scholarly journals QSAR, pharmacophore modeling and molecular docking studies to identify structural alerts for some nitrogen heterocycles as dual inhibitor of telomerase reverse transcriptase and human telomeric G-quadruplex DNA

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
R. D. Jawarkar ◽  
R. L. Bakal ◽  
P. N. Khatale ◽  
Israa Lewaa ◽  
Chetan M. Jain ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Carbon Atom ◽  
Reverse Transcriptase ◽  
Qsar Model ◽  
Pharmacophore Modeling ◽  
Telomerase Reverse Transcriptase ◽  
Quadruplex Dna ◽  
Pharmacophore Modelling ◽  
G Quadruplex ◽  
Dual Inhibition

Abstract Background Telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA are amongst the favorable target for researchers to discover novel and more effective anticancer agents. To understand and elucidate structure activity relationship and mechanism of inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA, a QSAR modeling and molecular docking were conducted. Results Two robust QSAR model were obtained which consist of full set QSAR model (R2: 0.8174, CCCtr: 0.8995, Q2loo: 0.7881, Q2LMO: 0.7814) and divided set QSAR model (R2: 0.8217, CCCtr: 0.9021, Q2loo: 0.7886, Q2LMO: 0.7783, Q2-F1: 0.7078, Q2-F2: 0.6865, Q2-F3: 0.7346) for envisaging the inhibitory activity of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The analysis reveals that carbon atom exactly at 3 bonds from aromatic carbon atom, nitrogen atom exactly at six bonds from planer nitrogen atom, aromatic carbon atom within 2 A0 from the center of mass of molecule and occurrence of element hydrogen within 2 A0 from donar atom are the key pharmacophoric features important for dual inhibition of TERT and human telomeric G-quadruplex DNA. To validate this analysis, pharmacophore modeling and the molecular docking is performed. Molecular docking analysis support QSAR analysis and revealed that, dual inhibition of TERT and human telomeric DNA is mainly contributed from hydrophobic and hydrogen bonding interactions. Conclusion The findings of molecular docking, pharmacophore modelling, and QSAR are all consistent and in strong agreement. The validated QSAR analyses can detect structural alerts, pharmacophore modelling can classify a molecule's consensus pharmacophore involving hydrophobic and acceptor regions, whereas docking analysis can reveal the mechanism of dual inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The combination of QSAR, pharmacophore modeling and molecular docking may be useful for the future drug design of dual inhibitors to combat the devastating issue of resistance. Graphical abstract

A Combined approach of Pharmacophore Modeling, QSAR Study, Molecular Docking and in silico ADME/Tox prediction of 4-Arylthio & 4- Aryloxy-3- Iodopyridine-2(1H)-one analogs to identify potential Reverse Transcriptase inhibitor: Anti-HIV agents

2020 ◽  
Vol 17 ◽  
Author(s):  
Debadash Panigrahi ◽  
Amiyakanta Mishra ◽  
Susanta Kumar Sahu ◽  
Mohd. Afzal Azam ◽  
C.M. Vyshaag
Keyword(s):  
Molecular Docking ◽  
Reverse Transcriptase ◽  
Active Site ◽  
3D Qsar ◽  
Qsar Model ◽  
Pharmacophore Modeling ◽  
Reverse Transcriptase Inhibitors ◽  
Rt Inhibitors ◽  
Anti Hiv ◽  
Exclusion Method

Background: Reverse transcriptase is an important therapeutic target to treat AIDS caused by the Human Immunodeficiency Virus (HIV). Despite many effective anti-HIV drugs, reverse transcriptase (RT) inhibitors remain the cornerstone of the drug regimen to treat AIDS. In the present work, we have expedited the use of different computational modules and presented an easy, cost-effective and high throughput screening method to identify potential reverse transcriptase inhibitors. Methods: A congeneric series of 4-Arylthio & 4-Aryloxy-3- Iodopyridine-2(1H)-one analogs having anti-HIV activity were subjected to structure-based 2D, 3D QSAR, Pharmacophore Modeling, and Molecular Docking to elucidate the structural properties required for the design of potent HIV-RT inhibitors. Prediction of preliminary Pharmacokinetic and the Drug Likeliness profile was performed for these compounds by in silico ADME study. Results: The 2D and 3D- QSAR models were developed by correlating two and three-dimensional descriptors with activity (pIC50) by sphere exclusion method and k-nearest neighbor molecular field analysis approach, respectively. The significant 2D- QSAR model developed by Partial Least Square associated with the Sphere Exclusion method (PLS-SE) having r2 and q2 values 0.9509 and 0.8038 respectively. The 3D-QSAR model by Step Wise variable selection method (SW-kNN MFA) is more significant which has a cross-validated squared correlation coefficient q2= 0.8509 and a non-cross-validated correlation coefficient pred_r2= 0.8102. The pharmacophore hypothesis was developed which comprised 5 features includes 3 aliphatic regions (Ala), 1 H-bond donor (HDr) and 1 H-bond acceptor (HAc). Docking studies of the selected inhibitors with the active site of reverse transcriptase enzyme showed hydrogen bond and π - π interaction with LYS-101, LYS-103, TYR- 181, TYR-188 and TRP-229 residues present at the active site. All the candidates with good bioavailability and ADMET drug likeliness properties. Conclusion: The results of the present work provide more useful information and important structural insights for the discovery, design of novel and potent reverse transcriptase inhibitors with high therapeutic windows in the future.

Hybrid Imidazole-Pyridine Derivatives: An Approach to Novel Anticancer DNA Intercalators

2020 ◽  
Vol 27 (1) ◽  
pp. 154-169 ◽  
Author(s):  
Claudiu N. Lungu ◽  
Bogdan Ionel Bratanovici ◽  
Maria Mirabela Grigore ◽  
Vasilichia Antoci ◽  
Ionel I. Mangalagiu
Keyword(s):  
Experimental Data ◽  
Antimicrobial Properties ◽  
Qsar Model ◽  
Therapeutic Effectiveness ◽  
Computational Results ◽  
Pyridine Derivatives ◽  
Quadruplex Dna ◽  
Dna Intercalators ◽  
Structure Activity ◽  
G Quadruplex

Lack of specificity and subsequent therapeutic effectiveness of antimicrobial and antitumoral drugs is a common difficulty in therapy. The aim of this study is to investigate, both by experimental and computational methods, the antitumoral and antimicrobial properties of a series of synthesized imidazole-pyridine derivatives. Interaction with three targets was discussed: Dickerson-Drew dodecamer (PDB id 2ADU), G-quadruplex DNA string (PDB id 2F8U) and DNA strain in complex with dioxygenase (PDB id 3S5A). Docking energies were computed and represented graphically. On them, a QSAR model was developed in order to further investigate the structure-activity relationship. Results showed that synthesized compounds have antitumoral and antimicrobial properties. Computational results agreed with the experimental data.

scholarly journals Molecular Docking and Biophysical Studies for Antiproliferative Assessment of Synthetic Pyrazolo-Pyrimidinones Tethered with Hydrazide-Hydrazones

2021 ◽  
Vol 22 (5) ◽  
pp. 2742
Author(s):  
Mabrouk Horchani ◽  
Gerardo Della Sala ◽  
Alessia Caso ◽  
Federica D’Aria ◽  
Germana Esposito ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Condensation Reaction ◽  
Growth Factor Receptor ◽  
Phase Cell ◽  
Cancer Disease ◽  
Quadruplex Dna ◽  
Docking Simulations ◽  
G Quadruplex ◽  
Therapeutic Alternatives

Chemotherapy represents the most applied approach to cancer treatment. Owing to the frequent onset of chemoresistance and tumor relapses, there is an urgent need to discover novel and more effective anticancer drugs. In the search for therapeutic alternatives to treat the cancer disease, a series of hybrid pyrazolo[3,4-d]pyrimidin-4(5H)-ones tethered with hydrazide-hydrazones, 5a–h, was synthesized from condensation reaction of pyrazolopyrimidinone-hydrazide 4 with a series of arylaldehydes in ethanol, in acid catalysis. In vitro assessment of antiproliferative effects against MCF-7 breast cancer cells, unveiled that 5a, 5e, 5g, and 5h were the most effective compounds of the series and exerted their cytotoxic activity through apoptosis induction and G0/G1 phase cell-cycle arrest. To explore their mechanism at a molecular level, 5a, 5e, 5g, and 5h were evaluated for their binding interactions with two well-known anticancer targets, namely the epidermal growth factor receptor (EGFR) and the G-quadruplex DNA structures. Molecular docking simulations highlighted high binding affinity of 5a, 5e, 5g, and 5h towards EGFR. Circular dichroism (CD) experiments suggested 5a as a stabilizer agent of the G-quadruplex from the Kirsten ras (KRAS) oncogene promoter. In the light of these findings, we propose the pyrazolo-pyrimidinone scaffold bearing a hydrazide-hydrazone moiety as a lead skeleton for designing novel anticancer compounds.

scholarly journals Discovery of a Natural Product-Like c-myc G-Quadruplex DNA Groove-Binder by Molecular Docking

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e43278 ◽  
Author(s):  
Dik-Lung Ma ◽  
Daniel Shiu-Hin Chan ◽  
Wai-Chung Fu ◽  
Hong-Zhang He ◽  
Hui Yang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Natural Product ◽  
Quadruplex Dna ◽  
G Quadruplex

scholarly journals In silico prediction of telomerase reverse transcriptase inhibitors using modified retinol for the treatment of arsenical cancer

2016 ◽  
Vol 9 (3) ◽  
pp. 164
Author(s):  
Kipchu Tshering ◽  
Mir Misbahuddin
Keyword(s):  
Molecular Docking ◽  
Reverse Transcriptase ◽  
In Silico ◽  
Telomerase Activity ◽  
Telomerase Reverse Transcriptase ◽  
Toxicity Evaluation ◽  
Reverse Transcriptase Inhibitors ◽  
Reverse Transcriptase Enzyme ◽  
New Compounds ◽  
High Binding Affinity

<p align="left">Retinol molecule was modified to predict the inhibitors of telomerase reverse transcriptase for the treatment of arsenical cancer through <em>in silico</em> study. Telomerase activity is expressed in the cancerous conditions which can be the target for anticancer activity by inhibiting telomerase reverse transcriptase enzyme. The inhibitors were predicted through molecular docking of modified retinol with telomerase reverse transcriptase. Taking into account of low binding energy and high binding affinity two new compounds, compound number 606 and compound number 609 were predicted as the inhibitors of telomerase reverse transcriptase for the treatment of arsenical cancer. The prediction of these two compounds was further supported by drug-likeness test through Administration, Distribution, Metabolism, Excretion and Toxicity evaluation. The compounds were also compared with some of the known inhibitors of telomerase reverse transcriptase. </p>

Structural Investigations of Aroylindole Derivatives through 3D-QSAR and Multiple Pharmacophore Modeling for the Search of Novel Colchicines Inhibitor

2020 ◽  
Vol 17 ◽  
Author(s):  
Vijay K. Patel ◽  
Harish Rajak
Keyword(s):  
Virtual Screening ◽  
Anticancer Agents ◽  
Structural Alignment ◽  
Pharmacophore Model ◽  
3D Qsar ◽  
Qsar Model ◽  
Structural Features ◽  
Pharmacophore Modeling ◽  
Structural Investigations ◽  
Pharmacophore Modelling

Background : The ligand and structure based integrated strategies are being repeatedly and effectively employed for the precise search and design of novel ligands against various disease targets. Aroylindole derivative have a similar structural analogy as Combretastatin A-4, and exhibited potent anticancer activity on several cancer cell lines. Objective: To identify structural features of aroylindole derivatives through 3D-QSAR and multiple pharmacophore modelling for the search of novel colchicines inhibitor via virtual screening. Method: The present study utilizes ligand and structure based methodology for the establishment of structure activity correlation among trimethoxyaroylindole derivatives and search of novel colchicines inhibitor via virtual screening. The 3DQSAR studies were performed using Phase module and provided details of relationship between structure and biological activity. A single ligand based pharmacophore model was generated from Phase on compound 3 and compound 29 and three energetically optimized structure based pharmacophore models were generated from e-pharmacophore for co-crystallized ligand, compound 3 and compound 29 with protein PBD ID 1SA0, 5EYP and 5LYJ. These pharmacophoric features containing hit-like compounds were collected from commercially available ZINC database and screened using virtual screening workflow. Results and Discussion: The 3D-QSAR model studies with good PLSs statistics for factor four was characterized by the best prediction coefficient Q2 (0.8122), regression R2 (0.9405), SD (0.2581), F (102.7), P (1.56e-015), RMSE (0.402), Stability (0.5411) and Pearson-r (0.9397). The generated e-pharmacophores have GH scores over 0.5 and AUAC ≥ 0.7 indicated that all the pharmacophores were suitable for pharmacophore-based virtual screening. The virtual screened compounds ZINC12323179, ZINC01642724, ZINC14238006 have showed similar structural alignment as co-crystallized ligand and showed the hydrogen bonding of ligand with ASN101, SER178, THR179, VAL238, CYS241 amino acid of protein. Conclusion: The study illustrates that the ligand and structure based pharmacophoric approach is beneficial for identification of structurally diverse hits, having better binding affinity on colchicines binding site as novel anticancer agents.

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