Development of potential inhibitors of cell division protein kinase 2 by ligand based drug design

2021 ◽  
pp. 1-10
Author(s):  
Vildan Enisoğlu Atalay ◽  
Büşra Savaş
Keyword(s):  
Hydrogen Bond ◽  
Cell Division ◽  
Drug Design ◽  
Discovery Studio ◽  
Cyclin Dependent Kinases ◽  
Hydrogen Bond Interactions ◽  
Damage Repair ◽  
Cancer Types ◽  
Potential Inhibitors ◽  
Cycle Regulation

Cyclin-dependent kinases (CDKs) are commonly known by their role in cell cycle regulation which affects cancer mechanism. In many cancer types, CDKs show extreme activity or CDK inhibiting proteins are dysfunctional. Specifically, CDK2 plays an indispensable role in cell division especially in the G1/S phase and DNA damage repair. Therefore, it is important to find new potential CDK2 inhibitors. In this study, ligand-based drug design is used to design new potential CDK2 inhibitors. Y8 L ligand is obtained from the X-ray crystal structure of human CDK2 (PDB ID: 2XNB) (www.pdb.org) and used as a structure model. By adding hydrophilic and hydrophobic groups to the structure, a training set of 36 molecules is generated. Each molecule examined with Spartan’14 and optimized structures are used for docking to CDK2 structure by AutoDock and AutoDock Vina programs. Ligand-amino acid interactions are analysed with Discovery Studio Visualizer. Van der Waals, Pi-Pi T-shaped, alkyl, pi-alkyl, conventional hydrogen bond and carbon-hydrogen bond interactions are observed. By docking results and viewed interactions, some molecules are identified and discussed as potential CDK2 inhibitors. Additionally, 8 different QSAR descriptors obtained from Spartan’14, Preadmet and ALOGPS 2.1 programs are investigated with multiple linear regulation (MLR) analysis with SPSS program for their impact on affinity value.

scholarly journals Targeting NEDDylation as a Novel Approach to Improve the Treatment of Head and Neck Cancer

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3250
Author(s):  
Trace M. Jones ◽  
Jennifer S. Carew ◽  
Julie E. Bauman ◽  
Steffan T. Nawrocki
Keyword(s):  
Head And Neck Cancer ◽  
Head And Neck ◽  
Patient Outcomes ◽  
Neck Cancer ◽  
Cellular Stress Response ◽  
Novel Approach ◽  
Damage Repair ◽  
Cancer Types ◽  
Cycle Regulation ◽  
Substrate Proteins

Head and neck cancer is diagnosed in nearly 900,000 new patients worldwide each year. Despite this alarming number, patient outcomes, particularly for those diagnosed with late-stage and human papillomavirus (HPV)-negative disease, have only marginally improved in the last three decades. New therapeutics that target novel pathways are desperately needed. NEDDylation is a key cellular process by which NEDD8 proteins are conjugated to substrate proteins in order to modulate their function. NEDDylation is closely tied to appropriate protein degradation, particularly proteins involved in cell cycle regulation, DNA damage repair, and cellular stress response. Components of the NEDDylation pathway are frequently overexpressed or hyperactivated in many cancer types including head and neck cancer, which contribute to disease progression and drug resistance. Therefore, targeting NEDDylation could have a major impact for malignancies with alterations in the pathway, and this has already been demonstrated in preclinical studies and clinical trials. Here, we will survey the mechanisms by which aberrant NEDDylation contributes to disease pathogenesis and discuss the potential clinical implications of inhibiting NEDDylation as a novel approach for the treatment of head and neck cancer.

Biological Role of CDK 11 and 12 in Cell Cycle and its Function in Tumorigenesis

2020 ◽  
Author(s):  
Shamim Mushtaq
Keyword(s):  
Breast Cancer ◽  
Cell Cycle ◽  
Web Of Science ◽  
The Body ◽  
Main Role ◽  
Hallmarks Of Cancer ◽  
Cyclin Dependent Kinases ◽  
Tumor Studies ◽  
Cycle Regulation

Uninhibited proliferation and abnormal cell cycle regulation are the hallmarks of cancer. The main role of cyclin dependent kinases is to regulate the cell cycle and cell proliferation. These protein kinases are frequently down regulated or up regulated in various cancers. Two CDK family members, CDK 11 and 12, have contradicting views about their roles in different cancers. For example, one study suggests that the CDK 11 isoforms, p58, inhibits growth of breast cancer whereas, the CDK 11 isoform, p110, is highly expressed in breast tumor. Studies regarding CDK 12 show variation of opinion towards different parts of the body, however there is a consensus that upregulation of cdk12 increases the risk of breast cancer. Hence, CDK 11 and CDK 12 need to be analyzed to confirm their mechanism and their role regarding therapeutics, prognostic value, and ethnicity in cancer. This article gives an outline on both CDKs of information known up to date from Medline, PubMed, Google Scholar and Web of Science search engines, which were explored and thirty relevant researches were finalized.

scholarly journals Bis[2-(2-hydroxymethyl)pyridine-κ2N,O](pivalato-κO)copper(II)

2012 ◽  
Vol 68 (8) ◽  
pp. m1055-m1055 ◽  
Author(s):  
M. Mobin Shaikh ◽  
Veenu Mishra ◽  
Priti Ram ◽  
Anil Birla
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Octahedral Geometry ◽  
Title Complex ◽  
Distorted Octahedral Geometry ◽  
Pyridine Ligands ◽  
Hydrogen Bond Interactions ◽  
Distorted Octahedral

The structure of the centrosymmetric title complex, [Cu(C5H9O2)2(C6H7NO)2], has the CuIIatom on a centre of inversion. The CuIIatom is six-coordinate with a distorted octahedral geometry, defined by the N and O atoms of the chelating 2-(2-hydroxymethyl)pyridine ligands and two carboxylate O atoms from two monodentate pivalate ions. The crystal packing is stabilized by intermolecular C—H...O and intramolecular O—H...O hydrogen-bond interactions.

Rietveld refinement of the cocrystal 2,4-dihydroxybenzoic acid–N′-(propan-2-ylidene)nicotinohydrazide (1/1)

2012 ◽  
Vol 68 (9) ◽  
pp. o335-o337 ◽  
Author(s):  
Saul H. Lapidus ◽  
Andreas Lemmerer ◽  
Joel Bernstein ◽  
Peter W. Stephens
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Powder Diffraction ◽  
Supramolecular Assembly ◽  
Covalent Bond ◽  
Analytical Tool ◽  
Powder Diffraction Data ◽  
Dihydroxybenzoic Acid ◽  
Bond Forming ◽  
Hydrogen Bond Interactions

A further example of using a covalent-bond-forming reaction to alter supramolecular assembly by modification of hydrogen-bonding possibilities is presented. This concept was introduced by Lemmerer, Bernstein & Kahlenberg [CrystEngComm(2011),13, 55–59]. The title structure, C9H11N3O·C7H6O4, which consists of a reacted niazid molecule,viz.N′-(propan-2-ylidene)nicotinohydrazide, and 2,4-dihydroxybenzoic acid, was solved from powder diffraction data using simulated annealing. The results further demonstrate the relevance and utility of powder diffraction as an analytical tool in the study of cocrystals and their hydrogen-bond interactions.

scholarly journals Doubly ionic hydrogen bond interactions within the choline chloride–urea deep eutectic solvent

2016 ◽  
Vol 18 (27) ◽  
pp. 18145-18160 ◽  
Author(s):  
Claire R. Ashworth ◽  
Richard P. Matthews ◽  
Tom Welton ◽  
Patricia A. Hunt
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Computational Analysis ◽  
Choline Chloride ◽  
Deep Eutectic Solvent ◽  
Hydrogen Bond Interactions

Computational analysis indicates flexibility and diversity in the hydrogen bonding, but limited charge delocalisation, within the choline chloride–urea eutectic.

scholarly journals The Emerging Role of Cyclin-Dependent Kinases (CDKs) in Pancreatic Ductal Adenocarcinoma

2018 ◽  
Vol 19 (10) ◽  
pp. 3219 ◽  
Author(s):  
Balbina García-Reyes ◽  
Anna-Laura Kretz ◽  
Jan-Philipp Ruff ◽  
Silvia von Karstedt ◽  
Andreas Hillenbrand ◽  
...  
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Therapeutic Potential ◽  
Current Knowledge ◽  
Ductal Adenocarcinoma ◽  
Transcriptional Elongation ◽  
Cyclin Dependent Kinases ◽  
Dismal Prognosis ◽  
The Family ◽  
Cycle Regulation

The family of cyclin-dependent kinases (CDKs) has critical functions in cell cycle regulation and controlling of transcriptional elongation. Moreover, dysregulated CDKs have been linked to cancer initiation and progression. Pharmacological CDK inhibition has recently emerged as a novel and promising approach in cancer therapy. This idea is of particular interest to combat pancreatic ductal adenocarcinoma (PDAC), a cancer entity with a dismal prognosis which is owed mainly to PDAC’s resistance to conventional therapies. Here, we review the current knowledge of CDK biology, its role in cancer and the therapeutic potential to target CDKs as a novel treatment strategy for PDAC.

scholarly journals PHYTOCHEMICALS AS POTENTIAL INHIBITORS OF LANOSTEROL 14 Α-DEMETHYLASE (CYP51) ENZYME: AN IN SILICO STUDY ON SIXTY MOLECULES

2020 ◽  
pp. 18-30
Author(s):  
ASHWINI KHANDERAO JADHAV ◽  
PATHAN KAMRAN KHAN ◽  
SANKUNNY MOHAN KARUPPAYIL
Keyword(s):  
Hydrogen Bond ◽  
Candida Albicans ◽  
Docking Study ◽  
Docking Studies ◽  
Antifungal Drugs ◽  
Ergosterol Biosynthesis ◽  
Binding Residue ◽  
Therapeutic Drugs ◽  
Ergosterol Synthesis ◽  
Potential Inhibitors

Lanosterol 14 α-demethylase (CYP51) is a key protein involved in ergosterol biosynthesis of Candida albicans and a crucial target for ergosterol synthesis inhibition. However, in the last two decades drug resistance is reported under clinical situations to most of the prescribed antifungal drugs like azole group of drugs. In this study, molecular docking of sixty plant molecules with Lanosterol 14 α-demethylase protein has been done. The homology modeling tool PHYRE2 was used to predict the structure of Lanosterol 14 α-demethylase. Predicted structure was used for docking studies with sixty plant molecules by using Autodock 1.5.6 cr2™. Among the sixty plant molecules, forty-seven were found to form hydrogen bond and the rest of the plant molecules did not form a hydrogen bond with Lanosterol 14 α-demethylase. Docking study of a library of sixty molecules revealed that 48 plant molecules showed an excellent and good binding affinity with predicted protein model Lanosterol 14 α-demethylase of Candida albicans. The binding residue comparison of docked molecules with that of Ketoconazole revealed, fourteen molecules have similar binding residue. These fourteen molecules may have a similar mode of action as that of Ketoconazole. These molecules should be screened and used to discover new antifungal therapeutic drugs.

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