCB1-deficient sarcomas, we recently completed the clinical trial of the EZH2 inhibitor tazemetostat. However, the principles of tumor response to epigenetic therapy in general, and tazemetostat in particular, remain unknown. Using functional genomics and diverse experimental models, we define molecular mechanisms of tazemetostat resistance in SMARCB1-deficient tumors. We found distinct acquired mutations that converge on the RB1/E2F axis and decouple EZH2-dependent differentiation and cell-cycle control. This allows tumor cells to escape tazemetostat-induced G1 arrest, suggests a general mechanism for effective therapy, and provides prospective biomarkers for therapy stratification, including PRICKLE1. On the basis of this, we develop a combination strategy to circumvent tazemetostat resistance using bypass targeting of AURKB. This offers a paradigm for rational epigenetic combination therapy suitable for translation to clinical trials for epithelioid sarcomas, rhabdoid tumors, and other epigenetically dysregulated cancers. SIGNIFICANCE Genomic studies of patient epithelioid sarcomas and rhabdoid tumors identify mutations converging on a common pathway for response to EZH2 inhibition. Resistance mutations decouple drug-induced differentiation from cell-cycle control. We identify an epigenetic combination strategy to overcome resistance and improve durability of response, supporting its investigation in clinical trials. See related commentary by Paolini and Souroullas, p. 903. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Yaniv Kazansky
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Cameron
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen S. Mueller
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Phillip Demarest
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Noemi Arrighetti
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Valentina Zuco
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Kyoto Prefectural University of Medicine
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rui Qu
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mrinal M. Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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9
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Hamed OA, Abou-Elmagd El-Sayed N, Mahmoud WR, F Elmasry G. Molecular docking approach for the design and synthesis of new pyrazolopyrimidine analogs of roscovitine as potential CDK2 inhibitors endowed with pronounced anticancer activity. Bioorg Chem 2024; 147:107413. [PMID: 38696844 DOI: 10.1016/j.bioorg.2024.107413] [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: 12/09/2023] [Revised: 03/13/2024] [Accepted: 04/27/2024] [Indexed: 05/04/2024]
Abstract
Cyclin-dependent kinase 2 (CDK2) is a vital protein for controlling cell cycle progression that is critically associated with various malignancies and its inhibition could offer a convenient therapeutic approach in designing anticancer remedies. Consequently, this study aimed to design and synthesize new CDK2 inhibitors featuring roscovitine as a template model. The purine ring of roscovitine was bioisosterically replaced with the pyrazolo[3,4-d]pyrimidine scaffold, in addition to some modifications in the side chains. A preliminary molecular docking study for the target chemotypes in the CDK2 binding domain revealed their ability to accomplish similar binding patterns and interactions to that of the lead compound roscovitine. Afterwards, synthesis of the new derivatives was accomplished. Then, the initial anticancer screening at a single dose by the NCI revealed that compounds 7a, 9c, 11c, 17a and 17b achieved the highest GI% values reaching up to 150 % indicating their remarkable activity. These derivatives were subsequently selected to undertake five-dose testing, where compounds 7a, 9c, 11c and 17a unveiled the most pronounced activity against almost the full panel with GI50 ranges; 1.41-28.2, 0.116-2.39, 0.578-60.6 and 1.75-42.4 µM, respectively and full panel GI50 (MG-MID); 8.24, 0.6, 2.46 and 6.84 µM, respectively. CDK2 inhibition assay presented compounds 7a and 9c as the most potent inhibitors with IC50 values of 0.262 and 0.281 µM, respectively which are nearly 2.4 folds higher than the reference ligand roscovitine (IC50 = 0.641 µM). Besides, flow cytometric analysis on the most susceptible and safe cell lines depicted that 7a caused cell cycle arrest at G1/S phase in renal cancer cell line (RXF393) while 9c led to cell growth arrest at S phase in breast cancer cell line (T-47D) along with pronounced apoptotic induction in the mentioned cell lines. These findings afforded new anticancer pyrazolo[3,4-d]pyrimidine, roscovitine analogs, acting via CDK2 inhibition.
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Affiliation(s)
- Ola Alaa Hamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Nehad Abou-Elmagd El-Sayed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Walaa R Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Ghada F Elmasry
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt.
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10
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Ahmad Sheikh K, Parveen D, Mumtaz Alam M, Azam F, Ahmed Khan M, Akhter M, Tasneem S, Meenu, Parvez S, Imtiyaz K, Rizvi MA, Shaquiquzzaman M. Exploring cyclopropylamine containing cyanopyrimidines as LSD1 inhibitors: Design, synthesis, ADMET, MD analysis and anticancer activity profiling. Bioorg Chem 2024; 147:107336. [PMID: 38636431 DOI: 10.1016/j.bioorg.2024.107336] [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: 10/25/2023] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024]
Abstract
In this series we report the structure-based design, synthesis and anticancer activity evaluation of a series of eighteen cyclopropylamine containing cyanopyrimidine derivatives. The computational predictions of ADMET properties revealed appropriate aqueous solubility, high GI absorption, no BBB permeability, no Lipinski rule violations, medium total clearance and no mutagenic, tumorigenic, irritant and reproductive toxic risks for most of the compounds. Compounds VIIb, VIIi and VIIm emerged as the most potent anticancer agents among all compounds evaluated against 60 cancer cell lines through the one-dose (10 µM) sulforhodamine B assay. Further, the multiple dose cell viability studies against cancer cell lines MOLT-4, A549 and HCT-116 revealed results consistent with the one-dose assay, besides sparing normal cell line HEK-293. The three potent compounds also displayed potent LSD1 inhibitory activity with IC50 values of 2.25, 1.80 and 6.08 µM. The n-propyl-thio/isopropyl-thio group bonded to the pyrimidine ring and unsubstituted/ electron donating group (at the para- position) attached to the phenyl ring resulted in enhanced anticancer activity. However, against leukemia cancer, the electron donating isopropyl group remarkably enhanced anti-cancer activity. Our findings provide important leads, which merit further optimization to result in better cancer therapeutics.
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Affiliation(s)
- Khursheed Ahmad Sheikh
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Darakhshan Parveen
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - M Mumtaz Alam
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India.
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Saudi Arabia
| | - Mohammad Ahmed Khan
- Department of Pharmacology, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Mymoona Akhter
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Sharba Tasneem
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Meenu
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Khalid Imtiyaz
- Genome Biology Lab, Department of Bioscience, Jamia Millia Islamia, New Delhi 110025, India
| | - Moshahid A Rizvi
- Genome Biology Lab, Department of Bioscience, Jamia Millia Islamia, New Delhi 110025, India
| | - M Shaquiquzzaman
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India.
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11
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Ibrahim BT, Allam HA, El-Dydamony NM, Fouad MA, Mohammed ER. Exploring new quinazolin-4(3H)-one derivatives as CDK2 inhibitors: Design, synthesis, and anticancer evaluation. Drug Dev Res 2024; 85:e22163. [PMID: 38419305 DOI: 10.1002/ddr.22163] [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: 11/20/2023] [Revised: 01/13/2024] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Abstract
In the present work, five series of new 2,3-disubstituted quinazolin-4(3H)-ones 4a-c, 5a-d, 6a-g, 7a,b, and 9a-c were designed, synthesized, and screened in vitro for their cytotoxic activity against 60 cancer cell lines by the National Cancer Institute, USA. Five candidates 4c, 6a, 6b, 6d, and 6g revealed promising cytotoxicity with significant percentage growth inhibition in the range of 81.98%-96.45% against the central nervous system (CNS) (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The in vitro cytotoxic half maximal inhibitory concentration (IC50 ) values for the most active compounds 4c, 6a, 6b, 6d, and 6g against the most sensitive cell lines were evaluated. Additionally, screening their cyclin-dependent kinase 2 (CDK2) inhibitory activity was performed. Ortho-chloro-benzylideneamino derivative 6b emerged as the most potent compound with IC50 = 0.67 µM compared to Roscovitine (IC50 = 0.64 µM). The most active candidates arrested the cell cycle at G1, S phases, or both, leading to cell death and inducing apoptosis against CNS (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The molecular docking study verified the resulting outcomes for the most active candidates in the CDK2-binding pocket. Finally, physicochemical, and pharmacokinetic properties deduced that compounds 4c, 6a, 6b, 6d, and 6g displayed significant drug-likeness properties. According to the obtained results, the newly targeted compounds are regarded as promising scaffolds for the continued development of novel CDK2 inhibitors.
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Affiliation(s)
- Basant T Ibrahim
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City, Egypt
| | | | - Nehad M El-Dydamony
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City, Egypt
| | - Marwa A Fouad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, New Giza University, Cairo, Egypt
| | - Eman R Mohammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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12
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Bitencourt-Ferreira G, Villarreal MA, Quiroga R, Biziukova N, Poroikov V, Tarasova O, de Azevedo Junior WF. Exploring Scoring Function Space: Developing Computational Models for Drug Discovery. Curr Med Chem 2024; 31:2361-2377. [PMID: 36944627 DOI: 10.2174/0929867330666230321103731] [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: 06/23/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 03/23/2023]
Abstract
BACKGROUND The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHODS We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.
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Affiliation(s)
| | - Marcos A Villarreal
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Rodrigo Quiroga
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Nadezhda Biziukova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Olga Tarasova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Walter F de Azevedo Junior
- Pontifical Catholic University of Rio Grande do Sul - PUCRS, Porto Alegre-RS, Brazil
- Specialization Program in Bioinformatics, The Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681 Porto Alegre / RS 90619-900, Brazil
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13
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Barakat A, Alshahrani S, Al-Majid AM, Alamary AS, Haukka M, Abu-Serie MM, Domingo LR, Ashraf S, Ul-Haq Z, Nafie MS, Teleb M. New spiro-indeno[1,2- b]quinoxalines clubbed with benzimidazole scaffold as CDK2 inhibitors for halting non-small cell lung cancer; stereoselective synthesis, molecular dynamics and structural insights. J Enzyme Inhib Med Chem 2023; 38:2281260. [PMID: 37994663 PMCID: PMC11003489 DOI: 10.1080/14756366.2023.2281260] [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: 09/25/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
Despite the crucial role of CDK2 in tumorigenesis, few inhibitors reached clinical trials for managing lung cancer, the leading cause of cancer death. Herein, we report combinatorial stereoselective synthesis of rationally designed spiroindeno[1,2-b]quinoxaline-based CDK2 inhibitors for NSCLC therapy. The design relied on merging pharmacophoric motifs and biomimetic scaffold hopping into this privileged skeleton via cost-effective one-pot multicomponent [3 + 2] cycloaddition reaction. Absolute configuration was assigned by single crystal x-ray diffraction analysis and reaction mechanism was studied by Molecular Electron Density Theory. Initial MTT screening of the series against A549 cells and normal lung fibroblasts Wi-38 elected 6b as the study hit regarding potency (IC50 = 54 nM) and safety (SI = 6.64). In vitro CDK2 inhibition assay revealed that 6b (IC50 = 177 nM) was comparable to roscovitine (IC50 = 141 nM). Docking and molecular dynamic simulations suggested that 6b was stabilised into CDK2 cavity by hydrophobic interactions with key aminoacids.
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Affiliation(s)
- Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saeed Alshahrani
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Matti Haukka
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Marwa M. Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Egypt
| | - Luis R. Domingo
- Department of Organic Chemistry, University of Valencia, Burjassot, Valencia, Spain
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Mohamed S. Nafie
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, UAE
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
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14
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Kazansky Y, Cameron D, Mueller HS, Demarest P, Zaffaroni N, Arrighetti N, Zuco V, Kuwahara Y, Somwar R, Ladanyi M, Qu R, De Stanchina E, Dela Cruz FS, Kung AL, Gounder M, Kentsis A. Overcoming clinical resistance to EZH2 inhibition using rational epigenetic combination therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527192. [PMID: 36798379 PMCID: PMC9934575 DOI: 10.1101/2023.02.06.527192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Essential epigenetic dependencies have become evident in many cancers. Based on the functional antagonism between BAF/SWI/SNF and PRC2 in SMARCB1-deficient sarcomas, we and colleagues recently completed the clinical trial of the EZH2 inhibitor tazemetostat. However, the principles of tumor response to epigenetic therapy in general, and tazemetostat in particular, remain unknown. Using functional genomics of patient tumors and diverse experimental models, we sought to define molecular mechanisms of tazemetostat resistance in SMARCB1-deficient sarcomas and rhabdoid tumors. We found distinct classes of acquired mutations that converge on the RB1/E2F axis and decouple EZH2-dependent differentiation and cell cycle control. This allows tumor cells to escape tazemetostat-induced G1 arrest despite EZH2 inhibition, and suggests a general mechanism for effective EZH2 therapy. This also enables us to develop combination strategies to circumvent tazemetostat resistance using cell cycle bypass targeting via AURKB, and synthetic lethal targeting of PGBD5-dependent DNA damage repair via ATR. This reveals prospective biomarkers for therapy stratification, including PRICKLE1 associated with tazemetostat resistance. In all, this work offers a paradigm for rational epigenetic combination therapy suitable for immediate translation to clinical trials for epithelioid sarcomas, rhabdoid tumors, and other epigenetically dysregulated cancers.
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15
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Zaki WA, El-Sayed SM, Alswah M, El-Morsy A, Bayoumi AH, Mayhoub AS, Moustafa WH, Awaji AA, Roh EJ, Hassan AH, Mahmoud K. Design, Synthesis, In Vitro, and In Silico Studies of New N5-Substituted-pyrazolo[3,4- d]pyrimidinone Derivatives as Anticancer CDK2 Inhibitors. Pharmaceuticals (Basel) 2023; 16:1593. [PMID: 38004458 PMCID: PMC10674233 DOI: 10.3390/ph16111593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
CDK2 is a key player in cell cycle processes. It has a crucial role in the progression of various cancers. Hepatocellular carcinoma (HCC) and colorectal cancer (CRC) are two common cancers that affect humans worldwide. The available therapeutic options suffer from many drawbacks including high toxicity and decreased specificity. Therefore, there is a need for more effective and safer therapeutic agents. A series of new pyrazolo[3,4-d]pyrimidine analogs was designed, synthesized, and evaluated as anticancer agents against the CRC and HCC cells, HCT116, and HepG2, respectively. Pyrazolo[3,4-d]pyrimidinone derivatives bearing N5-2-(4-halophenyl) acetamide substituents were identified as the most potent amongst evaluated compounds. Further evaluation of CDK2 kinase inhibition of two potential cytotoxic compounds 4a and 4b confirmed their CDK2 inhibitory activity. Compound 4a was more potent than the reference roscovitine regarding the CDK2 inhibitory activity (IC50 values: 0.21 and 0.25 µM, respectively). In silico molecular docking provided insights into the molecular interactions of compounds 4a and 4b with important amino acids within the ATP-binding site of CDK2 (Ile10, Leu83, and Leu134). Overall, compounds 4a and 4b were identified as interesting CDK2 inhibitors eliciting antiproliferative activity against the CRC and HCC cells, HCT116 and HepG2, respectively, for future further investigations and development.
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Affiliation(s)
- Waheed A. Zaki
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Selwan M. El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed Alswah
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed El-Morsy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
- Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University, Najaf 54001, Iraq
| | - Ashraf H. Bayoumi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Abrahman S. Mayhoub
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
- Nanoscience Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October, Giza 12578, Egypt
| | - Walaa H. Moustafa
- Microbiology and Immunology Department, Faculty of Pharmacy, Helwan University, Cairo 19448, Egypt
| | - Aeshah A. Awaji
- Department of Biology, Faculty of Science, University College of Taymaa, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Eun Joo Roh
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Ahmed H.E. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Kazem Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Egypt
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16
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Husseiny EM, Abulkhair HS, Saleh A, Altwaijry N, Zidan RA, Abdulrahman FG. Molecular overlay-guided design of new CDK2 inhibitor thiazepinopurines: Synthesis, anticancer, and mechanistic investigations. Bioorg Chem 2023; 140:106789. [PMID: 37611530 DOI: 10.1016/j.bioorg.2023.106789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]
Abstract
Adopting the molecular overlay approach, three novel sets of thiazepinopurines with expected cytotoxicity and CDK2 inhibition potential were designed and synthesized. This was accomplished through the heteroannelation of purines, for the first time, with thiazepine. The obtained thiazepinopurines derivatives were assessed for their cytotoxicity toward tumor cells of three different types, HepG2, MCF-7, and PC-3 as well as one normal cell (WI38). Among the studied compounds, 3b and 3c exhibited significant antiproliferative activity against tumor cells presenting IC50 range of 5.52-17.09 µM in comparison with Roscovitine (9.32-13.82 µM). Additionally, both compounds displayed superior selectivity indices (SI = 3.00-7.15) toward tested cancer cells. The 4-chlorophenyl analog 3b has shown the best selectivity index, and hence it has been subjected to additional investigations to determine its proper mechanistic effect. Accordingly, the CDK2 inhibition potential, apoptosis induction, and cell cycle analysis of MCF-7 were evaluated. Results revealed that this analog displayed a potent CDK2 inhibition potential with an IC50 value of 0.219 µM. Findings also showed that 3b was thought to arrest MCF-7 cell cycle at S phase together with apoptosis induction by the increased expression of Bax, Caspase-8, and -9 markers with a concomitant decrease in Bcl-2 expression. Besides, the probable interaction of 3b with CDK2 binding pocket was investigated by molecular docking.
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Affiliation(s)
- Ebtehal M Husseiny
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City 11754, Cairo, Egypt
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University-Egypt, International Coastal Road, New Damietta 34518, Egypt
| | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Riham A Zidan
- Department of Biochemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Fatma G Abdulrahman
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City 11754, Cairo, Egypt
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17
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Azmy EM, Hagras M, Ewida MA, Doghish AS, Gamil Khidr E, El-Husseiny AA, Gomaa MH, Refaat HM, Ismail NSM, Nassar IF, Lashin WH. Development of pyrolo[2,3-c]pyrazole, pyrolo[2,3-d]pyrimidine and their bioisosteres as novel CDK2 inhibitors with potent in vitro apoptotic anti-proliferative activity: Synthesis, biological evaluation and molecular dynamics investigations. Bioorg Chem 2023; 139:106729. [PMID: 37467621 DOI: 10.1016/j.bioorg.2023.106729] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
Inhibiting the CDK2/cyclin A2 enzyme has been validated in multiple clinical manifestations related to multiple types of cancer. Herein, novel series of pyrolo[2,3-c]pyrazole, pyrolo[2,3-c]isoaxazole and pyrolo[2,3-d]pyrimidine, pyrolo[3,2-c]pyridine & indole based analogs were designed, synthesized and biologically evaluated for their in vitro antiproliferative activity where the obtained results revealed that most of the newly synthesized compounds showed significant cytotoxic activity towards MCF-7 (breast cancer cell lines) and HepG-2 (hepatocellular carcinoma) with IC50 ranging from 3.20 µM to 10.05 µM & from 2.18 µM to 13.49 µM, respectively, compared to that of Sorafenib (IC50 9.76 & 13.19 µM, respectively). The in vitro inhibitory profile of the most promising compounds (9, 11, 14, 15, 16, 17 and 20) towards CDK2/CyclinA2 was evaluated. Compounds 14 & 15 exhibited potent inhibitory profile against CDK2 with (IC50 0.11 and 0.262 µM, respectively comparable to Sorafenib IC50 0.184 µM. Western blotting of 14 & 15 at MCF-7 cell line confirmed the diminishing activity on CDK2. Furthermore, both compounds exserted a significant cell cycle arrest and apoptosis. Moreover, the normal cell line cytotoxicity for both compounds revealed low cytotoxic results in normal cells rather than cancer cells. Molecular docking and dynamic simulation validated the potentiality of the newly synthesized compounds to have high binding affinity within CDK2 binding pocket. 3DQSAR pharmacophore, in-silico ADME/TOPKAT studies and drug-likeness showed proper pharmacokinetic properties and helped in structure requirements prediction. The obtained model and pattern of substitution could be used for further development of CDK2 inhibitors.
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Affiliation(s)
- Eman M Azmy
- Chemistry Department, Faculty of Women, Ain Shams University, Heliopolis, Egypt
| | - Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Menna A Ewida
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Emad Gamil Khidr
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Maher H Gomaa
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Hanan M Refaat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
| | - Nasser S M Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt.
| | - Ibrahim F Nassar
- Faculty of Specific Education, Ain Shams University, 365 Ramsis Street, Abassia, Cairo, Egypt
| | - Walaa H Lashin
- Chemistry Department, Faculty of Women, Ain Shams University, Heliopolis, Egypt
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18
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Ahmad B, Saeed A, Castrosanto MA, Amir Zia M, Farooq U, Abbas Z, Khan S. Identification of natural marine compounds as potential inhibitors of CDK2 using molecular docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2023; 41:8506-8516. [PMID: 36300512 DOI: 10.1080/07391102.2022.2135594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
The multifunctional enzyme cyclin-dependent kinase 2 (CDK2) protein is essential for cell proliferation, transcription and modulation of the cell cycle. There is a dysfunction that is connected to various diseases, such as cancer, making it an important treatment target in oncology and beyond. The goal of this study is to identify novel CDK2 ATP binding site inhibitors using in silico drug designing. To find competitive inhibitors for the ATP site, molecular docking, molecular dynamics (MD) simulation and free-binding energy calculations were used. Natural compounds retrieved from marine sources (fungi and algae) were docked against protein, and the best-binding compounds were further evaluated using MD simulations. LIG1, LIG2 and LIG3 (ΔGPB = -19.98, -15.82 and -12.98 kcal/mol, respectively) were placed in the top positions based on their overall binding energy calculated using MMPBSA approach. Stability of the complexes was confirmed by carefully analyzing the rmsd and rmsf patterns retrieved from the MD trajectories. Several residues and areas (Leu124, Val123, Phe80, Leu83, Glu81, Arg 126, Asn132, Leu134, Gln131, Lys88 and Glu195) appear to be critical for inhibitor retention across the active pocket, according to RMSD and RMSF. The dynamics of the ligands inside the active pocket were mapped using principle component analysis. It has been observed that LIG1-3 appear to be the best possible inhibitors due to their high binding energies, interaction pattern and retention inside the active pocket.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Basharat Ahmad
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Aamir Saeed
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Melvin A Castrosanto
- College of Arts and Sciences, Institute of Chemistry, University of the Philippines Los Banos, Laguna, Philippines
| | - Muhammad Amir Zia
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad - Abbottabad Campus, Abbottabad, Pakistan
| | - Zaheer Abbas
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Sara Khan
- Department of Chemistry, COMSATS University Islamabad - Abbottabad Campus, Abbottabad, Pakistan
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19
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Ezzat MAF, Elmasry GF, El-Mageed MMAA, Fouad MA, Abdel-Aziz HA, Elewa SI. Design, synthesis, and biological evaluation of furan-bearing pyrazolo[3,4-b]pyridines as novel inhibitors of CDK2 and P53-MDM2 protein-protein interaction. Drug Dev Res 2023; 84:1183-1203. [PMID: 37191966 DOI: 10.1002/ddr.22079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/17/2023]
Abstract
The novel series of furan-bearing pyrazolo[3,4-b]pyridines were designed as cyclin-dependent kinase 2 (CDK2) inhibitors and as p53-murine double minute 2 (MDM2) inhibitors. The newly synthesized compounds were screened for their antiproliferative activity toward hepatocellular carcinoma (HepG2) and breast cancer (MCF7) cell lines. The most active compounds on both cell lines were additionally evaluated for their in vitro CDK2 inhibitory activity. Compounds 7b and 12f displayed enhanced activity (half-maximal inhibitory concentration [IC50 ] = 0.46 and 0.27 µM, respectively) in comparison to the standard roscovitine (IC50 = 1.41 ± 0.03 µM), in addition to, cell cycle arrest at S phase and G1/S transition phase in MCF7 cells treated with both compounds, respectively. Moreover, the most active spiro-oxindole derivative against MCF7 cell line, 16a, exhibited enhanced inhibitory activity against p53-MDM2 interaction in vitro (IC50 = 3.09 ± 0.12 µM) compared to nutlin, and increased the levels of both p53 and p21 by nearly fourfold in comparison to the negative control. Molecular docking studies demonstrated the plausible interaction patterns of the most potent derivatives 17b and 12f in the CDK2 binding pocket and the spiro-oxindole 16a with p53-MDM2 complex, respectively. Consequently, the new chemotypes 7b, 12f, and 16a can be presented as promising antitumor hits for further studies and optimization.
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Affiliation(s)
| | - Ghada F Elmasry
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Marwa A Fouad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, NewGiza University, Cairo, Egypt
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Giza, Egypt
| | - Safaa I Elewa
- Organic Chemistry Department, Faculty of Women's for Arts, Science and Education, Ain Shams University, Cairo, Egypt
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20
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Farghaly TA, Abbas EMH, Al-Sheikh MA, Medrasi HY, Masaret GS, Pashameah RA, Qurban J, Harras MF. Synthesis of tricyclic and tetracyclic benzo[6,7]cycloheptane derivatives linked morpholine moiety as CDK2 inhibitors. Drug Dev Res 2023; 84:1127-1141. [PMID: 37170788 DOI: 10.1002/ddr.22074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/11/2023] [Accepted: 04/29/2023] [Indexed: 05/13/2023]
Abstract
With the aim of developing cyclin-dependent kinase 2 (CDK2) inhibitors with strong antibreast cancer efficacy, new tricyclic and tetracyclic benzo[6,7]cycloheptane derivatives were synthesized. The newly synthesized tri- and tetracyclic derivatives were achieved from the reaction of 4-(4-morpholin-4-yl-phenyl)-1,3,4,5,6,7-hexahydro-benzo[6,7]cyclohepta[1,2-d]pyrimidine-2-thione (5) with α-haloketone derivatives as hydrazonyl chlorides, phenacyl bromide derivatives, chloroacetone, and ethyl substituted acetate derivatives. The MCF-7 and MDA-MB-231 breast cancer cell lines were utilized to examine the anticancer properties. Compounds 5 and 8 were shown to be the most effective, with half-maximal inhibitory concentration (IC50 ) values between 5.73 and 9.11 µM, which are on the level with doxorubicin. Mechanistic studies showed that 5 and 8 caused tumor cell death by inducing apoptosis and they also produced cancer arrest in the S phase of the cell cycle. In addition, compounds 5 and 8 showed strong anti-CDK2 action (IC50 = 0.112 and 0.18 µM, respectively) comparable to roscovitine (IC50 = 0.127 µM). Moreover, the docking result demonstrated that derivatives 5 and 8 fit into the CDK2 active site in the proper orientation.
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Affiliation(s)
- Thoraya A Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Eman M H Abbas
- Chemistry of National and Microbial Products Department, National Research Centre, Giza, Egypt
| | - Mariam A Al-Sheikh
- Department of Chemistry, Faculty of Science, University of Jeddah, AlFaisaliah, Jeddah, Saudi Arabia
| | - Hanadi Y Medrasi
- Department of Chemistry, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ghada S Masaret
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jihan Qurban
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Marwa F Harras
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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21
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Moussaoui M, Baassi M, Baammi S, Soufi H, Salah M, Daoud R, El Allali A, Belghiti ME, Belaaouad S. In silico design of novel CDK2 inhibitors through QSAR, ADMET, molecular docking and molecular dynamics simulation studies. J Biomol Struct Dyn 2023; 41:13646-13662. [PMID: 37203327 DOI: 10.1080/07391102.2023.2212304] [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: 08/23/2022] [Accepted: 02/04/2023] [Indexed: 05/20/2023]
Abstract
The present study aims to investigate about the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the DFT method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R2 = 0.725, R2adj = 0.653, MSE = 0.060, R2test = 0.827, Q2cv = 0.536). The energy EHOMO orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Further, new Thiazole derivatives have been designed and their activities and pharmacokinetic properties have been predicted using the validated QSAR model. The designed molecules were then assessed to molecular docking (MD), and molecular dynamic (MDs) simulation accompanied by the calculation of the binding affinity using MMPBSA script according to 100 ns a simulation trajectory, to study both their affinity and their stability towards CDK2 as a target protein for the cancer disease treatment. This research concluded with the identification of four new CDK2 inhibitors which are A1, A3, A5, and A6 showing good pharmacokinetic properties. The MDs results revealed that the newly designed compound A5 remained stable in the active center of the discovered CDK2 protein, indicating its potential as a novel inhibitor for the treatment of hepatocellular carcinoma. The current findings may eventually contribute to the development of robust CDK2 inhibitors in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed Moussaoui
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mouna Baassi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Hatim Soufi
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohammed Salah
- Team of Chemoinformatics Research and Spectroscopy and Quantum Chemistry, Department of chemistry, Faculty of Science, University Chouaib Doukkali, El Jadida, Morocco
| | - Rachid Daoud
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - M E Belghiti
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
- Laboratory of Nernest Technology, Sherbrook, Quebec, Canada
| | - Said Belaaouad
- Laboratory of Physical Chemistry of Materials, Faculty of Sciences Ben M'Sick, Hassan II University of Casablanca, Casablanca, Morocco
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22
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Quintela M, James DW, Garcia J, Edwards K, Margarit L, Das N, Lutchman-Singh K, Beynon AL, Rioja I, Prinjha RK, Harker NR, Gonzalez D, Steven Conlan R, Francis LW. In silico enhancer mining reveals SNS-032 and EHMT2 inhibitors as therapeutic candidates in high-grade serous ovarian cancer. Br J Cancer 2023:10.1038/s41416-023-02274-2. [PMID: 37120667 DOI: 10.1038/s41416-023-02274-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Epigenomic dysregulation has been linked to solid tumour malignancies, including ovarian cancers. Profiling of re-programmed enhancer locations associated with disease has the potential to improve stratification and thus therapeutic choices. Ovarian cancers are subdivided into histological subtypes that have significant molecular and clinical differences, with high-grade serous carcinoma representing the most common and aggressive subtype. METHODS We interrogated the enhancer landscape(s) of normal ovary and subtype-specific ovarian cancer states using publicly available data. With an initial focus on H3K27ac histone mark, we developed a computational pipeline to predict drug compound activity based on epigenomic stratification. Lastly, we substantiated our predictions in vitro using patient-derived clinical samples and cell lines. RESULTS Using our in silico approach, we highlighted recurrent and privative enhancer landscapes and identified the differential enrichment of a total of 164 transcription factors involved in 201 protein complexes across the subtypes. We pinpointed SNS-032 and EHMT2 inhibitors BIX-01294 and UNC0646 as therapeutic candidates in high-grade serous carcinoma, as well as probed the efficacy of specific inhibitors in vitro. CONCLUSION Here, we report the first attempt to exploit ovarian cancer epigenomic landscapes for drug discovery. This computational pipeline holds enormous potential for translating epigenomic profiling into therapeutic leads.
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Affiliation(s)
- Marcos Quintela
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - David W James
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Jetzabel Garcia
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Kadie Edwards
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Lavinia Margarit
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
- Cwm Taf Morgannwg University Health Board, Swansea, SA2 8QA, UK
| | - Nagindra Das
- Swansea Bay University Health Board, Swansea, SA12 7BR, UK
| | | | | | - Inmaculada Rioja
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Rab K Prinjha
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Nicola R Harker
- Immunology Research Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage, SG1 2NY, UK
| | - Deyarina Gonzalez
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - R Steven Conlan
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK
| | - Lewis W Francis
- Swansea University Medical School, Swansea University, Swansea, SA2 8PP, UK.
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23
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Tong J, Tan X, Hao S, Ermine K, Lu X, Liu Z, Jha A, Yu J, Zhang L. Inhibition of multiple CDKs potentiates colon cancer chemotherapy via p73-mediated DR5 induction. Oncogene 2023; 42:869-880. [PMID: 36721000 PMCID: PMC10364554 DOI: 10.1038/s41388-023-02598-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/01/2023]
Abstract
Targeting cyclin-dependent kinases (CDKs) has recently emerged as a promising therapeutic approach against cancer. However, the anticancer mechanisms of different CDK inhibitors (CDKIs) are not well understood. Our recent study revealed that selective CDK4/6 inhibitors sensitize colorectal cancer (CRC) cells to therapy-induced apoptosis by inducing Death Receptor 5 (DR5) via the p53 family member p73. In this study, we investigated if this pathway is involved in anticancer effects of different CDKIs. We found that less-selective CDKIs, including flavopiridol, roscovitine, dinaciclib, and SNS-032, induced DR5 via p73-mediated transcriptional activation. The induction of DR5 by these CDKIs was mediated by dephosphorylation of p73 at Threonine 86 and p73 nuclear translocation. Knockdown of a common target of these CDKIs, including CDK1, 2, or 9, recapitulated p73-mediated DR5 induction. CDKIs strongly synergized with 5-fluorouracil (5-FU), the most commonly used CRC chemotherapy agent, in vitro and in vivo to promote growth suppression and apoptosis, which required DR5 and p73. Together, these findings indicate p73-mediated DR5 induction as a potential tumor suppressive mechanism and a critical target engaged by different CDKIs in potentiating therapy-induced apoptosis in CRC cells. These findings help better understand the anticancer mechanisms of CDKIs and may help facilitate their clinical development and applications in CRC.
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Affiliation(s)
- Jingshan Tong
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Xiao Tan
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Suisui Hao
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Kaylee Ermine
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Xinyan Lu
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Zhaojin Liu
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Anupma Jha
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Jian Yu
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Lin Zhang
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
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24
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Soleman DM, Eldahshan OA, Ibrahim MH, Ogaly HA, Galal HM, Batiha GES, Elkousy RH. GC/MS Analysis, Cytotoxicity, and Antiviral Activities of Annona glabra Hexane Extract Supported by In Silico Study. Molecules 2023; 28:molecules28041628. [PMID: 36838616 PMCID: PMC9966597 DOI: 10.3390/molecules28041628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Annona glabra Linn is employed in conventional medicine to treat a number of human disorders, including cancer and viruses. In the present investigation, the significant phytochemical components of Annona glabra hexane extract were identified using gas chromatography-mass spectrometry (GC-MS) analysis. Three major compounds were identified in the hexane extract: tritriacontane (30.23%), 13, 17-dimethyl-tritriacontane (22.44%), and limonene (18.97%). MTT assay was used to assess the cytotoxicity of the extract on six human cancer cell lines including liver (HepG-2), pancreas (PANC-1), lung (A-549), breast (MCF-7, HTB-22), prostate (PC-3), and colon (CACO-2, ATB-37). The extract exhibited significant cytotoxic activity against both CACO-2 and A-549 cancer cell lines (IC50 = 47 ± 0.74 μg/mL and 56.82 ± 0.92 μg/mL) in comparison with doxorubicin (IC50 = 31.91 ± 0.81 μg/mL and 23.39 ± 0.43 μg/mL) and of SI of 3.8 and 3.1, respectively. It also induced moderate-to-weak activities against the other cancerous cell lines: PC-3, PANC-1, MCF-7, and HepG-2 (IC50 = 81.86 ± 3.26, 57.34 ± 0.77, 80.31 ± 4.13, and 57.01 ± 0.85 μg/mL) in comparison to doxorubicin (IC50 = 32.9 ± 1.74, 19.07 ± 0.2, 15.48 ± 0.84 and 5.4 ± 0.22 μg/mL, respectively) and SI of 2.2, 3.1, 2.2, and 3.1, respectively. In vitro anti-HSV1 (Herpes simplex 1 virus) and HAV (Hepatitis A virus) activity was evaluated using MTT colorimetric assay with three different protocols to test protective, anti-replicative, and anti-infective antiviral activities, and three separate replications of each experiment were conducted. The plant extract showed promising protective and virucidal activity against HSV1 with no significant difference with acyclovir (79.55 ± 1.67 vs. 68.44 ± 7.62 and 70.91 ± 7.02 vs. 83.76 ± 5.67), while it showed mild protective antiviral activity against HAV (48.08 ±3.46) with no significant difference vs. acyclovir (36.89 ± 6.61). The selected main compounds were examined for their bioactivity through in silico molecular docking, which exhibited that limonene could possess the strongest antiviral properties. These findings support Annona glabra's conventional use, which is an effective source of antiviral and anticancer substances that could be used in pharmaceuticals.
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Affiliation(s)
- Dalia M. Soleman
- Department of Pharmacognosy, Faculty of Pharmacy, Misr International University, Cairo P.O. Box 41611, Egypt
| | - Omayma A. Eldahshan
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Center for Drug Discovery Research and Development, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Correspondence: (O.A.E.); (R.H.E.)
| | - Mona H. Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (for Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
| | - Hanan A. Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha 61421, Saudi Arabia
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Heba M. Galal
- Department of Medical Physiology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
- Department of Medical Physiology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Rawah H. Elkousy
- Department of Pharmacognosy, Faculty of Pharmacy (for Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
- Correspondence: (O.A.E.); (R.H.E.)
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25
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Suto A, Yano Y, Yamamoto Y, Noguchi H, Takeda A, Yamamoto S, Kagawa T, Yoshida K, Hinokio K, Kuwahara A, Yasui T, Iwasa T. Effects of activation with a Ca ionophore and roscovitine on the development of human oocytes that failed to fertilize after ICSI. THE JOURNAL OF MEDICAL INVESTIGATION 2023; 70:321-324. [PMID: 37940514 DOI: 10.2152/jmi.70.321] [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] [Indexed: 11/10/2023]
Abstract
OBJECTIVE The effects of oocyte activation with a Ca ionophore and roscovitine (Ca+R), a selective inhibitor of M-phase promoting factor, on unfertilized oocytes after intracytoplasmic sperm injection (ICSI) or testicular sperm extraction (TESE)-ICSI were evaluated. METHOD Oocytes without pronuclei at 18 hours after ICSI were judged to be unfertilized and were exposed to the Ca ionophore A23187 (5 ?M) with or without roscovitine (50 ?M). The activation rate was measured 3, 7, and 18 hours later. Oocytes with two polar bodies and two pronuclei with a sperm tail were judged to have been activated. RESULTS At 18 hours, the activation rates in the control, Ca ionophore, and Ca+R groups were 3.5% (4/112), 26.9% (7/26), and 32.1% (17/53), respectively. The activation rate of the Ca+R group was significantly higher than that of the control and similar to that of the Ca ionophore group. Among the oocytes that remained unfertilized after TESE-ICSI, the activation rates of the Ca ionophore and Ca+R groups were 22.2% (2/9) and 43.8% (7/16), respectively. CONCLUSIONS Sequential treatment with an Ca ionophore and roscovitine activates oocytes that remain unfertilized after ICSI. In TESE-ICSI, the activation rate tended to be increased by the co-administration of roscovitine with a Ca ionophore. J. Med. Invest. 70 : 321-324, August, 2023.
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Affiliation(s)
- Ayako Suto
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Yuya Yano
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Yuri Yamamoto
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Hiroki Noguchi
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Asuka Takeda
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Shota Yamamoto
- School of Medicine, Tokushima University, Tokushima, Japan
- Department of Renal and Genitourinary Surgery, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | | | - Kanako Yoshida
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Kenji Hinokio
- School of Medicine, Tokushima University, Tokushima, Japan
| | - Akira Kuwahara
- School of Medicine, Tokushima University, Tokushima, Japan
| | | | - Takeshi Iwasa
- School of Medicine, Tokushima University, Tokushima, Japan
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26
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Abdelazeem NM, El-Hussieny M, El-Rashedy AA, Elsayed GH. Design, Synthesis, Docking Studies and Biological Evaluation of Novel Benzochromenopyrimidines via Silica Sulfuric Acid Catalyzed Reaction on Apoptosis in Human Cancer Cells. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2150237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nagwa M. Abdelazeem
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Giza, Egypt
| | - Marwa El-Hussieny
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Giza, Egypt
| | - Ahmed A. El-Rashedy
- Natural and Microbial Products Department, National Research Center (NRC), Giza, Egypt
| | - Ghada H. Elsayed
- Hormones Department, National Research Centre, Giza, Egypt
- Stem Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Giza, Egypt
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27
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Liu J, Zhang M, Dong H, Liu J, Mao A, Ning G, Cao Y, Zhang Y, Wang Q. Chemokine signaling synchronizes angioblast proliferation and differentiation during pharyngeal arch artery vasculogenesis. Development 2022; 149:285824. [PMID: 36468454 PMCID: PMC10114070 DOI: 10.1242/dev.200754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/14/2022] [Indexed: 12/09/2022]
Abstract
Developmentally, the great vessels of the heart originate from the pharyngeal arch arteries (PAAs). During PAA vasculogenesis, PAA precursors undergo sequential cell fate decisions that are accompanied by proliferative expansion. However, how these two processes are synchronized remains poorly understood. Here, we find that the zebrafish chemokine receptor Cxcr4a is expressed in PAA precursors, and genetic ablation of either cxcr4a or the ligand gene cxcl12b causes PAA stenosis. Cxcr4a is required for the activation of the downstream PI3K/AKT cascade, which promotes not only PAA angioblast proliferation, but also differentiation. AKT has a well-known role in accelerating cell-cycle progression through the activation of cyclin-dependent kinases. Despite this, we demonstrate that AKT phosphorylates Etv2 and Scl, the key regulators of angioblast commitment, on conserved serine residues, thereby protecting them from ubiquitin-mediated proteasomal degradation. Altogether, our study reveals a central role for chemokine signaling in PAA vasculogenesis through orchestrating angioblast proliferation and differentiation.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingming Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Haojian Dong
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China.,Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jingwen Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Aihua Mao
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Guozhu Ning
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Cao
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiyue Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Qiang Wang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
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28
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Khedr MA, Zaghary WA, Elsherif GE, Azzam RA, Elgemeie GH. Purine analogs: synthesis, evaluation and molecular dynamics of pyrazolopyrimidines based benzothiazole as anticancer and antimicrobial CDK inhibitors. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:77-104. [PMID: 35949161 DOI: 10.1080/15257770.2022.2109169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Cyclin dependent kinases (CDKs) enzymes regulate cell proliferation and transcriptional processes and can be considered as important targets for the development of anticancer and antimicrobial drugs. In this work, novel benzothiazolyl pyrazolopyrimidine carboxamide and benzothiazolyl pyrazolopyrimidine carbonitrile derivatives were synthesized and characterized. The synthetic process was carried out via the reaction of ylidine benzothiazole derivatives with pyrazolocarboxamide and pyrazolocarbonitrile through a Michael addition pathway. Docking studies were done against CDK2 and CDK9 enzymes and revealed that compound 8a showed high free energy of binding against CDK2 (-8.10 kcal/mol) while compound 15a showed the highest free energy of binding against CDK2 (-8.16 kcal/mol) and CDK9 (-7.87 kcal/mol). Molecular dynamics simulations were conducted to compare the stability of binding of the most active compound 15a and the potent reference drugs roscovitine and dinaciclib. A CDK enzyme assay was done against CDK2 and CDK9 for the previously mentioned top-ranked compounds, 8a and 15a. It was found that compound 15a was the most potent inhibitor for both enzymes with IC50 of 127 ± 1.01 nM and 65 ± 0.50 nM. The anticancer activity of the synthesized compounds was also determined by NCI against 60 cell lines. Compound 8a showed the highest cytotoxic activity against a large number of the tested cell lines. The antimicrobial activity of the synthesized compounds was determined against various gram positive and gram-negative bacteria as well as fungi. The results showed that compound 15a had the strongest antibacterial activity.
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Affiliation(s)
- Mohammed A Khedr
- Department of Pharmaceutical Chemistry, Faculty of pharmacy, Helwan University, Helwan, Cairo, Egypt.,Department of pharmaceutical sciences, College of clinical pharmacy, King Faisal University, Kingdom of Saudi Arabia
| | - Wafaa A Zaghary
- Department of Pharmaceutical Chemistry, Faculty of pharmacy, Helwan University, Helwan, Cairo, Egypt
| | - Gihad E Elsherif
- Department of Pharmaceutical Chemistry, Faculty of pharmacy, Helwan University, Helwan, Cairo, Egypt
| | - Rasha A Azzam
- Department of Chemistry, Faculty of Science, Helwan University, Cairo, Egypt
| | - Galal H Elgemeie
- Department of Chemistry, Faculty of Science, Helwan University, Cairo, Egypt
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29
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Shi Z, Tian L, Qiang T, Li J, Xing Y, Ren X, Liu C, Liang C. From Structure Modification to Drug Launch: A Systematic Review of the Ongoing Development of Cyclin-Dependent Kinase Inhibitors for Multiple Cancer Therapy. J Med Chem 2022; 65:6390-6418. [PMID: 35485642 DOI: 10.1021/acs.jmedchem.1c02064] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discuss more than 50 cyclin-dependent kinase (CDK) inhibitors that have been approved or have undergone clinical trials and their therapeutic application in multiple cancers. This review discusses the design strategies, structure-activity relationships, and efficacy performances of these selective or nonselective CDK inhibitors. The theoretical basis of early broad-spectrum CDK inhibitors is similar to the scope of chemotherapy, but because their toxicity is greater than the benefit, there is no clinical therapeutic window. The notion that selective CDK inhibitors have a safer therapeutic potential than pan-CDK inhibitors has been widely recognized during the research process. Four CDK4/6 inhibitors have been approved for the treatment of breast cancer or for prophylactic administration during chemotherapy to protect bone marrow and immune system function. Furthermore, the emerging strategies in the field of CDK inhibitors are summarized briefly, and CDKs continue to be widely pursued as emerging anticancer drug targets for drug discovery.
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Affiliation(s)
- Zhenfeng Shi
- Department of Urology Surgery Center, The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830002, P. R. China
| | - Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yue Xing
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang 550025, P. R. China
| | - Chang Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Zhuhai 519030, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
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30
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Venkatanarayana M, Nuchu R, Babu HS. Ultrasound assisted effective synthesis of benzopril based indole derivatives, docking studies: And there in vitro anti-proliferative effects on various cancer cell lines. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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31
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Shimazaki T, Tachikawa M. Collaborative Approach between Explainable Artificial Intelligence and Simplified Chemical Interactions to Explore Active Ligands for Cyclin-Dependent Kinase 2. ACS OMEGA 2022; 7:10372-10381. [PMID: 35382271 PMCID: PMC8973106 DOI: 10.1021/acsomega.1c06976] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/09/2022] [Indexed: 05/13/2023]
Abstract
To improve virtual screening for drug discovery, we present a collaborative approach between explainable artificial intelligence (AI) and simplified chemical interaction scores to efficiently search for active ligands bound to the target receptor. In particular, we focus on cyclin-dependent kinase 2 (CDK2), which is well known as a cancer target protein. Docking simulation alone is insufficient to distinguish active ligands from decoy molecules. To identify active ligands, in this paper, machine learning is employed together with scoring functions that simplify the screened Coulomb and Lennard-Jones interactions between the ligands and residues of the target receptor. We demonstrate that these simplified interaction scores can significantly improve the classification ability of machine learning models. We also demonstrate that explainable AI together with the simplified scoring method can highlight the important residues of CDK2 for recognizing active ligands.
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Affiliation(s)
- Tomomi Shimazaki
- Graduate
School of Nanobioscience, Yokohama City
University, 22-2 Seto, Yokohama, Kanagawa 236-0027, Japan
| | - Masanori Tachikawa
- Graduate
School of Data Science, Yokohama City University, 22-2, Seto, Yokohama, Kanagawa 236-0027, Japan
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32
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Eze CC, Ezeokonkwo AM, Ugwu ID, Eze UF, Onyeyilim EL, Attah IS, Okonkwo IV. Azole-pyrimidine Hybrid Anticancer Agents: A Review of Molecular Structure, Structure Activity Relationship and Molecular Docking. Anticancer Agents Med Chem 2022; 22:2822-2851. [PMID: 35306990 DOI: 10.2174/1871520622666220318090147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/07/2021] [Accepted: 01/18/2022] [Indexed: 11/22/2022]
Abstract
Cancer has emerged as one of the leading causes of deaths globally partly due to the steady rise in anticancer drug resistance. Pyrimidine and pyrimidine-fused heterocycles are some of the privileged scaffolds in medicine, as they possess diverse biological properties. Pyrimidines containing azole nucleus possesses inestimable anticancer potency and has enormous potential to conduct the regulation of cellular pathways for selective anticancer activity. The present review outlines the molecular structure of pyrimidine-fused azoles with significant anticancer activity. The structure activity relationship and molecular docking studies have also been discussed. The current review is the first complete compilation of significant literature on the proposed topic from 2016 to 2020. The information contained in this review offers a useful insight to chemists in the design of new and potent anticancer azole-pyrimidine analogues.
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Affiliation(s)
- Chinweike Cosmas Eze
- Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | | | - Izuchukwu David Ugwu
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Uchenna Florence Eze
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Ebuka Leonard Onyeyilim
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Izuchi Solomon Attah
- Department of Pure & Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
| | - Ifeoma Vivian Okonkwo
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
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33
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Obakachi VA, Kehinde I, Kushwaha ND, Akinpelu OI, Kushwaha B, Merugu SR, Kayamba F, Kumalo HM, Karpoormath R. Structural based investigation of novel pyrazole-thiazole Hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2045016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Vincent A. Obakachi
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Idowu Kehinde
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Olayinka I. Akinpelu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Babita Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Srinivas Reddy Merugu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Francis Kayamba
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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34
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kumar Bhardwaj V, Das P, Purohit R. Identification and comparison of plant-derived scaffolds as selective CDK5 inhibitors against standard molecules: Insights from umbrella sampling simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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35
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Cole E, Gaertig J. Anterior-posterior pattern formation in ciliates. J Eukaryot Microbiol 2022; 69:e12890. [PMID: 35075744 PMCID: PMC9309198 DOI: 10.1111/jeu.12890] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
As single cells, ciliates build, duplicate, and even regenerate complex cortical patterns by largely unknown mechanisms that precisely position organelles along two cell‐wide axes: anterior–posterior and circumferential (left–right). We review our current understanding of intracellular patterning along the anterior–posterior axis in ciliates, with emphasis on how the new pattern emerges during cell division. We focus on the recent progress at the molecular level that has been driven by the discovery of genes whose mutations cause organelle positioning defects in the model ciliate Tetrahymena thermophila. These investigations have revealed a network of highly conserved kinases that are confined to either anterior or posterior domains in the cell cortex. These pattern‐regulating kinases create zones of cortical inhibition that by exclusion determine the precise placement of organelles. We discuss observations and models derived from classical microsurgical experiments in large ciliates (including Stentor) and interpret them in light of recent molecular findings in Tetrahymena. In particular, we address the involvement of intracellular gradients as vehicles for positioning organelles along the anterior‐posterior axis.
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Affiliation(s)
- Eric Cole
- Biology Department, St. Olaf College, Northfield, MN, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
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36
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Khodair AI, Bakare SB, Awad MK, Al‐Issa SA, Nafie MS. Design, synthesis, and computational explorations of novel 2‐thiohydantoin nucleosides with cytotoxic activities. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ahmed I. Khodair
- Chemistry Department, Faculty of Science Kafrelsheikh University Kafrelsheikh Egypt
| | - Safyah B. Bakare
- Faculty of Education Shaqra University Shaqra Kingdom of Saudi Arabia
| | - Mohamed K. Awad
- Theoretical Applied Chemistry Unit (TACU), Chemistry Department, Faculty of Science Tanta University Tanta Egypt
| | - Siham A. Al‐Issa
- Chemistry Department College of Science, Princess Nourah Bint Abdulrahman University Riyadh Saudi Arabia
| | - Mohamed S. Nafie
- Chemistry Department, Faculty of Science Suez Canal University Ismailia Egypt
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37
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Heo K, Basu H, Gutnick A, Wei W, Shlevkov E, Schwarz TL. Serine/Threonine Protein Phosphatase 2A Regulates the Transport of Axonal Mitochondria. Front Cell Neurosci 2022; 16:852245. [PMID: 35370563 PMCID: PMC8973303 DOI: 10.3389/fncel.2022.852245] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubule-based transport provides mitochondria to distant regions of neurons and is essential for neuronal health. To identify compounds that increase mitochondrial motility, we screened 1,641 small-molecules in a high-throughput screening platform. Indirubin and cantharidin increased mitochondrial motility in rat cortical neurons. Cantharidin is known to inhibit protein phosphatase 2A (PP2A). We therefore tested two other inhibitors of PP2A: LB-100 and okadaic acid. LB-100 increased mitochondrial motility, but okadaic acid did not. To resolve this discrepancy, we knocked down expression of the catalytic subunit of PP2A (PP2CA). This long-term inhibition of PP2A more than doubled retrograde transport of axonal mitochondria, confirming the importance of PP2A as a regulator of mitochondrial motility and as the likely mediator of cantharidin's effect.
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Affiliation(s)
- Keunjung Heo
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Himanish Basu
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Amos Gutnick
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Wei Wei
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Evgeny Shlevkov
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Thomas L Schwarz
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurobiology, Harvard Medical School, Boston, MA, United States
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38
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Meijer L, Hery-Arnaud G, Leven C, Nowak E, Hillion S, Renaudineau Y, Durieu I, Chiron R, Prevotat A, Fajac I, Hubert D, Murris-Espin M, Huge S, Danner-Boucher I, Ravoninjatovo B, Leroy S, Macey J, Urban T, Rault G, Mottier D, Berre RL. Safety and pharmacokinetics of Roscovitine (Seliciclib) in cystic fibrosis patients chronically infected with Pseudomonas aeruginosa, a randomized, placebo-controlled study. J Cyst Fibros 2021; 21:529-536. [PMID: 34961705 DOI: 10.1016/j.jcf.2021.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 01/20/2023]
Abstract
BACKGROUND The orally available kinase inhibitor R-roscovitine has undergone clinical trials against various cancers and is currently under clinical evaluation against Cushing disease and rheumatoid arthritis. Roscovitine displays biological properties suggesting potential benefits in CF: it partially corrects F508del-CFTR trafficking, stimulates the bactericidal properties of CF alveolar macrophages, and displays anti-inflammatory properties and analgesic effects. METHODS A phase 2 trial study (ROSCO-CF) was launched to evaluate the safety and effects of roscovitine in Pseudomonas aeruginosa infected adult CF patients carrying two CF causing mutations (at least one F508del-CFTR mutation) and harboring a FEV1 ≥40%. ROSCO-CF was a multicenter, double-blind, placebo-controlled, dose-ranging study (200, 400, 800 mg roscovitine, orally administered daily for 4 days/week/4 weeks). RESULTS Among the 34 volunteers enrolled, randomization assigned 11/8/8/7 to receive the 0 (placebo)/ 200/400/800 mg roscovitine doses, respectively. In these subjects with polypharmacy, roscovitine was relatively safe and well-tolerated, with no significant adverse effects (AEs) other than five serious AEs (SAEs) possibly related to roscovitine. Pharmacokinetics of roscovitine were rather variable among subjects. No significant efficacy, at the levels of inflammation, infection, spirometry, sweat chloride, pain and quality of life, was detected in roscovitine-treated groups compared to the placebo-treated group. CONCLUSION Roscovitine was relatively safe and well-tolerated in CF patients especially at the 200 and 400 mg doses. However, there were 5 subject withdrawals due to SAEs in the roscovitine group and none in the placebo group. The lack of evidence for efficacy of roscovitine (despite encouraging cellular and animal results) may be due to high pharmacokinetics variability, short duration of treatment, and/or inappropriate dosing protocol.
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Affiliation(s)
- Laurent Meijer
- ManRos Therapeutics, Presqu'île de Perharidy, Roscoff 29680, France.
| | - Geneviève Hery-Arnaud
- Unité de Bactériologie, Hôpital de la Cavale Blanche, CHRU Brest, Brest cedex 29609, France; Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest 29200, France
| | - Cyril Leven
- Département de Biochimie et Pharmaco-Toxicologie, CHRU Brest, Brest cedex 29609, France; Univ Brest, EA 3878, GETBO, Brest 29200, France
| | - Emmanuel Nowak
- INSERM CIC 1412, Brest University Hospital, Brest cedex 29609, France
| | - Sophie Hillion
- Laboratoire d'Immunologie et Immunothérapie, CHRU de Brest, INSERM U1227, 2 avenue Foch, BP824, 29609 Brest cedex, France
| | - Yves Renaudineau
- Laboratoire d'Immunologie et Immunothérapie, CHRU de Brest, INSERM U1227, 2 avenue Foch, BP824, 29609 Brest cedex, France
| | - Isabelle Durieu
- Research on Healthcare Performance (RESHAPE), INSERM U1290, Claude Bernard Lyon 1 University, 8 Avenue Rockefeller, 69003 Lyon, France; Department of Internal Medicine, Cystic Fibrosis Center, Hospices Civils de Lyon, Pierre-Bénite 69495, France
| | - Raphaël Chiron
- CHU Montpellier, Maladies Respiratoires, Hôpital Arnaud de Villeneuve, 371, avenue du Doyen Gaston Giraud, Montpellier 34295, France
| | - Anne Prevotat
- Service de pneumologie, CHR - Hôpital Calmette, Boulevard du Pr. Leclercq, Lille 59037, France
| | - Isabelle Fajac
- APHP.Centre - Université de Paris, 27 rue du Faubourg Saint-Jacques, Paris 75014, France
| | - Dominique Hubert
- APHP.Centre - Université de Paris, 27 rue du Faubourg Saint-Jacques, Paris 75014, France
| | - Marlène Murris-Espin
- CHU Toulouse, CRCM adulte, Service de Pneumologie, Clinique des Voies Respiratoires. Hôpital Larrey, 24 chemin de Pouvourville, Toulouse 31059, France
| | - Sandrine Huge
- Centre Hospitalier Bretagne Atlantique, CRCM Mixte 56, 20 Boulevard du général Maurice Guillaudot, Vannes cedex 56017, France
| | - Isabelle Danner-Boucher
- CHU de Nantes, Service de Pneumologie, Hôpital Nord Laennec, Boulevard Jacques-Monod, Nantes 44093, Saint-Herblain, France
| | - Bruno Ravoninjatovo
- Centre de Ressources et de Compétences de la Mucoviscidose, Maladies Respiratoires et Allergiques, Hôpital Maison Blanche - CHU Reims, 45 rue Cognacq-Jay, 51100 Reims, France
| | - Sylvie Leroy
- CHU de Nice, Hôpital Pasteur, Service de Pneumologie, Oncologie Thoracique et Soins Intensifs Respiratoires, 30 Voie Romaine, CS 51069, Nice cedex 1 06001, France
| | - Julie Macey
- CHU Bordeaux, Hôpital Haut-Lévêque, Service de Pneumologie, Avenue de Magellan, Pessac cedex 33604, France
| | - Thierry Urban
- Département de Pneumologie, CHU Angers, Site de Larrey, 4 rue de Larrey, Angers cedex 49933, France
| | - Gilles Rault
- Fondation Ildys, Centre de Perharidy, Roscoff cedex 29684, France
| | - Dominique Mottier
- Département de Biochimie et Pharmaco-Toxicologie, CHRU Brest, Brest cedex 29609, France
| | - Rozenn Le Berre
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest 29200, France; Département de Médecine Interne et Pneumologie, CHRU Brest, Brest cedex 29609, France
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de Azevedo WF. Protein-ligand interactions. High-resolution structures of CDK2. Curr Drug Targets 2021; 23:438-440. [PMID: 34906055 DOI: 10.2174/1389450122666211214113205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022]
Affiliation(s)
- Walter Filgueira de Azevedo
- Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900. Brazil
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40
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Hit Identification of a Novel Quinazoline Sulfonamide as a Promising EphB3 Inhibitor: Design, Virtual Combinatorial Library, Synthesis, Biological Evaluation, and Docking Simulation Studies. Pharmaceuticals (Basel) 2021; 14:ph14121247. [PMID: 34959648 PMCID: PMC8708751 DOI: 10.3390/ph14121247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
EphB3 is a major key player in a variety of cellular activities, including cell migration, proliferation, and apoptosis. However, the exact role of EphB3 in cancer remains ambiguous. Accordingly, new EphB3 inhibitors can increase the understanding of the exact roles of the receptor and may act as promising therapeutic candidates. Herein, a hybrid approach of structure-based design and virtual combinatorial library generated 34 quinazoline sulfonamides as potential selective EphB3 inhibitors. A molecular docking study over EphB3 predicted the binding affinities of the generated library, and the top seven hit compounds (3a and 4a–f), with GlideScore ≥ −6.20 Kcal/mol, were chosen for further MM-GBSA calculations. Out of the seven top hits, compound 4c showed the highest MM-GBSA binding free energy (−74.13 Kcal/mol). To validate these predicted results, compounds 3a and 4a–f were synthesized and characterized using NMR, HRMS, and HPLC. The biological evaluation revealed compound 4c as a potent EphB3 inhibitory lead (IC50 = 1.04 µM). The screening of 4c over a mini-panel of kinases consisting of EGFR, Aurora A, Aurora B, CDK2/cyclin A, EphB1, EphB2, EphB4, ERBB2/HER2, and KDR/VEGFR2, showed a promising selective profile against EphB3 isoform. A dose-dependent assay of compound 4c and a molecular docking study over the different forms of EphB provided insights into the elicited biological activities and highlighted reasonable explanations of the selectivity.
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Adamantane-Substituted Purines and Their β-Cyclodextrin Complexes: Synthesis and Biological Activity. Int J Mol Sci 2021; 22:ijms222312675. [PMID: 34884480 PMCID: PMC8657435 DOI: 10.3390/ijms222312675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/05/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) play an important role in the cell-division cycle. Synthetic inhibitors of CDKs are based on 2,6,9-trisubstituted purines and are developed as potential anticancer drugs; however, they have low solubility in water. In this study, we proved that the pharmaco-chemical properties of purine-based inhibitors can be improved by appropriate substitution with the adamantane moiety. We prepared ten new purine derivatives with adamantane skeletons that were linked at position 6 using phenylene spacers of variable geometry and polarity. We demonstrated that the adamantane skeleton does not compromise the biological activity, and some of the new purines displayed even higher inhibition activity towards CDK2/cyclin E than the parental compounds. These findings were supported by a docking study, which showed an adamantane scaffold inside the binding pocket participating in the complex stabilisation with non-polar interactions. In addition, we demonstrated that β-cyclodextrin (CD) increases the drug’s solubility in water, although this is at the cost of reducing the biochemical and cellular effect. Most likely, the drug concentration, which is necessary for target engagement, was decreased by competitive drug binding within the complex with β-CD.
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42
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Satake SI, Konishi S. Topographical distance between presynaptic Ca 2+ channels and exocytotic Ca 2+ sensors contributes to differential facilitatory actions of roscovitine on neurotransmitter release at cerebellar glutamatergic and GABAergic synapses. Eur J Neurosci 2021; 54:7048-7062. [PMID: 34622493 DOI: 10.1111/ejn.15487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022]
Abstract
Calcium influx into presynaptic terminals through voltage-gated Ca2+ channels triggers univesicular or multivesicular release of neurotransmitters depending on the characteristics of the release machinery. However, the mechanisms underlying multivesicular release (MVR) and its regulation remain unclear. Previous studies showed that in rat cerebellum, the cyclin-dependent kinase inhibitor roscovitine profoundly increases excitatory postsynaptic current (EPSC) amplitudes at granule cell (GC)-Purkinje cell (PC) synapses by enhancing the MVR of glutamate. This compound can also moderately augment the amplitude and prolong the decay time of inhibitory postsynaptic currents (IPSCs) at molecular layer interneuron (MLI)-PC synapses via MVR enhancement and GABA spillover, thus allowing for persistent activation of perisynaptic GABA receptors. The enhanced MVR may depend on the driving force for Cav 2.1 channel-mediated Ca2+ influx. To determine whether the distinct spatiotemporal dynamics of presynaptic Ca2+ influence MVR, we compared the effects of slow and fast Ca2+ chelators, that is, EGTA and BAPTA, respectively, on roscovitine-induced actions at GC-PC and MLI-PC synapses. Membrane-permeable EGTA-AM decreased GC-PC EPSC and MLI-PC IPSC amplitudes to a similar extent but suppressed the roscovitine-induced enhancement of EPSCs. In contrast, BAPTA-AM attenuated the effects of roscovitine on IPSCs. These results suggest that roscovitine augmented glutamate release by activating the release machinery located distally from the Cav 2.1 channel clusters, while it enhanced GABA release in a manner less dependent on those at distal sites. Therefore, the spatial relationships among Ca2+ channels, buffers, and sensors are critical determinants of the differential facilitatory actions of roscovitine on glutamatergic and GABAergic synapses in the cerebellar cortex.
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Affiliation(s)
- Shin' Ichiro Satake
- Brain Research Support Center, National Institute for Physiological Sciences (NIPS), Okazaki, Japan.,School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Shiro Konishi
- Department of Neurophysiology, Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Sanuki, Japan
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Synthesis, in vitro anticancer activity and in silico studies of certain pyrazole-based derivatives as potential inhibitors of cyclin dependent kinases (CDKs). Bioorg Chem 2021; 116:105347. [PMID: 34555628 DOI: 10.1016/j.bioorg.2021.105347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
New diphenyl-1H-pyrazoles were synthesized and screened for CDK2 inhibition where 8d, 9b, 9c, and 9e exhibited promising activity (IC50 = 51.21, 41.36, 29.31, and 40.54 nM respectively) compared to R-Roscovitine (IC50 = 43.25 nM). Furthermore, preliminary anti-proliferative activity screening of some selected compounds on 60 cancer cell lines was performed at the (NCI/USA). Compounds 8a-c displayed promising growth inhibitory activity (mean %GI; 73.74, 94.32 and 74.19, respectively). Additionally, they were further selected by the NCI for five-dose assay, exhibiting pronounced activity against almost the full panel (GI50 ranges; 0.181-5.19, 1.07-4.12 and 1.07-4.82 µM, respectively) and (Full panel GI50 (MG-MID); 2.838, 2.306 and 2.770 µM, respectively). Screening the synthesized compounds 8a-c for inhibition of CDK isoforms revealed that compound 8a exhibited nearly equal inhibition to all the tested CDK isoforms, while compound 8b inhibits CDK4/D1 preferentially than the other isoforms and compound 8c inhibits CDK1, CDK2 and CDK4 more than CDK7. Flow cytometry cell cycle assay of 8a-c on Non-small cell lung carcinoma (NSCL HOP-92) cell line revealed S phase arrest by 8a and G1/S phase arrest by 8b and 8c. Apoptotic induction in HOP-92 cell line was also observed upon treatment with compounds 8a-c. Docking to CDK2 ATP binding site revealed similar interactions as the co-crystallized ligand R-Roscovitine (PDB code; 3ddq). These findings present compounds 8a-c as promising anti-proliferative agents.
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Nandi S, Dey R, Dey S, Samadder A, Saxena A. Naturally Sourced CDK Inhibitors and Current Trends in Structure-Based Synthetic Anticancer Drug Design by Crystallography. Anticancer Agents Med Chem 2021; 22:485-498. [PMID: 34503422 DOI: 10.2174/1871520621666210908101751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 06/12/2021] [Accepted: 07/12/2021] [Indexed: 11/22/2022]
Abstract
Cyclin-dependent kinases (CDKs) are the chief regulators in cell proliferation; the kinase activities are largely regulated by their interactions with CDK inhibitors (CKIs) and Cyclins. The association of different CDKs with CDKIs and Cyclins at the cell-cycle checkpoints of different stages of mitotic cell cycle function act more likely as the molecular switches that regulate different transcriptional events required for progression through the cell cycle. A fine balance in response to extracellular and intracellular signals is highly maintained in the orchestrated function of CDKs along with Cyclins and CDKIs for normal cell proliferation. This fine-tuning in mitotic cell cycle progression sometimes gets lost due to dysregulation of CDKs. The aberrant functioning of the CDKIs is therefore studied for its contributions as a vital hallmark of cancers. It has attracted our focus to maneuver cancer therapy. Hence, several synthetic CDKIs and their crystallography-based drug design have been explained to understand their mode of action with CDKs. Since most of the synthetic drugs function by inhibiting the CDK4/6 kinases by competitively binding to their ATP binding cleft, these synthetic drugs are reported to attack the normal, healthy growing cells adjacent to the cancer cells leading to the decrease in the life span of the cancer patients. The quest for traditional natural medicines may have a great impact on the treatment of cancer. Therefore, in the present studies, a search for naturally sourced CDK inhibitors has been briefly focused. Additionally, some synthetic crystallography-based drug design has been explained to elucidate different avenues to develop better anticancer chemotherapeutics, converting natural scaffolds into inhibitors of the CDK mediated abnormal signal transduction with lesser side effects.
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Affiliation(s)
- Sisir Nandi
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713. India
| | - Rishita Dey
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713. India
| | - Sudatta Dey
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235. India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235. India
| | - Anil Saxena
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713. India
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Self assembly of a novel Cu(II) complex, (C6H9N2)2[CuCl4]: experimental, computational, and molecular docking survey. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02195-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Talapati SR, Goyal M, Nataraj V, Pothuganti M, R SM, Gore S, Ramachandra M, Antony T, More SS, Rao NK. Structural and binding studies of cyclin-dependent kinase 2 with NU6140 inhibitor. Chem Biol Drug Des 2021; 98:857-868. [PMID: 34423559 DOI: 10.1111/cbdd.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) is an established target protein for therapeutic intervention in various diseases, including cancer. Reported inhibitors of CDK2 target the ATP-binding pocket to inhibit the kinase activity. Many small molecule CDK2 inhibitors have been discovered, and their crystal structure with CDK2 or CDK2-cyclin A complex has been published. NU6140 is a CDK2 inhibitor with moderate potency and selectivity. Herein, we report the cocrystal structure determination of NU6140 in complex with CDK2 and confirmation of the binding using various biophysical methods. Our data show that NU6140 binds to CDK2 with a Kd of 800 nM as determined by SPR and stabilizes the protein against thermal denaturation (ΔTm -5°C). The cocrystal structure determined in our study shows that NU6140 binds in the ATP-binding pocket as expected for this class of compounds and interacts with Leu83 and Glu81 with regular hydrogen bonds and with Asp145 via water-mediated H-bond. Based on these data, we propose structural modifications of NU6140 to introduce new interactions with CDK2 that can improve its potency while retaining the selectivity.
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Affiliation(s)
- Sumalatha Rani Talapati
- Aurigene Discovery Technologies Ltd, Bangalore, India.,School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Megha Goyal
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | | | | | - Sreevidya M R
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | - Suraj Gore
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | | | - Thomas Antony
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | - Sunil S More
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
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Jawa Y, Yadav P, Gupta S, Mathan SV, Pandey J, Saxena AK, Kateriya S, Tiku AB, Mondal N, Bhattacharya J, Ahmad S, Chaturvedi R, Tyagi RK, Tandon V, Singh RP. Current Insights and Advancements in Head and Neck Cancer: Emerging Biomarkers and Therapeutics with Cues from Single Cell and 3D Model Omics Profiling. Front Oncol 2021; 11:676948. [PMID: 34490084 PMCID: PMC8418074 DOI: 10.3389/fonc.2021.676948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancer (HNC) is among the ten leading malignancies worldwide, with India solely contributing one-third of global oral cancer cases. The current focus of all cutting-edge strategies against this global malignancy are directed towards the heterogeneous tumor microenvironment that obstructs most treatment blueprints. Subsequent to the portrayal of established information, the review details the application of single cell technology, organoids and spheroid technology in relevance to head and neck cancer and the tumor microenvironment acknowledging the resistance pattern of the heterogeneous cell population in HNC. Bioinformatic tools are used for study of differentially expressed genes and further omics data analysis. However, these tools have several challenges and limitations when analyzing single-cell gene expression data that are discussed briefly. The review further examines the omics of HNC, through comprehensive analyses of genomics, transcriptomics, proteomics, metabolomics, and epigenomics profiles. Patterns of alterations vary between patients, thus heterogeneity and molecular alterations between patients have driven the clinical significance of molecular targeted therapies. The analyses of potential molecular targets in HNC are discussed with connotation to the alteration of key pathways in HNC followed by a comprehensive study of protein kinases as novel drug targets including its ATPase and additional binding pockets, non-catalytic domains and single residues. We herein review, the therapeutic agents targeting the potential biomarkers in light of new molecular targeted therapies. In the final analysis, this review suggests that the development of improved target-specific personalized therapies can combat HNC's global plight.
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Affiliation(s)
- Yashika Jawa
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shruti Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sivapar V. Mathan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jyoti Pandey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ajay K. Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ashu B. Tiku
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neelima Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh K. Tyagi
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rana P. Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Patel M, Pandey N, Timaniya J, Parikh P, Chauhan A, Jain N, Patel K. Coumarin-carbazole based functionalized pyrazolines: synthesis, characterization, anticancer investigation and molecular docking. RSC Adv 2021; 11:27627-27644. [PMID: 35480680 PMCID: PMC9037808 DOI: 10.1039/d1ra03970a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
A series of novel pyrazoline scaffolds from coumarin-carbazole chalcones were synthesized. We explored various acetyl, amide, and phenyl substituents at the N-1 position of the pyrazoline core. The synthesized compounds were characterized by FTIR, 1H-NMR, 13C-NMR, DEPT, and mass spectroscopic techniques. The in vitro cytotoxicity study of all the synthesized compounds was evaluated against HeLa, NCI-H520 and NRK-52E cell lines. Compounds 4a and 7b became the most active compounds and exhibited their potential to arrest the cell cycle progression and induce apoptosis in both the cell lines. In addition, molecular docking studies revealed a higher binding affinity of both the molecules with CDK2 protein. Based on the obtained results, a comprehensive analysis is warranted to establish the role of compounds 4a and 7b as promising cancer therapeutic agents.
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Affiliation(s)
- Mrugesh Patel
- Department of Advanced Organic Chemistry, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat 388421 India
| | - Nilesh Pandey
- Department of Medical Laboratory Technology, Charotar Institute of Paramedical Sciences, Charotar University of Science and Technology Gujarat 388421 India
| | - Jignesh Timaniya
- Department of Advanced Organic Chemistry, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat 388421 India
| | - Paranjay Parikh
- Department of Advanced Organic Chemistry, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat 388421 India
| | - Alex Chauhan
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat 388421 India
| | - Neeraj Jain
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat 388421 India
| | - Kaushal Patel
- Department of Advanced Organic Chemistry, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat 388421 India
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Veit-Acosta M, de Azevedo Junior WF. Computational Prediction of Binding Affinity for CDK2-ligand Complexes. A Protein Target for Cancer Drug Discovery. Curr Med Chem 2021; 29:2438-2455. [PMID: 34365938 DOI: 10.2174/0929867328666210806105810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND CDK2 participates in the control of eukaryotic cell-cycle progression. Due to the great interest in CDK2 for drug development and the relative easiness in crystallizing this enzyme, we have over 400 structural studies focused on this protein target. This structural data is the basis for the development of computational models to estimate CDK2-ligand binding affinity. OBJECTIVE This work focuses on the recent developments in the application of supervised machine learning modeling to develop scoring functions to predict the binding affinity of CDK2. METHOD We employed the structures available at the protein data bank and the ligand information accessed from the BindingDB, Binding MOAD, and PDBbind to evaluate the predictive performance of machine learning techniques combined with physical modeling used to calculate binding affinity. We compared this hybrid methodology with classical scoring functions available in docking programs. RESULTS Our comparative analysis of previously published models indicated that a model created using a combination of a mass-spring system and cross-validated Elastic Net to predict the binding affinity of CDK2-inhibitor complexes outperformed classical scoring functions available in AutoDock4 and AutoDock Vina. CONCLUSION All studies reviewed here suggest that targeted machine learning models are superior to classical scoring functions to calculate binding affinities. Specifically for CDK2, we see that the combination of physical modeling with supervised machine learning techniques exhibits improved predictive performance to calculate the protein-ligand binding affinity. These results find theoretical support in the application of the concept of scoring function space.
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Affiliation(s)
- Martina Veit-Acosta
- Western Michigan University, 1903 Western, Michigan Ave, Kalamazoo, MI 49008. United States
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Discovery of New Pyrazolopyridine, Furopyridine, and Pyridine Derivatives as CDK2 Inhibitors: Design, Synthesis, Docking Studies, and Anti-Proliferative Activity. Molecules 2021; 26:molecules26133923. [PMID: 34206976 PMCID: PMC8272136 DOI: 10.3390/molecules26133923] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
New pyridine, pyrazoloyridine, and furopyridine derivatives substituted with naphthyl and thienyl moieties were designed and synthesized starting from 6-(naphthalen-2-yl)-2-oxo-4-(thiophen-2-yl)-1,2-dihydropyridine-3-carbonitrile (1). The chloro, methoxy, cholroacetoxy, imidazolyl, azide, and arylamino derivatives were prepared to obtain the pyridine-−C2 functionalized derivatives. The derived pyrazolpyridine-N-glycosides were synthesized via heterocyclization of the C2-thioxopyridine derivative followed by glycosylation using glucose and galactose. The furopyridine derivative 14 and the tricyclic pyrido[3′,2′:4,5]furo[3,2-d]pyrimidine 15 were prepared via heterocyclization of the ester derivative followed by a reaction with formamide. The newly synthesized compounds were evaluated for their ability to in vitro inhibit the CDK2 enzyme. In addition, the cytotoxicity of the compounds was tested against four different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549). The CDK2/cyclin A2 enzyme inhibitory results revealed that pyridone 1, 2-chloro-6-(naphthalen-2-yl)-4-(thiophen-2-yl)nicotinonitrile (4), 6-(naphthalen-2-yl)-4-(thiophen-2-yl)-1H-pyrazolo[3,4-b]pyridin-3-amine (8), S-(3-cyano-6-(naphthaen-2-yl)-4-(thiophen-2-yl)pyridin-2-yl) 2-chloroethanethioate (11), and ethyl 3-amino-6-(naphthalen-2-yl)-4-(thiophen-2-yl)furo[2,3-b]pyridine-2-carboxylate (14) are among the most active inhibitors with IC50 values of 0.57, 0.24, 0.65, 0.50, and 0.93 µM, respectively, compared to roscovitine (IC50 0.394 μM). Most compounds showed significant inhibition on different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549) with IC50 ranges of 31.3–49.0, 19.3–55.5, 22.7–44.8, and 36.8–70.7 μM, respectively compared to doxorubicin (IC50 40.0, 64.8, 24.7 and 58.1 µM, respectively). Furthermore, a molecular docking study suggests that most of the target compounds have a similar binding mode as a reference compound in the active site of the CDK2 enzyme. The structural requirements controlling the CDK2 inhibitory activity were determined through the generation of a statistically significant 2D-QSAR model.
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