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Ali GME, Ewida MA, Elmetwali AM, Ewida HA, George RF, Mahmoud WR, Ismail NSM, Ahmed MS, Georgey HH. Discovery of pyrazole-based analogs as CDK2 inhibitors with apoptotic-inducing activity: design, synthesis and molecular dynamics study. RSC Adv 2024; 14:34537-34555. [PMID: 39479486 PMCID: PMC11520566 DOI: 10.1039/d4ra06500j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 10/10/2024] [Indexed: 11/02/2024] Open
Abstract
The discovery of novel CDK2 inhibitors is crucial for developing targeted anticancer therapies. Thus, in this study, we aimed to design, synthesize, and evaluate a series of novel pyrazole derivatives (2a-g, 7a-d, 8a and b, 9, and 10) for their potential as CDK2/cyclin A2 enzyme inhibitors. The newly synthesized compounds were screened in vitro at 50 μM for CDK2 inhibition, followed by IC50 profiling of the most promising candidates. Compounds 4, 7a, 7d, and 9 exhibited the strongest inhibition, with IC50 values of 3.82, 2.0, 1.47, and 0.96 μM, respectively. To assess their anti-proliferative effects, all target compounds were further screened against a panel of 60 National Cancer Institute (NCI) cell lines representing various carcinoma types. Among them, compound 4 demonstrated exceptional anti-proliferative activity with a mean growth inhibition (GI) of 96.47% across the panel, while compound 9 showed a mean GI of 65.90%. Additionally, compounds 2b and 7c exhibited notable inhibition against MCF7 breast cancer cells, with GI rates of 86.1% and 79.41%, respectively. Compound 4 was selected for further five-dose concentration evaluations, displaying a full-panel GI50 value of 3.81 μM, with a subpanel range of 2.36-9.17 μM. Western blot analysis of compounds 4 and 9 in HCT-116 cell lines confirmed their inhibitory effects on CDK2. Furthermore, compound 4 induced significant cell cycle arrest at the G1 phase and promoted apoptosis. In silico molecular docking studies revealed that compounds 4, 7a, 7d, and 9 adopt a similar binding mode as AT7519 (I) within the CDK2 binding site. Molecular dynamics simulations further validated the stability of these compounds within the catalytic domain of CDK2. ADME/TOPKAT analyses indicated their favorable pharmacokinetic profiles, which were confirmed by their low toxicity in normal cell lines. Based on these findings, it was concluded that the synthesized pyrazole derivatives, particularly compound 4, show potent CDK2 inhibition and significant anticancer activity, with promising drug-like properties and minimal toxicity. This positions them as strong candidates for further development as CDK2-targeting anticancer agents.
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Affiliation(s)
- Ghada M E Ali
- Central Administration of Drug Control, EDA P.O. Box: 29 Cairo Egypt
| | - Menna A Ewida
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt Cairo 11835 Egypt
| | - Amira M Elmetwali
- Central Administration of Drug Control, EDA P.O. Box: 29 Cairo Egypt
| | - Heba A Ewida
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Future University in Egypt Cairo 11835 Egypt
- Pharmaceutical Sciences Department, School of Pharmacy, Texas Tech University Health Science Center Amarillo Texas USA
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Walaa R Mahmoud
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Nasser S M Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt Cairo 11835 Egypt
| | - Mahmoud S Ahmed
- Pharmaceutical Sciences Department, School of Pharmacy, Texas Tech University Health Science Center Amarillo Texas USA
| | - Hanan H Georgey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University 11786 Cairo Egypt
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2
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Bose K, Shajahan A, Sreekumar N, Aneesh TP. Heterocyclic Compounds as CDK9 Inhibitors: Structural Diversity, Mechanism of Action, and Therapeutic Potential in Cancer and Beyond. Chem Biodivers 2024:e202401797. [PMID: 39267257 DOI: 10.1002/cbdv.202401797] [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: 07/28/2024] [Revised: 09/12/2024] [Accepted: 09/12/2024] [Indexed: 09/17/2024]
Abstract
Cyclin-dependent kinases (CDKs) are crucial proteins involved in key cellular processes, such as cell division and transcription. Their dysregulation plays a significant role in cancer development. Inhibiting cyclin-dependent kinase 9 (CDK9) impacts several survival pathways in cancer cells, presenting a promising therapeutic approach for various cancers. CDK9, in association with cyclin T1, forms the positive transcription elongation factor b (P-TEFb) complex, which phosphorylates the C-terminal domain (CTD) of RNA polymerase II (Pol II). This phosphorylation promotes the transition from transcription initiation to elongation. This review examines recent advancements in CDK9 modulators, with a particular emphasis on compounds currently in clinical trials.
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Affiliation(s)
- Kuntal Bose
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, 682041, India
| | - Afiya Shajahan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, 682041, India
| | - Nandana Sreekumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, 682041, India
| | - T P Aneesh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, Kerala, 682041, India
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3
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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4
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Hakami AA, Alorfi HS, Farghaly TA, Hussein MA. A new polyazomethine-based pyrazole moiety and its reinforced nanocomposites @ ZnO for antimicrobial applications. Des Monomers Polym 2024; 27:1-20. [PMID: 38756722 PMCID: PMC11097710 DOI: 10.1080/15685551.2024.2352897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/04/2024] [Indexed: 05/18/2024] Open
Abstract
A new class of biologically active polyazomethine/pyrazole and their related nanocomposites, polyazomethine/pyrazole/zinc oxide nanoparticles, have been successfully synthesized through the polycondensation technique in the form of polyazomethine pyrazole (PAZm/Py4-6) and polyazomethine/pyrazole/zinc oxide nanoparticles (PAZm/Py/ZnOa-c). The polymeric nanocomposites were prepared with a 5% loading of zinc oxide nanofiller using the same preparation technique, in addition to the help of ultrasonic radiation. The characteristics of the new polymers, such as solubility, viscometry, and molecular weight, were examined. All the polymers were completely soluble in the following solvents: concentrated sulfuric acid, formic acid, dimethylformamide, dimethyl sulfoxide, and tetrahydrofuran. Furthermore, the weight loss of the polyazomethine pyrazole (4, 5, and 6) at 800 °C was 67%, 95%, and 86%, respectively, which indicates the thermal stability of these polymers. At 800 °C, the polyazomethine/pyrazole/zinc oxide nanoparticles (a, b, and c) lost 74%, 68%, and 75% of their weight, respectively. This shows that adding zinc oxide nanoparticles made these compounds more stable at high temperatures. The X-Ray diffraction pattern of the polyazomethine pyrazole (PAZm/Py4-6) shows a number of sharp peaks with varying intensities. The polymers that were studied had straight crystal structures. Furthermore, the measurements of polyazomethine/pyrazole/zinc oxide nanoparticles (PAZm/Py/ZnOa-c) indicate a good merging of zinc oxide nanoparticles into the matrix of polymers. The antimicrobial activity of polymers and polymer nanocomposites was tested against some selected bacteria and fungi. The synthesized polymer (c) shows the highest activity against the two types of gram-negative bacteria selected. Most tested compounds were found to be effective against gram-positive bacteria except polyazomethine pyrazole (PAZm/Py5) and polyazomethine pyrazole (PAZm/Py6), which do not exhibit any activity. The synthesized polymers and their related nanocomposites were tested for their ability to kill the chosen fungi. All of them were effective against Aspergillus flavus, but only polyazomethine pyrazole (PAZm/Py4) and polyazomethine/pyrazole/zinc oxide (PAZm/Py/ZnOc) were effective against Candida albicans.
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Affiliation(s)
- Aqilah A. Hakami
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hajar S. Alorfi
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thoraya A. Farghaly
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
| | - Mahmoud A. Hussein
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
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Odeh DM, Allam HA, Baselious F, Mahmoud WR, Odeh MM, Ibrahim HS, Abdel-Aziz HA, Mohammed ER. Design, synthesis, and biological evaluation of dinaciclib and CAN508 hybrids as CDK inhibitors. Drug Dev Res 2024; 85:e22193. [PMID: 38685605 DOI: 10.1002/ddr.22193] [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: 02/23/2024] [Revised: 03/26/2024] [Accepted: 04/14/2024] [Indexed: 05/02/2024]
Abstract
The scaffolds of two known CDK inhibitors (CAN508 and dinaciclib) were the starting point for synthesizing two series of pyarazolo[1,5-a]pyrimidines to obtain potent inhibitors with proper selectivity. The study presented four promising compounds; 10d, 10e, 16a, and 16c based on cytotoxic studies. Compound 16a revealed superior activity in the preliminary anticancer screening with GI % = 79.02-99.13 against 15 cancer cell lines at 10 μM from NCI full panel 60 cancer cell lines and was then selected for further investigation. Furthermore, the four compounds revealed good safety profile toward the normal cell lines WI-38. These four compounds were subjected to CDK inhibitory activity against four different isoforms. All of them showed potent inhibition against CDK5/P25 and CDK9/CYCLINT. Compound 10d revealed the best activity against CDK5/P25 (IC50 = 0.063 µM) with proper selectivity index against CDK1 and CDK2. Compound 16c exhibited the highest inhibitory activity against CDK9/CYCLINT (IC50 = 0.074 µM) with good selectivity index against other isoforms. Finally, docking simulations were performed for compounds 10e and 16c accompanied by molecular dynamic simulations to understand their behavior in the active site of the two CDKs with respect to both CAN508 and dinaciclib.
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Affiliation(s)
- Dana M Odeh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Fady Baselious
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Walaa R Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mohanad M Odeh
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Hany S Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo, Egypt
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Cairo, Dokki, Egypt
| | - Eman R Mohammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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6
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Lusardi M, Spallarossa A, Brullo C. Amino-Pyrazoles in Medicinal Chemistry: A Review. Int J Mol Sci 2023; 24:ijms24097834. [PMID: 37175540 PMCID: PMC10177828 DOI: 10.3390/ijms24097834] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
A pyrazole nucleus is an easy-to-prepare scaffold with large therapeutic potential. Consequently, the search for new pyrazole-based compounds is of great interest to the academic community as well as industry. In the last ten years, a large number of papers and reviews on the design, synthesis, and biological evaluation of different classes of pyrazoles and many pyrazole-containing compounds have been published. However, an overview of pyrazole derivatives bearing a free amino group at the 3, 4, or 5 position (namely, 3-aminopyrazoles, 4-aminopyrazoles, and 5-aminopyrazoles, respectively) and their biological properties is still missing, despite the fact that aminopyrazoles are advantageous frameworks able to provide useful ligands for receptors or enzymes, such as p38MAPK, and different kinases, COX and others, as well as targets important for bacterial and virus infections. With the aim to fill this gap, the present review focuses on aminopyrazole-based compounds studied as active agents in different therapeutic areas, with particular attention on the design and structure-activity relationships defined by each class of compounds. In particular, the most relevant results have been obtained for anticancer/anti-inflammatory compounds, as the recent approval of Pirtobrutinib demonstrates. The data reported here are collected from different databases (Scifinder, Web of Science, Scopus, Google Scholar, and Pubmed) using "aminopyrazole" as the keyword.
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Affiliation(s)
- Matteo Lusardi
- Department of Pharmacy (DIFAR), Section of Medicinal Chemistry, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Andrea Spallarossa
- Department of Pharmacy (DIFAR), Section of Medicinal Chemistry, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Chiara Brullo
- Department of Pharmacy (DIFAR), Section of Medicinal Chemistry, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
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7
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Recent Advancement in Drug Design and Discovery of Pyrazole Biomolecules as Cancer and Inflammation Therapeutics. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248708. [PMID: 36557840 PMCID: PMC9780894 DOI: 10.3390/molecules27248708] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/27/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022]
Abstract
Pyrazole, an important pharmacophore and a privileged scaffold of immense significance, is a five-membered heterocyclic moiety with an extensive therapeutic profile, viz., anti-inflammatory, anti-microbial, anti-anxiety, anticancer, analgesic, antipyretic, etc. Due to the expansion of pyrazolecent red pharmacological molecules at a quicker pace, there is an urgent need to put emphasis on recent literature with hitherto available information to recognize the status of this scaffold for pharmaceutical research. The reported potential pyrazole-containing compounds are highlighted in the manuscript for the treatment of cancer and inflammation, and the results are mentioned in % inhibition of inflammation, % growth inhibition, IC50, etc. Pyrazole is an important heterocyclic moiety with a strong pharmacological profile, which may act as an important pharmacophore for the drug discovery process. In the struggle to cultivate suitable anti-inflammatory and anticancer agents, chemists have now focused on pyrazole biomolecules. This review conceals the recent expansion of pyrazole biomolecules as anti-inflammatory and anticancer agents with an aim to provide better correlation among different research going around the world.
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Dileep C, Chandini K, Sridhar M, Ajay Kumar K. Structure property relationship of two pyrazole derivatives: Insights from crystal structure and computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Aggarwal R, Kumar S, Virender, Kumar A, Mohan B, Sharma D, Kumar V. Development of heterocyclic 2,7-diamino-3-phenylazo-6-phenylpyrazolo[1,5-a]pyrimidine as antimicrobial agent and selective probe for UV–visible and colorimetric detection of Hg2+ ions. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Targeting cyclin-dependent kinase 9 in cancer therapy. Acta Pharmacol Sin 2022; 43:1633-1645. [PMID: 34811514 PMCID: PMC9253122 DOI: 10.1038/s41401-021-00796-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinase (CDK) 9 associates mainly with cyclin T1 and forms the positive transcription elongation factor b (p-TEFb) complex responsible for transcriptional regulation. It has been shown that CDK9 modulates the expression and activity of oncogenes, such as MYC and murine double minute 4 (MDM4), and it also plays an important role in development and/or maintenance of the malignant cell phenotype. Malfunction of CDK9 is frequently observed in numerous cancers. Recent studies have highlighted the function of CDK9 through a variety of mechanisms in cancers, including the formation of new complexes and epigenetic alterations. Due to the importance of CDK9 activation in cancer cells, CDK9 inhibitors have emerged as promising candidates for cancer therapy. Natural product-derived and chemically synthesized CDK9 inhibitors are being examined in preclinical and clinical research. In this review, we summarize the current knowledge on the role of CDK9 in transcriptional regulation, epigenetic regulation, and different cellular factor interactions, focusing on new advances. We show the importance of CDK9 in mediating tumorigenesis and tumor progression. Then, we provide an overview of some CDK9 inhibitors supported by multiple oncologic preclinical and clinical investigations. Finally, we discuss the perspective and challenge of CDK9 modulation in cancer.
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Natural Protein Kinase Inhibitors, Staurosporine, and Chelerythrine Suppress Wheat Blast Disease Caused by Magnaporthe oryzae Triticum. Microorganisms 2022; 10:microorganisms10061186. [PMID: 35744705 PMCID: PMC9230996 DOI: 10.3390/microorganisms10061186] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 01/01/2023] Open
Abstract
Protein kinases (PKs), being key regulatory enzymes of a wide range of signaling pathways, are potential targets for antifungal agents. Wheat blast disease, caused by Magnaporthe oryzae Triticum (MoT), is an existential threat to world food security. During the screening process of natural metabolites against MoT fungus, we find that two protein kinase inhibitors, staurosporine and chelerythrine chloride, remarkably inhibit MoT hyphal growth. This study further investigates the effects of staurosporine and chelerythrine chloride on MoT hyphal growth, conidia production, and development as well as wheat blast inhibition in comparison to a commercial fungicide, Nativo®75WG. The growth of MoT mycelia is significantly inhibited by these compounds in a dose-dependent manner. These natural compounds greatly reduce conidia production in MoT mycelia along with suppression of conidial germination and triggered lysis, resulting in deformed germ tubes and appressoria. These metabolites greatly suppress blast development in artificially inoculated wheat plants in the field. This is the first report of the antagonistic effect of these two natural PKC inhibitory alkaloids on MoT fungal developmental processes in vitro and suppression of wheat blast disease on both leaves and spikes in vivo. Further research is needed to identify their precise mechanism of action to consider them as biopesticides or lead compounds for controlling wheat blast.
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Ratnani S, Bargujar S, Khulbe M, Kathuria A. Applications of Choline Chlorine based Deep Eutectic Solvents as Sustainable Media and catalyst in the synthesis of Heterocyclic Scaffolds. CURR ORG CHEM 2022. [DOI: 10.2174/1385272826666220602105646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Deep eutectic solvents (DESs), also referred to as low transition temperature mixtures (LTTMs), have emerged as sustainable and cheap alternatives to conventional organic solvents in organic synthesis. This is attributed to their exceptional characteristics viz. easy preparation with readily available cheap materials, water compatibility, non-flammability, non-toxicity, biocompatibility, biodegradability, etc. All these properties label them as versatile and cost-effective green solvents. The first reported DES, choline chloride urea mixture has appeared as an innocuous solvent and catalyst in many organic transformations. This prospective DES combination has been applied extensively to the synthesis of a wide range of heterocyclic compounds including quinolones, spirooxindoles, etc. The conditions employed are relatively mild and do not require additional acid catalysts or organic solvents. This eco-friendly blend for the synthesis of heterocycles reports excellent yields of products with shorter reaction times and a simple workup procedure. Evaluating these merits, this review focuses on the recent literature published on the use of choline chlorine-based DESs in the synthesis of a few important heterocyclic compounds.
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Affiliation(s)
- Sonia Ratnani
- Department of Chemistry, Ramjas College, University of Delhi, Delhi - 110007, India
| | - Savita Bargujar
- Department of Chemistry, Ramjas College, University of Delhi, Delhi - 110007, India
| | - Mihir Khulbe
- Department of Chemistry, Ramjas College, University of Delhi, Delhi - 110007, India
| | - Abha Kathuria
- Department of Chemistry, Ramjas College, University of Delhi, Delhi - 110007, India
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Ismail MMF, Khalifa MM, El-Sehrawi HMA, Sabour R. Design, Synthesis and Antimicrobial Evaluation of New Arylazopyrazole and Arylazopyrazolo[1,5- a]pyrimidine Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2020.1830811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Magda M. F. Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Maha M. Khalifa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Hend M. A. El-Sehrawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Rehab Sabour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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14
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Essa BM, Selim AA, Sayed GH, Anwer KE. Conventional and microwave-assisted synthesis, anticancer evaluation, 99mTc-coupling and In-vivo study of some novel pyrazolone derivatives. Bioorg Chem 2022; 125:105846. [PMID: 35512493 DOI: 10.1016/j.bioorg.2022.105846] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/31/2022] [Accepted: 04/25/2022] [Indexed: 12/25/2022]
Abstract
New pyrazolone derivatives were successfully synthesized by both microwave-assisted and conventional techniques. Compound 3 (3-(3-Methyl-5-oxo-4,5-dihydro-1H-pyrazol-1-yl)-3-oxopropanehydrazide) displayed remarkable anti-cancer activity (IC50 obtained at 8.71 and 10.63 µM for HCT-116 and MCF-7, respectively. Moreover, biodistribution study using radiolabeling approach revealed a remarked uptake of [99mTc]Tc-compound 3 complex into tumour induced in mice. The biodistribution showed high accumulation in tumour tissues with T/NT of 6.92 after 60 min post injection. As a result of these promising data, the newly synthesized compounds especially compound 3 affords a potential radio-carrier that could be used as a tumour marker and can be used for cancer therapy after further preclinical studies.
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Affiliation(s)
- Basma M Essa
- Radioactive Isotopes and Generators Department, Egyptian Atomic Energy Authority, 13759 Cairo, Egypt
| | - Adli A Selim
- Labelled Compounds Department, Egyptian Atomic Energy Authority, 13759 Cairo, Egypt.
| | - Galal H Sayed
- Heterocyclic Synthesis Lab., Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, 11566 Cairo, Egypt
| | - Kurls E Anwer
- Heterocyclic Synthesis Lab., Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, 11566 Cairo, Egypt
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15
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Novel orthodiphenyl five-member N-heteroaromatic compounds as potent anticancer cell agents. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02894-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Oskouie AA, Ahmadi MS, Taherkhani A. Identification of Prognostic Biomarkers in Papillary Thyroid Cancer and Developing Non-Invasive Diagnostic Models Through Integrated Bioinformatics Analysis. Microrna 2022; 11:73-87. [PMID: 35068400 DOI: 10.2174/2211536611666220124115445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most frequent subtype of thyroid carcinoma, mainly detected in patients with benign thyroid nodules (BTN). Due to the invasiveness of accurate diagnostic tests, there is a need to discover applicable biomarkers for PTC. So, in this study, we aimed to identify the genes associated with prognosis in PTC. Besides, we performed a machine learning tool to develop a non-invasive diagnostic approach for PTC. METHODS For the study purposes, the miRNA dataset GSE130512 was downloaded from the GEO database and then analyzed to identify the common differentially expressed miRNAs in patients with non-metastatic PTC (nm-PTC)/metastatic PTC (m-PTC) compared with BTNs. The SVM was also applied to differentiate patients with PTC from those patients with BTN using the common DEMs. A protein-protein interaction network was also constructed based on the targets of the common DEMs. Next, functional analysis was performed, the hub genes were determined, and survival analysis was then executed. RESULTS A total of three common miRNAs were found to be differentially expressed among patients with nm-PTC/m-PTC compared with BTNs. In addition, it was established that the autophagosome maturation, ciliary basal body-plasma membrane docking, antigen processing as ubiquitination & proteasome degradation, and class I MHC mediated antigen processing & presentation are associated with the pathogenesis of PTC. Furthermore, it was illustrated that RPS6KB1, CCNT1, SP1, and CHD4 might serve as new potential biomarkers for PTC prognosis. CONCLUSION RPS6KB1, CCNT1, SP1, and CHD4 may be considered new potential biomarkers used for prognostic aims in PTC. However, performing validation tests is inevitable in the future.
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Affiliation(s)
- Afsaneh Arefi Oskouie
- Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeed Ahmadi
- Department of Otorhinolaryngology, Besat Hospital, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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17
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Jansen CU, Uhd J, Andersen JB, Hultqvist LD, Jakobsen TH, Nilsson M, Nielsen TE, Givskov M, Tolker-Nielsen T, Qvortrup KM. SAR study of 4-arylazo-3,5-diamino-1 H-pyrazoles: identification of small molecules that induce dispersal of Pseudomonas aeruginosa biofilms. RSC Med Chem 2021; 12:1868-1878. [PMID: 34841247 DOI: 10.1039/d1md00275a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
By screening of a collection of 50 000 small-molecule compounds, we recently identified 4-arylazo-3,5-diamino-1H-pyrazoles as a novel group of anti-biofilm agents. Here, we report a SAR study based on 60 analogues by examining ways in which the pharmacophore can be further optimized, for example, via substitutions in the aryl ring. The SAR study revealed the very potent anti-biofilm compound 4-(2-(2-fluorophenyl)hydrazineylidene)-5-imino-4,5-dihydro-1H-pyrazol-3-amine (2).
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Affiliation(s)
- Charlotte U Jansen
- Department of Chemistry, Technical University of Denmark DK-2800 Lyngby Denmark
| | - Jesper Uhd
- Department of Chemistry, Technical University of Denmark DK-2800 Lyngby Denmark
| | - Jens B Andersen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark
| | - Louise D Hultqvist
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark
| | - Tim H Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark
| | - Martin Nilsson
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark
| | - Thomas E Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University Singapore
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen DK-2200 Copenhagen Denmark
| | - Katrine M Qvortrup
- Department of Chemistry, Technical University of Denmark DK-2800 Lyngby Denmark
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18
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Alzahrani AY, Ammar YA, Salem MA, Abu-Elghait M, Ragab A. Design, synthesis, molecular modeling, and antimicrobial potential of novel 3-[(1H-pyrazol-3-yl)imino]indolin-2-one derivatives as DNA gyrase inhibitors. Arch Pharm (Weinheim) 2021; 355:e2100266. [PMID: 34747519 DOI: 10.1002/ardp.202100266] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022]
Abstract
A series of 3-[(1H-pyrazol-3-yl)imino]indolin-2-one derivatives were designed using the molecular hybridization method, characterized using different spectroscopic techniques, and evaluated for their in vitro antimicrobial activity. Most of the target compounds demonstrated good to moderate antimicrobial activity compared with ciprofloxacin and fluconazole. Four compounds (8b, 9a, 9c, and 10a) showed encouraging results, with minimal inhibitory concentration (MIC) values (53.45-258.32 µM) comparable to those of norfloxacin (100.31-200.63 µM) and ciprofloxacin (48.33-96.68 µM). Noticeably, the four derivatives revealed excellent bactericidal and fungicidal activities, except for the bacteriostatic potential of compounds 8b and 9a against Escherichia coli and Staphylococcus aureus, respectively. The time-killing kinetic study against S. aureus confirmed the efficacy of these derivatives. Furthermore, two of the four promising derivatives, 9a and 10a, could prevent the formation of biofilms of S. aureus without affecting the bacterial growth at low concentrations. A combination study with seven commercial antibiotics against the multidrug-resistant bacterium P. aeruginosa showed a notable reduction in the antibiotic MIC values, represented mainly through a synergistic or additive effect. The enzymatic assay implied that the most active derivatives had inhibition potency against DNA gyrase comparable to that of ciprofloxacin. Molecular docking and density functional theory calculations were performed to explore the binding mode and study the reactivity of the promising compounds.
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Affiliation(s)
- Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail, Assir, Saudi Arabia
| | - Yousry A Ammar
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed A Salem
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail, Assir, Saudi Arabia.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohammed Abu-Elghait
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ahmed Ragab
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
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19
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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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20
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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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21
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Toman D, Jorda R, Ajani H, Kryštof V, Cankař P. Synthesis of 4-styrylpyrazoles and evaluation of their inhibitory effects on cyclin-dependent kinases. Med Chem 2021; 18:484-496. [PMID: 34365958 DOI: 10.2174/1573406417666210806095710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/02/2021] [Accepted: 04/05/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cycle-regulating and transcriptional cyclin-dependent kinases (CDKs) are attractive targets in cancer drug development. Several CDK inhibitors have already been obtained or are close to regulatory approval for clinical applications. OBJECTIVE Phenylazopyrazole CAN508 has been described as the first selective CDK9 inhibitor with an IC50 of 350 nM. Since the azo-moiety is not a suitable functionality for drugs due to pharmacological reasons, the preparation of carbo-analogues of CAN508 with similar biological activities is desirable. The present work is focused on the synthesis of carbo-analogues similar to CAN508 and their CDK inhibition activity. METHODS Herein, the synthesis of 21 novel carbo analogues of CAN508 and their intermediates is reported. Subsequently, target compounds 8a - 8u were evaluated for protein kinase inhibition (CDK2/cyclin E, CDK4/cyclin D, CDK9/cyclin T) and antiproliferative activities in cell lines (K562, MCF-7, MV4-11). Moreover, the binding mode of derivative 8s in the active site of CDK9 was revealed by molecular docking. RESULTS Compounds 8a - 8u were obtained from key intermediate 7, which was prepared by linear synthesis involving Vilsmeier-Haack, Knoevenagel, Hunsdiecker, and Suzuki-Miyaura reactions. Styrylpyrazoles 8t and 8u were the most potent CDK9 inhibitors with IC50 values of approximately 1 µM. Molecular modelling suggested binding in the active site of CDK9 and CDK2. The flow cytometric analysis of MV4-11 cells treated with the most active styrylpyrazoles showed a significant G1-arrest. CONCLUSION The prepared styrylpyrazoles showed inhibition activity towards CDKs and can provide a novel chemotype of kinase inhibitors.
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Affiliation(s)
- Daniel Toman
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46 Olomouc. Czech Republic
| | - Radek Jorda
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc. Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Vladimír Kryštof
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc. Czech Republic
| | - Petr Cankař
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46 Olomouc. Czech Republic
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22
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Andersen JB, Hultqvist LD, Jansen CU, Jakobsen TH, Nilsson M, Rybtke M, Uhd J, Fritz BG, Seifert R, Berthelsen J, Nielsen TE, Qvortrup K, Givskov M, Tolker-Nielsen T. Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms. NPJ Biofilms Microbiomes 2021; 7:59. [PMID: 34244523 PMCID: PMC8271024 DOI: 10.1038/s41522-021-00225-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial biofilms are involved in a number of infections that cannot be cured, as microbes in biofilms resist host immune defenses and antibiotic therapies. With no strict biofilm-antibiotic in the current pipelines, there is an unmet need for drug candidates that enable the current antibiotics to eradicate bacteria in biofilms. We used high-throughput screening to identify chemical compounds that reduce the intracellular c-di-GMP content in Pseudomonas aeruginosa. This led to the identification of a small molecule that efficiently depletes P. aeruginosa for c-di-GMP, inhibits biofilm formation, and disperses established biofilm. A combination of our lead compound with standard of care antibiotics showed improved eradication of an implant-associated infection established in mice. Genetic analyses provided evidence that the anti-biofilm compound stimulates the activity of the c-di-GMP phosphodiesterase BifA in P. aeruginosa. Our work constitutes a proof of concept for c-di-GMP phosphodiesterase-activating drugs administered in combination with antibiotics as a viable treatment strategy for otherwise recalcitrant infections.
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Affiliation(s)
- Jens Bo Andersen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louise Dahl Hultqvist
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Holm Jakobsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Nilsson
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Uhd
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Blaine Gabriel Fritz
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roland Seifert
- Institute of Pharmacology and Research Core Unit Metabolomics, Hannover Medical School Carl-Neuberg-Straße 1, Hannover, Germany
| | - Jens Berthelsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Eiland Nielsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Michael Givskov
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Shawky AM, Ibrahim NA, Abdalla AN, Abourehab MAS, Gouda AM. Novel pyrrolizines bearing 3,4,5-trimethoxyphenyl moiety: design, synthesis, molecular docking, and biological evaluation as potential multi-target cytotoxic agents. J Enzyme Inhib Med Chem 2021; 36:1313-1333. [PMID: 34154478 PMCID: PMC8221158 DOI: 10.1080/14756366.2021.1937618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
In the present study, two new series of pyrrolizines bearing 3,4,5-trimethoxyphenyl moiety were designed, synthesised, and evaluated for their cytotoxic activity. The benzamide derivatives 16a-e showed higher cytotoxicity than their corresponding Schiff bases 15a-e. Compounds 16a,b,d also inhibited the growth of MCF-7/ADR cells with IC50 in the range of 0.52-6.26 μM. Interestingly, the new compounds were less cytotoxic against normal MRC-5 cells (IC50=0.155-17.08 μM). Mechanistic studies revealed the ability of compounds 16a,b,d to inhibit tubulin polymerisation and multiple oncogenic kinases. Moreover, compounds 16a,b,d induced preG1 and G2/M cell cycle arrest and early apoptosis in MCF-7 cells. The molecular docking analyses of compounds 16a,b,d into the active site in tubulin, CDK-2, and EGFR proteins revealed higher binding affinities compared to the co-crystallised ligands. These preliminary results suggested that compounds 16a,b,d could serve as promising lead compounds for the future development of new potent anticancer agents.HighlightsTwo new series of pyrrolizines bearing 3,4,5-trimethoxyphenyl moieties were synthesized.Compounds 16a,b,d displayed the highest cytotoxicity against the three cancer cell lines.Kinase profiling test revealed inhibition of multiple oncogenic kinases by compounds 16a,b,d.Compounds 16a,b,d exhibited weak to moderate inhibition of tubulin-polymerization.Compounds 16a,b,d induced preG1 and G2/M cell cycle arrest and early apoptosis in MCF-7 cells.Docking studies revealed high binding affinities for compounds 16a,b towards tubulin and CDK-2.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia.,Central Laboratory for Micro-analysis, Minia University, Minia, Egypt
| | - Nashwa A Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmacology and Toxicology, Medicinal and Aromatic Plants Research Institute, National Center for Research, Khartoum, Sudan
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Ahmed M Gouda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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24
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Bitencourt-Ferreira G, Rizzotto C, de Azevedo Junior WF. Machine Learning-Based Scoring Functions, Development and Applications with SAnDReS. Curr Med Chem 2021; 28:1746-1756. [PMID: 32410551 DOI: 10.2174/0929867327666200515101820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Analysis of atomic coordinates of protein-ligand complexes can provide three-dimensional data to generate computational models to evaluate binding affinity and thermodynamic state functions. Application of machine learning techniques can create models to assess protein-ligand potential energy and binding affinity. These methods show superior predictive performance when compared with classical scoring functions available in docking programs. OBJECTIVE Our purpose here is to review the development and application of the program SAnDReS. We describe the creation of machine learning models to assess the binding affinity of protein-ligand complexes. METHODS SAnDReS implements machine learning methods available in the scikit-learn library. This program is available for download at https://github.com/azevedolab/sandres. SAnDReS uses crystallographic structures, binding and thermodynamic data to create targeted scoring functions. RESULTS Recent applications of the program SAnDReS to drug targets such as Coagulation factor Xa, cyclin-dependent kinases and HIV-1 protease were able to create targeted scoring functions to predict inhibition of these proteins. These targeted models outperform classical scoring functions. CONCLUSION Here, we reviewed the development of machine learning scoring functions to predict binding affinity through the application of the program SAnDReS. Our studies show the superior predictive performance of the SAnDReS-developed models when compared with classical scoring functions available in the programs such as AutoDock4, Molegro Virtual Docker and AutoDock Vina.
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Affiliation(s)
| | - Camila Rizzotto
- Pontifical Catholic University of Rio Grande do Sul - PUCRS, Porto Alegre-RS, Brazil
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25
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Goel B, Tripathi N, Bhardwaj N, Jain SK. Small Molecule CDK Inhibitors for the Therapeutic Management of Cancer. Curr Top Med Chem 2021; 20:1535-1563. [PMID: 32416692 DOI: 10.2174/1568026620666200516152756] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 01/03/2023]
Abstract
Cyclin-dependent kinases (CDKs) are a group of multifunctional enzymes consisting of catalytic and regulatory subunits. The regulatory subunit, cyclin, remains dissociated under normal circumstances, and complexation of cyclin with the catalytic subunit of CDK leads to its activation for phosphorylation of protein substrates. The primary role of CDKs is in the regulation of the cell cycle. Retinoblastoma protein (Rb) is one of the widely investigated tumor suppressor protein substrates of CDK, which prevents cells from entering into cell-cycle under normal conditions. Phosphorylation of Rb by CDKs causes its inactivation and ultimately allows cells to enter a new cell cycle. Many cancers are associated with hyperactivation of CDKs as a result of mutation of the CDK genes or CDK inhibitor genes. Therefore, CDK modulators are of great interest to explore as novel therapeutic agents against cancer and led to the discovery of several CDK inhibitors to clinics. This review focuses on the current progress and development of anti-cancer CDK inhibitors from preclinical to clinical and synthetic to natural small molecules.
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Affiliation(s)
- Bharat Goel
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
| | - Nancy Tripathi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
| | - Nivedita Bhardwaj
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
| | - Shreyans K Jain
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi-221005, India
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26
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Bobrova AV, Krasnov PO, Povarov IG, Bobrov PS, Lyubyashkin AV, Suboch GA, Tovbis MS. Facile synthesis and sulfonylation of 4-aminopyrazoles. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Bitencourt-Ferreira G, Duarte da Silva A, Filgueira de Azevedo W. Application of Machine Learning Techniques to Predict Binding Affinity for Drug Targets: A Study of Cyclin-Dependent Kinase 2. Curr Med Chem 2021; 28:253-265. [PMID: 31729287 DOI: 10.2174/2213275912666191102162959] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/22/2019] [Accepted: 09/24/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The elucidation of the structure of cyclin-dependent kinase 2 (CDK2) made it possible to develop targeted scoring functions for virtual screening aimed to identify new inhibitors for this enzyme. CDK2 is a protein target for the development of drugs intended to modulate cellcycle progression and control. Such drugs have potential anticancer activities. OBJECTIVE Our goal here is to review recent applications of machine learning methods to predict ligand- binding affinity for protein targets. To assess the predictive performance of classical scoring functions and targeted scoring functions, we focused our analysis on CDK2 structures. METHODS We have experimental structural data for hundreds of binary complexes of CDK2 with different ligands, many of them with inhibition constant information. We investigate here computational methods to calculate the binding affinity of CDK2 through classical scoring functions and machine- learning models. RESULTS Analysis of the predictive performance of classical scoring functions available in docking programs such as Molegro Virtual Docker, AutoDock4, and Autodock Vina indicated that these methods failed to predict binding affinity with significant correlation with experimental data. Targeted scoring functions developed through supervised machine learning techniques showed a significant correlation with experimental data. CONCLUSION Here, we described the application of supervised machine learning techniques to generate a scoring function to predict binding affinity. Machine learning models showed superior predictive performance when compared with classical scoring functions. Analysis of the computational models obtained through machine learning could capture essential structural features responsible for binding affinity against CDK2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Laboratory of Computational Systems Biology. Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900 , Brazil
| | - Amauri Duarte da Silva
- Specialization Program in Bioinformatics. Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- Laboratory of Computational Systems Biology. Pontifical Catholic University of Rio Grande do Sul (PUCRS). Av. Ipiranga, 6681 Porto Alegre/RS 90619-900 , Brazil
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Upadhyay N, Tilekar K, Loiodice F, Anisimova NY, Spirina TS, Sokolova DV, Smirnova GB, Choe JY, Meyer-Almes FJ, Pokrovsky VS, Lavecchia A, Ramaa CS. Pharmacophore hybridization approach to discover novel pyrazoline-based hydantoin analogs with anti-tumor efficacy. Bioorg Chem 2021; 107:104527. [PMID: 33317839 DOI: 10.1016/j.bioorg.2020.104527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/20/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
In search for new and safer anti-cancer agents, a structurally guided pharmacophore hybridization strategy of two privileged scaffolds, namely diaryl pyrazolines and imidazolidine-2,4-dione (hydantoin), was adopted resulting in a newfangled series of compounds (H1-H22). Herein, a bio-isosteric replacement of "pyrrolidine-2,5-dione" moiety of our recently reported antitumor hybrid incorporating diaryl pyrazoline and pyrrolidine-2,5-dione scaffolds with "imidazoline-2,4-dione" moiety has been incorporated. Complete biological studies revealed the most potent analog among all i.e. compound H13, which was at-least 10-fold more potent compared to the corresponding pyrrolidine-2,5-dione, in colon and breast cancer cells. In-vitro studies showed activation of caspases, arrest of G0/G1 phase of cell cycle, decrease in the expression of anti-apoptotic protein (Bcl-2) and increased DNA damage. In-vivo assay on HT-29 (human colorectal adenocarcinoma) animal xenograft model unveiled the significant anti-tumor efficacy along with oral bioavailability with maximum TGI 36% (i.p.) and 44% (per os) at 50 mg/kg dose. These findings confirm the suitability of hybridized pyrazoline and imidazolidine-2,4-dione analog H13 for its anti-cancer potential and starting-point for the development of more efficacious analogs.
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Affiliation(s)
- Neha Upadhyay
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth's College of Pharmacy, Navi Mumbai, India
| | - Kalpana Tilekar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth's College of Pharmacy, Navi Mumbai, India
| | - Fulvio Loiodice
- Department of Pharmacy-Drug Science, University of Bari "Aldo Moro", Via E. Orabona, 4, 70126 Bari, Italy
| | - Natalia Yu Anisimova
- Laboratory of Combined Therapy, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | - Tatiana S Spirina
- Laboratory of Combined Therapy, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | - Darina V Sokolova
- Laboratory of Combined Therapy, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | - Galina B Smirnova
- Laboratory of Combined Therapy, N.N. Blokhin Cancer Research Center, Moscow, Russia
| | - Jun-Yong Choe
- East Carolina Diabetes and Obesity Institute, Department of Chemistry, East Carolina University, Greenville, NC, USA
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Science, Darmstadt, Germany
| | - Vadim S Pokrovsky
- Laboratory of Combined Therapy, N.N. Blokhin Cancer Research Center, Moscow, Russia; Department of Biochemistry, People's Friendship University, Moscow, Russia.
| | - Antonio Lavecchia
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Napoli "Federico II", Via D. Montesano, 49, 80131 Napoli, Italy.
| | - C S Ramaa
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth's College of Pharmacy, Navi Mumbai, India.
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Ismail MMF, Soliman DH, Sabour R, Farrag AM. Synthesis of new arylazopyrazoles as apoptosis inducers: Candidates to inhibit proliferation of MCF-7 cells. Arch Pharm (Weinheim) 2020; 354:e2000214. [PMID: 32924168 DOI: 10.1002/ardp.202000214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/15/2020] [Accepted: 08/20/2020] [Indexed: 11/08/2022]
Abstract
New 4-arylazo-3,5-diamino-1H-pyrazole derivatives substituted in the 4-aryl ring with the acetyl moiety were designed and synthesized. The antiproliferative activity of the novel arylazopyrazoles was examined against the MCF-7 cell line. Among all target compounds, 8b (IC50 3.0 µM) and 8f (IC50 4.0 µM) displayed higher cytotoxicity as compared with the reference standard imatinib (IC50 7.0 µM). Further studies to explore the mechanism of action were performed on the most active hit of our library, 8b, via anti-CDK2 kinase activity. It demonstrated good inhibitory effects for CDK2 (IC50 0.24 µM) with 62.5% inhibition, compared with imatinib. The cell cycle analysis in the MCF-7 cell line revealed apoptosis induction by 8b and cell cycle arrest at the S phase. Docking in the CDK2 active site and pharmacophore modeling confirmed the affinity of 8b to the CDK2 active site. Absorption, distribution, metabolism, and excretion studies revealed that our target compounds are orally bioavailable, with no permeation through the blood-brain barrier.
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Affiliation(s)
- Magda M F Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Dalia H Soliman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Rehab Sabour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Amel M Farrag
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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30
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Ismail MMF, Abdulwahab HG, Elnagdi MH. Design, synthesis, and in vitroanticancer screening of novel pyrazolinyl‐pyrazole/1, 2, 3‐triazole hybrids. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Magda M. F. Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy (Girls) Al‐Azhar University Cairo Egypt
| | - Hanan G. Abdulwahab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy (Girls) Al‐Azhar University Cairo Egypt
| | - Mohamed H. Elnagdi
- Department of Chemistry, Faculty of Science University of Kuwait Safat Kuwait
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31
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Synthesis, characterization, in vitro DNA photocleavage and cytotoxicity studies of 4-arylazo-1-phenyl-3-(2-thienyl)-5-hydroxy-5-trifluoromethylpyrazolines and regioisomeric 4-arylazo-1-phenyl-5(3)-(2-thienyl)-3(5)-trifluoromethylpyrazoles. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2020.109573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Bitencourt-Ferreira G, de Azevedo WF. Molecular Dynamics Simulations with NAMD2. Methods Mol Biol 2020; 2053:109-124. [PMID: 31452102 DOI: 10.1007/978-1-4939-9752-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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33
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Abstract
AutoDock is one of the most popular receptor-ligand docking simulation programs. It was first released in the early 1990s and is in continuous development and adapted to specific protein targets. AutoDock has been applied to a wide range of biological systems. It has been used not only for protein-ligand docking simulation but also for the prediction of binding affinity with good correlation with experimental binding affinity for several protein systems. The latest version makes use of a semi-empirical force field to evaluate protein-ligand binding affinity and for selecting the lowest energy pose in docking simulation. AutoDock4.2.6 has an arsenal of four search algorithms to carry out docking simulation including simulated annealing, genetic algorithm, and Lamarckian algorithm. In this chapter, we describe a tutorial about how to perform docking with AutoDock4. We focus our simulations on the protein target cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Val Oliveira Pintro
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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34
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Al-Otaibi FA, Bakhotmah DA. Synthesis and Biological Evaluation of New Fluorine Compounds Bearing 4-Amino-1,2,4-triazino[4,3-b]-1,2,4-triazin-8-one and the Related Derivatives as CDK2 Inhibitors of Tumor Cell. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1747098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Fatimah A. Al-Otaibi
- King Abdulaziz University, Jeddah, Saudi Arabia
- Tabuk University, Tabuk, Saudi Arabia
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35
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Silva D, Mendes E, Summers EJ, Neca A, Jacinto AC, Reis T, Agostinho P, Bolea I, Jimeno ML, Mateus ML, Oliveira‐Campos AMF, Unzeta M, Marco‐Contelles J, Majekova M, Ramsay RR, Carreiras MC. Synthesis, biological evaluation, and molecular modeling of nitrile‐containing compounds: Exploring multiple activities as anti‐Alzheimer agents. Drug Dev Res 2020; 81:215-231. [DOI: 10.1002/ddr.21594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/01/2019] [Accepted: 08/04/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Silva
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
| | - Eduarda Mendes
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
| | - Eleanor J. Summers
- Biomedical Sciences Research ComplexUniversity of St. Andrews St. Andrews UK
| | - Ana Neca
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
| | - Ana C. Jacinto
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
| | - Telma Reis
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
| | - Paula Agostinho
- Faculty of Medicine and Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
| | - Irene Bolea
- Institut de Neurociències i Departament de Bioquímica i Biologia Molecular, Facultat de MedicinaUniversitat Autònoma de Barcelona (UAB) Bellaterra (Barcelona) Spain
| | - M. Luisa Jimeno
- Centro de Química Orgánica “Lora Tamayo” (CSIC) Madrid Spain
| | - M. Luisa Mateus
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
| | | | - Mercedes Unzeta
- Institut de Neurociències i Departament de Bioquímica i Biologia Molecular, Facultat de MedicinaUniversitat Autònoma de Barcelona (UAB) Bellaterra (Barcelona) Spain
| | - José Marco‐Contelles
- Laboratory of Medicinal ChemistryInstitute of Organic Chemistry (CSIC) Madrid Spain
| | - Magdalena Majekova
- Center of Experimental MedicineInstitute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences Bratislava Slovakia
| | - Rona R. Ramsay
- Biomedical Sciences Research ComplexUniversity of St. Andrews St. Andrews UK
| | - M. Carmo Carreiras
- Research Institute for Medicines (iMed.ULisboa), Faculty of PharmacyUniversidade de Lisboa Lisbon Portugal
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36
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Said MA, Eldehna WM, Nocentini A, Fahim SH, Bonardi A, Elgazar AA, Kryštof V, Soliman DH, Abdel-Aziz HA, Gratteri P, Abou-Seri SM, Supuran CT. Sulfonamide-based ring-fused analogues for CAN508 as novel carbonic anhydrase inhibitors endowed with antitumor activity: Design, synthesis, and in vitro biological evaluation. Eur J Med Chem 2020; 189:112019. [PMID: 31972394 DOI: 10.1016/j.ejmech.2019.112019] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 11/17/2022]
Abstract
In the present study, we report the design and synthesis of novel CAN508 sulfonamide-based analogues (4, 8a-e, 9a-h and 10a-e) as novel carbonic anhydrase (CA) inhibitors with potential CDK inhibitory activity. A bioisosteric replacement approach was adopted to replace the phenolic OH of CAN508 with a sulfamoyl group to afford compound 4. Thereafter, a ring-fusion approach was utilized to furnish the 5/5 fused imidazopyrazoles 8a-e which were subsequently expanded to 6/5 pyrazolopyrimidines 9a-h and 10a-e. All the synthesized analogues were evaluated for their inhibitory activity toward isoforms hCA I, II, IX and XII. The target tumor-associated isoforms hCA IX and XII were effectively inhibited with KIs ranges 6-67.6 and 10.1-88.6 nM, respectively. Furthermore, all compounds were evaluated for their potential CDK2 and 9 inhibitory activities. Pyrazolopyrimidines 9d, 9e and 10b displayed weak CDK2 inhibitory activity (IC50 = 6.4, 8.0 and 11.6 μM, respectively), along with abolished CDK9 inhibitory activity. This trend suggested that pyrazolopyrimidine derivatives merit further optimization to furnish more effective CDK2 inhibitor lead. On account of their excellent activity and selectivity towards hCA IX and XII, pyrazolopyrimidines 10 were evaluated for their anti-proliferative activity toward breast cancer MCF-7 and MDA-MB-468 cell lines under normoxic and hypoxic conditions. The most potent anti-proliferative agents 10a, 10c and 10d significantly increased cell percentage at sub-G1 and G2-M phases with concomitant decrease in the S phase population in MCF-7 treated cells. Finally, a docking study was undertaken to investigate the binding mode for the most selective hCA IX and XII inhibitors 10a-e, within hCA II, IX and XII active sites.
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Affiliation(s)
- Mohamed A Said
- Department of Pharmaceutical Chemistry, College of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt.
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy; Department of NEUROFARBA - Pharmaceutical and Nutraceutical Section; Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Samar H Fahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Alessandro Bonardi
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy; Department of NEUROFARBA - Pharmaceutical and Nutraceutical Section; Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Abdullah A Elgazar
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany, The Czech Academy of Sciences, Slechtitelu 27, 78371, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Hnevotinská 5, 77900, Olomouc, Czech Republic
| | - Dalia H Soliman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al Azhar University, Cairo, P.O. Box 11471, Egypt
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Cairo, 12622, Egypt
| | - Paola Gratteri
- Department of NEUROFARBA - Pharmaceutical and Nutraceutical Section; Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Sahar M Abou-Seri
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt.
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy.
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37
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Abstract
Protein-ligand docking simulations are of central interest for computer-aided drug design. Docking is also of pivotal importance to understand the structural basis for protein-ligand binding affinity. In the last decades, we have seen an explosion in the number of three-dimensional structures of protein-ligand complexes available at the Protein Data Bank. These structures gave further support for the development and validation of in silico approaches to address the binding of small molecules to proteins. As a result, we have now dozens of open source programs and web servers to carry out molecular docking simulations. The development of the docking programs and the success of such simulations called the attention of a broad spectrum of researchers not necessarily familiar with computer simulations. In this scenario, it is essential for those involved in experimental studies of protein-ligand interactions and biophysical techniques to have a glimpse of the basics of the protein-ligand docking simulations. Applications of protein-ligand docking simulations to drug development and discovery were able to identify hits, inhibitors, and even drugs. In the present chapter, we cover the fundamental ideas behind protein-ligand docking programs for non-specialists, which may benefit from such knowledge when studying molecular recognition mechanism.
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38
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El-Sayed EH, Mohamed KS. Synthesis and Anti-inflammatory Evaluation of Some New Pyrazole, Pyrimidine, Pyrazolo[1,5-a]Pyrimidine, Imidazo[1,2-b]Pyrazole and Pyrazolo[5,1-b]Quinazoline Derivatives Containing Indane Moiety. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1653941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Khaled S. Mohamed
- Engineering Chemistry Department, Higher Institute for Engineering and Technology, New Damietta, Egypt
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Chen EW, Tay NQ, Brzostek J, Gascoigne NRJ, Rybakin V. A Dual Inhibitor of Cdc7/Cdk9 Potently Suppresses T Cell Activation. Front Immunol 2019; 10:1718. [PMID: 31402912 PMCID: PMC6670834 DOI: 10.3389/fimmu.2019.01718] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023] Open
Abstract
T cell activation is mediated by signaling pathways originating from the T cell receptor (TCR). Propagation of signals downstream of the TCR involves a cascade of numerous kinases, some of which have yet to be identified. Through a screening strategy that we have previously introduced, PHA-767491, an inhibitor of the kinases Cdc7 and Cdk9, was identified to impede TCR signaling. PHA-767491 suppressed several T cell activation phenomena, including the expression of activation markers, proliferation, and effector functions. We also observed a defect in TCR signaling pathways upon PHA-767491 treatment. Inhibition of Cdc7/Cdk9 impairs T cell responses, which could potentially be detrimental for the immune response to tumors, and also compromises the ability to resist infections. The Cdc7/Cdk9 inhibitor is a strong candidate as a cancer therapeutic, but its effect on the immune system poses a problem for clinical applications.
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Affiliation(s)
- Elijah W Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Neil Q Tay
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Immunology Programme, Centre for Life Sciences, Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Centre for Life Sciences (CeLS), NUS Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore, Singapore
| | - Joanna Brzostek
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nicholas R J Gascoigne
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Immunology Programme, Centre for Life Sciences, Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Centre for Life Sciences (CeLS), NUS Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore, Singapore
| | - Vasily Rybakin
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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40
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Jethava DJ, Acharya PT, Vasava MS, Bhoi MN, Bhavsar ZA, Rathwa SK, Rajani DP, Patel HD. Design, synthesis, biological evaluation and computational study of novel triazolo [4,3-a]pyrazin analogues. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Synthesis, In Vitro Antimicrobial and Cytotoxic Activities of Some New Pyrazolo[1,5- a]pyrimidine Derivatives. Molecules 2019; 24:molecules24061080. [PMID: 30893820 PMCID: PMC6471749 DOI: 10.3390/molecules24061080] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/06/2019] [Accepted: 03/13/2019] [Indexed: 12/31/2022] Open
Abstract
A new series of pyrazole 4⁻7 and pyrazolo[1,5-a]pyrimidine 8⁻13 were synthesized by using a simple, efficient procedure, and screened for their in-vitro antimicrobial and antitumor activities. Symmetrical and asymmetrical 3,6-diarylazo-2,5,7-triaminopyrazolo[1,5-a]pyrimidine were synthesized by the conventional method and also subjected to microwave irradiation and under ultrasound conditions. The biological results revealed that most of the tested compounds proved to be active as antibacterial and antifungal agents. The antitumor activity of the synthesized compounds was evaluated against human cancer cell lines, MCF-7, HCT-116, and HepG-2, as compared with Doxorubicin as a control.
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42
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Al-Mousawi SM, Moustafa MS, Elnagdi MH. Studies with 2-Arylhydrazononitriles: Further Investigations on the Utility of 2-Arylhydrazononitriles as Precursors to 1,2,3-Triazole Amines. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.3184/030823407x244869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
3-Oxo-2-arylhydrazonobutanenitriles react with hydroxylamine hydrochloride in ethanolic sodium acetate to yield either amidoximes or isoxazolamines depending on the nature of the substituent. The amidoximes cyclise in refluxing DMF containing piperidine to form 2-aryl-1,2,3-triazol-5-amines. The isoxazolamines rearranged into 1,2,3-triazolamines on refluxing in DMF. Amidoxime 2c cyclised in acetic anhydride to give 2-arylhydrazono-1,2,4-oxadiazole 9c, which rearranged to acetylamino-1,2,3-triazole 8c. The prepared acetyl-1,2,3-triazolamines 8b,c were utilised as precursors to triazolopyridines and pyrazolyltriazoles.
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Affiliation(s)
| | | | - Mohamed Hilmy Elnagdi
- Department of Chemistry, Faculty of Science, University of Kuwait, Safat 13060, PO Box 5969, Kuwait
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43
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Hosseini Nasab N, Safari J. The Novel Synthesis of Functionalized Indenopyrazolones Using Fe
3
O
4
nanoparticles stabilized on MMT: An Efficient Magnetically Recoverable Heterogeneous Nanocomposite Catalyst. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Narges Hosseini Nasab
- Department of Organic Chemistry, Faculty of ScienceUniversity of Kashan Kashan 87317 Islamic Republic of Iran
| | - Javad Safari
- Department of Organic Chemistry, Faculty of ScienceUniversity of Kashan Kashan 87317 Islamic Republic of Iran
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44
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Cheng W, Yang Z, Wang S, Li Y, Wei H, Tian X, Kan Q. Recent development of CDK inhibitors: An overview of CDK/inhibitor co-crystal structures. Eur J Med Chem 2019; 164:615-639. [PMID: 30639897 DOI: 10.1016/j.ejmech.2019.01.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
The cyclin-dependent protein kinases (CDKs) are protein-serine/threonine kinases that display crucial effects in regulation of cell cycle and transcription. While the excessive expression of CDKs is intimate related to the development of diseases including cancers, which provides opportunities for disease treatment. A large number of small molecules are explored targeting CDKs. CDK/inhibitor co-crystal structures play an important role during the exploration of inhibitors. So far nine kinds of CDK/inhibitor co-crystals have been determined, they account for the highest proportion among the Protein Data Bank (PDB) deposited crystal structures. Herein, we review main co-crystals of CDKs in complex with corresponding inhibitors reported in recent years, focusing our attention on the binding models and the pharmacological activities of inhibitors.
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Affiliation(s)
- Weiyan Cheng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhiheng Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Suhua Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ying Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Han Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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Bitencourt-Ferreira G, de Azevedo WF. Docking with GemDock. Methods Mol Biol 2019; 2053:169-188. [PMID: 31452105 DOI: 10.1007/978-1-4939-9752-7_11] [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: 06/10/2023]
Abstract
GEMDOCK is a protein-ligand docking software that makes use of an elegant biologically inspired computational methodology based on the differential evolution algorithm. As any docking program, GEMDOCK has two major features to predict the binding of a small-molecule ligand to the binding site of a protein target: the search algorithm and the scoring function to evaluate the generated poses. The GEMDOCK scoring function uses a piecewise potential energy function integrated into the differential evolutionary algorithm. GEMDOCK has been applied to a wide range of protein systems with docking accuracy similar to other docking programs such as Molegro Virtual Docker, AutoDock4, and AutoDock Vina. In this chapter, we explain how to carry out protein-ligand docking simulations with GEMDOCK. We focus this tutorial on the protein target cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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Abstract
Since the early 1980s, we have witnessed considerable progress in the development and application of docking programs to assess protein-ligand interactions. Most of these applications had as a goal the identification of potential new binders to protein targets. Another remarkable progress is taking place in the determination of the structures of protein-ligand complexes, mostly using X-ray diffraction crystallography. Considering these developments, we have a favorable scenario for the creation of a computational tool that integrates into one workflow all steps involved in molecular docking simulations. We had these goals in mind when we developed the program SAnDReS. This program allows the integration of all computational features related to modern docking studies into one workflow. SAnDReS not only carries out docking simulations but also evaluates several docking protocols allowing the selection of the best approach for a given protein system. SAnDReS is a free and open-source (GNU General Public License) computational environment for running docking simulations. Here, we describe the combination of SAnDReS and AutoDock4 for protein-ligand docking simulations. AutoDock4 is a free program that has been applied to over a thousand receptor-ligand docking simulations. The dataset described in this chapter is available for downloading at https://github.com/azevedolab/sandres.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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47
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Bitencourt-Ferreira G, Veit-Acosta M, de Azevedo WF. Van der Waals Potential in Protein Complexes. Methods Mol Biol 2019; 2053:79-91. [PMID: 31452100 DOI: 10.1007/978-1-4939-9752-7_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Van der Waals forces are determinants of the formation of protein-ligand complexes. Physical models based on the Lennard-Jones potential can estimate van der Waals interactions with considerable accuracy and with a computational complexity that allows its application to molecular docking simulations and virtual screening of large databases of small organic molecules. Several empirical scoring functions used to evaluate protein-ligand interactions approximate van der Waals interactions with the Lennard-Jones potential. In this chapter, we present the main concepts necessary to understand van der Waals interactions relevant to molecular recognition of a ligand by the binding pocket of a protein target. We describe the Lennard-Jones potential and its application to calculate potential energy for an ensemble of structures to highlight the main features related to the importance of this interaction for binding affinity.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Martina Veit-Acosta
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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Abstract
Molegro Virtual Docker is a protein-ligand docking simulation program that allows us to carry out docking simulations in a fully integrated computational package. MVD has been successfully applied to hundreds of different proteins, with docking performance similar to other docking programs such as AutoDock4 and AutoDock Vina. The program MVD has four search algorithms and four native scoring functions. Considering that we may have water molecules or not in the docking simulations, we have a total of 32 docking protocols. The integration of the programs SAnDReS ( https://github.com/azevedolab/sandres ) and MVD opens the possibility to carry out a detailed statistical analysis of docking results, which adds to the native capabilities of the program MVD. In this chapter, we describe a tutorial to carry out docking simulations with MVD and how to perform a statistical analysis of the docking results with the program SAnDReS. To illustrate the integration of both programs, we describe the redocking simulation focused the cyclin-dependent kinase 2 in complex with a competitive inhibitor.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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49
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Abstract
Molecular docking is the major computational technique employed in the early stages of computer-aided drug discovery. The availability of free software to carry out docking simulations of protein-ligand systems has allowed for an increasing number of studies using this technique. Among the available free docking programs, we discuss the use of ArgusLab ( http://www.arguslab.com/arguslab.com/ArgusLab.html ) for protein-ligand docking simulation. This easy-to-use computational tool makes use of a genetic algorithm as a search algorithm and a fast scoring function that allows users with minimal experience in the simulations of protein-ligand simulations to carry out docking simulations. In this chapter, we present a detailed tutorial to perform docking simulations using ArgusLab.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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50
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Abstract
Homology modeling is a computational approach to generate three-dimensional structures of protein targets when experimental data about similar proteins are available. Although experimental methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy successfully solved the structures of nearly 150,000 macromolecules, there is still a gap in our structural knowledge. We can fulfill this gap with computational methodologies. Our goal in this chapter is to explain how to perform homology modeling of protein targets for drug development. We choose as a homology modeling tool the program MODELLER. To illustrate its use, we describe how to model the structure of human cyclin-dependent kinase 3 using MODELLER. We explain the modeling procedure of CDK3 apoenzyme and the structure of this enzyme in complex with roscovitine.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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