Investigation of novel compounds via in silico approaches of EGFR inhibitors as anticancer agents

Before the experimental studies of a compound to be synthesized from in vitro to in vivo, it is possible to save both time and money with in silico approaches only with Computer Aided Drug Design (CADD) methods. In other words, compounds that can be new drug candidates can be suggested by drug design using computational drug discovery strategies. In this study, all molecules in the ChEMBL Database were virtual screened based on drugs with inhibitory properties on the Epidermal Growth Factor Receptor (EGFR), one of the receptor tyrosine kinases, which is effective in cancer cells. During this High-Throughput Screening (HTS), the number of compounds was minimized according to the parameters of the reference drugs, physicochemical properties such as logP, M.W., HBA, HDB, RosLip. As a result of in silico approaches and molecular docking analysis, ten compounds with the highest docking scores were determined and a model compound that could be a new drug candidate was proposed.     

Synthesis of functionalized aminopyrazole and pyrazolopyrimidine derivatives: Molecular modeling and docking as anticancer agents

Three new functionalized 4-aminopyrazole derivatives were synthesized and cyclized with phenyl isothiocyanate to yield the corresponding three pyrazolo[4,3-d]pyrimidine analogues. The DFT quantum chemical calculations were utilized in the determination of the frontier molecular orbital energies and Fukui’s indices. The data showed that they have a low HOMO-LUMO energy gap, ranging from 1.16 to 2.35 eV for 5 and 6, respectively. The newly created analogues' cytotoxic qualities were evaluated in comparison to the reference 5-florouracil (5-Fu) using an in vitro MTT cytotoxicity screening investigation toward four different cell lines, including HCT-116, HepG2, MCF-7, and WI38. The results showed variable potency against human cell lines, with MCF-7 and HepG-2 showing cytotoxic selectivity. The most potent agent against MCF-7 and HCT-116 human cancer cells were found to be aminopyrazole and pyrazolopyrimidine derivatives 4–9. The structure–activity relationships (SAR) for the synthesized compounds were discussed. The examined compounds had superior cytotoxic properties; the most potent derivative 7, had an IC₅₀ ranged from 11.51 ± 0.35 to 21.25 ± 0.37 µM. Meanwhile, quantum chemical computation used independent variables E_H, E_L, ΔE_H-L, χ and η were applied to determine the best way to describe activity. As a result, an increase in the HOMO-LUMO gap and hardness will result in an increase in the anticancer activity. While the E_H, E_L, and showed negative coefficients, increasing them will decrease the anticancer activity. Furthermore, 5IVE protein's crystal structure for KDM5A was docked with the newly created aminopyrazole and pyrazolopyrimidine derivatives to afford the theoretical prediction on the KDM5A enzyme.     

Novel benzimidazole derivatives as anti-cervical cancer agents of potential multi-targeting kinase inhibitory activity

Multi-target EGFR, HER2, VEGFR-2 and PDGFR is an improved strategy for the treatment of solid tumors. This work deals with synthesis of an array of new 6-benzoyl benzimidazole derivatives utlizing1-(6-benzoyl-2-(3,4-dimethoxyphenyl)-1H benzo[d] imidazol-1-yl)propan-2-one (1) as a starting compound. The new compounds were screened as cytotoxic agents against cervical cancer cells (Hela) and Doxorubicin served as a reference drug. Most of the tested compounds showed promising anticancer activity in addition to their safety towards the normal cell line. The most potent candidates were evaluated as EGFR, HER2, PDGFR-β and VEGFR2 inhibitors in comparison to Erlotinib. Compounds 9 and 13 exhibited promising suppression effects. Also, the latter compounds exhibited their ability to induce cellular apoptosis alongside cell cycle arrest at the G2/M phase and accumulation of cells in pre-G1 phase. Molecular docking analysis suggested that compounds 2c, 3f, 9, 12 and 13 tightly interacts with the amino acid residues in the active binding site of HER2 kinase.     

Thymus musilii Velen. as a promising source of potent bioactive compounds with its pharmacological properties: In vitro and in silico analysis

For the first time, we reported the phytochemical composition of the volatile oil from Thymus musilii Velen (T. musilii). The antioxidant and antimicrobial activities against various food-borne and clinical pathogenic microorganisms were also tested. The thyme oil was particularly rich in thymol (67.697 ± 0.938%), and thymyl acetate (12.993 ± 0.221%). The strongest antioxidant activity of the essential oil was registered with the tests: ABTS (IC₅₀ = 5.6 × 10⁻⁴ mg/mL) and β-carotene/linoleic acid (IC₅₀ = 3.2 × 10⁻³ mg/mL). This thymol-chemotype oil was active against all microorganisms tested with an inhibition growth zone ranging from 21.33 ± 1.52 mm for Proteus mirabilis (P. mirabilis) to 37.33 ± 1.15 mm for Candida vaginalis (C. vaginalis) strain. Overall, the tested oil exhibited bactericidal and fungicidal activities and only a small quantity of the tested essential oil was found to be sufficient for inhibiting the growth of the tested microorganisms. Furthermore, molecular docking results implies that, among the bioactive compounds, β-caryophyllene interacted strongly with the active site residues of TyrRS, GLMS and Gyrase enzymes and consequently support our in vitro results with the highest inhibition potential of this essential oil against tested pathogens, especially Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Our results suggested that essential oil of T. musiliii exhibited strong biological activities with a promising source of various natural compounds.     

In-silico profiling,design, molecular docking computation,and drug kinetic model evaluation of novel curcumin derivatives as potential anticancer agents

The alarming trend of leukemia cell lines that are multidrug-resistant has prompted scientists to scramble for effective new anticancer treatments. Therefore, it remains an intriguing scientific task to optimize curcumin by trying to introduce molecular alteration to its vital structure to improve the biological effect against the P388 cell line or get around resistance phenomena. Regardless of the wide range of medications that are now being studied, Prednisone remains the most important and efficient part of chemotherapy that the WHO recommends. This article discusses the QSAR-oriented model and in silico assessment of some potent curcumin derivatives' anticancer activity against the P388 cell line. The solidity and propensity for prediction of the model were ensured by using stringent validation procedures. The activity of these derivatives was shown to be unrelated to lipophilicity, while shorter N-N distances and short substituents result in quite bioactive molecules. This information was used to design potent molecules that demonstrate good quality as per the assessment based on the Lead-Like Soft rule is acceptable for drug-like molecules. Also, molecule d2 does not possess any toxic effects risk alerts, suggesting drug-adherent conduct. While Prednisone the reference drug has a toxicity risk alert in red, suggesting non-adherent conduct for Prednisone. Hence, the novel molecules are promising anticancer agents.     

1,3-Oxazole derivatives of cytisine as potential inhibitors of glutathione reductase of Candida spp.: QSAR modeling,docking analysis and experimental study of new anti-Candida agents

Natural products as well as their derivatives play a significant role in the discovery of new biologically active compounds in the different areas of our life especially in the field of medicine. The synthesis of compounds produced from natural products including cytisine is one approach for the wider use of natural substances in the development of new drugs. QSAR modeling was used to predict and select of biologically active cytisine-containing 1,3-oxazoles. The eleven most promising compounds were identified, synthesized and tested. The activity of the synthesized compounds was evaluated using the disc diffusion method against C. albicans M 885 (ATCC 10,231) strain and clinical fluconazole-resistant Candida krusei strain. Molecular docking of the most active compounds as potential inhibitors of the Candida spp. glutathione reductase was performed using the AutoDock Vina. The built classification models demonstrated good stability, robustness and predictive power. The eleven cytisine-containing 1,3-oxazoles were synthesized and their activity against Candida spp. was evaluated. Compounds 10, 11 as potential inhibitors of the Candida spp. glutathione reductase demonstrated the high activity against C. albicans M 885 (ATCC 10,231) strain and clinical fluconazole-resistant Candida krusei strain. The studied compounds 10, 11 present the interesting scaffold for further investigation as potential inhibitors of the Candida spp. glutathione reductase with the promising antifungal properties. The developed models are publicly available online at http://ochem.eu/article/120720 and could be used by scientists for design of new more effective drugs.     

A comparative QSAR analysis and molecular docking studies of phenyl piperidine derivatives as potent dual NK1R antagonists/serotonin transporter (SERT) inhibitors

Depression is a critical mood disorder that affects millions of patients. Available therapeutic antidepressant agents are associated with several undesirable side effects. Recently, it has been shown that Neurokinin 1 receptor (NK₁R) antagonists can potentiate the antidepressant effects of serotonin-selective reuptake inhibitors (SSRIs). In this study, a series of phenyl piperidine derivatives as potent dual NK₁R antagonists/serotonin transporter (SERT) inhibitors were applied to quantitative structure–activity relationship (QSAR) analysis. A collection of chemometrics methods such as multiple linear regression (MLR), factor analysis–based multiple linear regression (FA-MLR), principal component regression (PCR), and partial least squared combined with genetic algorithm for variable selection (GA-PLS) were applied to make relations between structural characteristics and NK₁R antagonism/SERT inhibitory of these compounds. The best multiple linear regression equation was obtained from GA-PLS and MLR for NK₁R and SERT, respectively. Based on the resulted model, an in silico-screening study was also conducted and new potent lead compounds based on new structural patterns were designed for both targets. Molecular docking studies of these compounds on both targets were also conducted and encouraging results were acquired. There was a good correlation between QSAR and docking results. The results obtained from validated docking studies indicate that the important amino acids inside the active site of the cavity that are responsible for essential interactions are Glu33, Asp395 and Arg26 for SERT and Ala30, Lys7, Asp31, Phe5 and Tyr82 for NK₁R receptors.     

Synthesis,pharmacological evaluation,and molecular modeling studies of novel isatin hybrids as potential anticancer agents

A novel series of isatin hybrids 5a-g was designed, synthesized, and characterized spectroscopically. The synthesized compounds were evaluated for their cytotoxic activity against the human breast cancer cell line (MCF-7) by in vitro MTT assay. Amongst the tested compounds, 5e compound bearing benzyl moiety at N₄ piperazine was found to be the most active with the promising IC₅₀ (12.47 µM). Moreover, the active compounds 5e and 5g were subjected to antitumor evaluation (in vivo) against Dalton’s ascitic lymphoma (DAL) cell line and the results suggested that the best active compound 5e can normalize the blood picture in comparison to the standard drug. An in silico molecular docking study using the crystal structure of Hsp90 protein described the role of significant protein–ligand interactions and revealed more insights into the binding mode. The drug-likeliness of the compounds was predicted based on Lipinski's rule of five and pharmacokinetic ADME parameters. Hence, the synthesized isatin hybrids could be novel starting point anticancer lead compounds demonstrating drug-like properties which can be explored further for anticancer drug discovery.     

Design,synthesis and evaluation of novel dehydroabietic acid-dithiocarbamate hybrids as potential multi-targeted compounds for tumor cytotoxicity

In the present study, novel representatives of the important group of biologically-active, dehydroabietic acid-bearing dithiocarbamate moiety, were synthesized and characterized by ¹H NMR, ¹³C NMR, HR-MS. The in vitro antiproliferative activity evaluation (MTT) indicated that these compounds exhibited potent inhibitory activities in various cancer cell lines (HepG-2, MCF-7, HeLa, T-24, MGC-803). Particularly, compound III-b possessed extraordinary cytotoxicity with low micromolar IC₅₀ values ranging from 4.07 to 38.84 µM against tested cancer cell lines, while displayed weak cytotoxicity on two normal cell lines (LO-2 and HEK 293 T). Subsequently, the potential mechanisms of representative compound III-b were elementarily investigated by Transwell experiment, which showed III-b can inhibit cancer cells migration. Annexin-V/PI dual staining showed that the compound can induce HepG-2 cells apoptosis in a dose-dependent manner. Meanwhile this apoptosis may be related to the upregulated protein expression of cleaved-caspase 3, cleaved-caspase 9, Bax and downregulated of Bcl-2 indicated by Western Blot. Later study further confirmed that ROS levels in HepG-2 cells increased significantly with the rise of concentrations. In addition, through the network pharmacology data analyzing, the core targets and signaling pathways of compound III-b for treatment of liver neoplasms were forecasted. Molecular docking model showed that compound III-b had high affinity with hub targets (CASP3, EGFR, HSP90AA1, MAPK1, ERBB2, MDM2), suggesting that compound III-b might target the hub protein to modulate signaling activity. Taken together, these data indicated that dehydroabietic acid structural modification following the “Molecular hybridization” principle is a feasible way to discover the potential multi-targeted antitumor compounds.