CoMFA and CoMSIA studies on a new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line

Abstract  A new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line is examined to determine the relationship between the structural properties and the biological activity of these compounds—the 3-D quantitative structure–activity relationship (3D-QSAR)—using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best CoMFA and CoMSIA models were obtained using the atom-based alignment of 33 compounds, 22 training compounds and 11 tested compounds, and these give desirable statistics; those for the CoMFA standard model were: r _cv² = 0.691, r ² = 0.998, S _press = 0.178, s = 0.014 and F = 1080.765, while CoMSIA combined steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields: r _cv² = 0.600, r ² = 0.988, S _press = 0.206, s = 0.034 and F = 284.433. The 3D-QSAR models calculated satisfactory test set activities. The 3D-QSAR contour plots correlated strongly with the experimental data for the binding topology. For this reason, these results would be beneficial for predicting affinities with the compounds of interest, and they are advantageous for guiding the design and synthesis of new and more effective anticancer agents. Graphical abstract   A new and more effective anticancer agent of xanthone derivatives against the oral human epidermoid carcinoma (KB) cell line, as investigated by CoMFA and CoMSIA analysis     

In vitro evaluation of antiproliferative effect of ethyl gallate against human oral squamous carcinoma cell line KB

Although some polyphenols are known to possess anticancer activity against different cancer cell lines through induction of apoptosis, the mode of antiproliferative effect of ethyl gallate against human oral squamous carcinoma cell line KB was not studied until now. Therefore, the antiproliferative effect of ethyl gallate was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay in comparison with the reference drug paclitaxel. Generation of reactive oxygen species, mitochondrial membrane potential loss, DNA damage and apoptosis were determined using 2,7-diacetyldichlorofluorescein fluorescence, uptake of rhodamine-123 by mitochondria, comet assay and acridine orange/ethidium bromide dual-dye staining method. Both ethyl gallate and paclitaxel exhibited cytotoxicity in a dose-dependent manner. The 50% inhibitory concentration for ethyl gallate was 30 and 20 μg/mL for paclitaxel. A volume of 50 μg/mL of ethyl gallate was found to be significantly effective (P < 0.05) in controlling the cancer cell proliferation leading to acute apoptosis.     

3D-QSAR (CoMFA,CoMSIA, HQSAR and topomer CoMFA), MD simulations and molecular docking studies on purinylpyridine derivatives as B-Raf inhibitors for the treatment of melanoma cancer

As per the World Health Organization (WHO), cancer is the second most leading cause of death after cardiovascular diseases in worldwide with around 9.88 million total new cases and 1.08 million were observed due to skin cancer in 2018. Amongst two types of skin cancer, progression of melanoma cancer is increasing day by day due to the environmental changes than non-melanoma cancer. Most of B-Raf mutation, specifically B-RafV600E, is responsible for the progression of the melanoma cancer. Here, various 3D-QSAR techniques like comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), molecular hologram QSAR (HQSAR) and topomer CoMFA were used to design novel B-Raf inhibitors by using 28 synthetic B-Raf inhibitors. Except for topomer CoMFA model, remaining models were generated by three different alignment methods in which distil-based alignment method was found best and gave prominent statistical values. After performing N-fold statistical validation, in CoMFA, q², r² and r²_pred values were found to be 0.638, 0.969 and 0.848, respectively. Similarly, q², r² and r²_pred values were found to be 0.796, 0.978 and 0.891 in CoMSIA (SHD) and 0.761, 0.973 and 0.852 in CoMSIA (SH) by N-fold statistical validation. In HQSAR analysis, statistical values were found for q² as 0.984, r² as 0.999 and r²_pred as 0.634 with 97 as best hologram length (BHL). The results of topomer CoMFA showed the q² value of 0.663 and the r² value of 0.967. Important features of purinylpyridine were identified by contour map analysis of all 3D-QSAR techniques, which could be useful to design the novel molecules as B-Raf inhibitors for the treatment of melanoma cancer.

     

CoMFA and CoMSIA 3D-quantitative structure-activity relationship model on benzodiazepine derivatives, inhibitors of phosphodiesterase IV

Recently, we reported structurally novel PDE4 inhibitors based on 1,4-benzodiazepine derivatives. The main interest in developing bezodiazepine-based PDE4 inhibitors is in their lack of adverse effects of emesis with respect to rolipram-like compounds. A large effort has thus been made toward the structural optimization of this series. In the absence of structural information on the inhibitor binding mode into the PDE4 active site, 2D-QSAR (H-QSAR) and two 3D-QSAR (CoMFA and CoMSIA) methods were applied to improve our understanding of the molecular mechanism controlling the PDE4 affinity of the benzodiazepine derivatives. As expected, the CoMSIA 3D contour maps have provided more information on the benzodiazepine interaction mode with the PDE4 active site whereas CoMFA has built the best tool for activity prediction. The 2D pharmacophoric model derived from CoMSIA fields is consistent with the crystal structure of the PDE4 active site reported recently. The combination of the 2D and 3D-QSAR models was used not only to predict new compounds from the structural optimization process, but also to screen a large library of bezodiazepine derivatives.     

CoMFA,CoMSIA, Topomer CoMFA,HQSAR, molecular docking and molecular dynamics simulations study of triazine morpholino derivatives as mTOR inhibitors for the treatment of breast cancer

mTOR has become a promising target for many types of cancer like breast, lung and renal cell carcinoma. CoMFA, CoMSIA, Topomer CoMFA and HQSAR were performed on the series of 39 triazine morpholino derivatives. CoMFA analysis showed q² value of 0.735, r²_cv value of 0.722 and r²_pred value of 0.769. CoMSIA analysis (SEHD) showed q² value of 0.761, r²_cv value of 0.775 and r²_pred value of 0.651. Topomer CoMFA analysis showed q² value of 0.693, r² (conventional correlation coefficient) value of 0.940 and r²_pred value of 0.720. HQSAR analysis showed q²,r²and r²_pred values of 0.694, 0.920 and 0.750, respectively. HQSAR analysis with the combination of atomic number (A), bond type (B) and atomic connections showed q² and r² values of 0.655 and 0.891, respectively. Contour maps from all studies provided significant insights. Molecular docking studies with molecular dynamics simulations were carried out on the highly potent compound 36. Furthermore, four acridine derivatives were designed and docking results of these designed compounds showed the same interactions as that of the standard PI-103 which proved the efficiency of 3D-QSAR and MD/MS study. In future, this study might be useful prior to synthesis for the designing of novel mTOR inhibitors.     

CoMFA and CoMSIA studies on 1,3-bis(benzylidene)-3,4-dihydro-1H-naphthalen-2-one, 2,6-bis(benzylidene)cyclohexanone, and 3,5-bis(benzylidene)-4-piperidone series of cytotoxic compounds

A number of 1,3-bis(benzylidene)-3,4-dihydro-1H-naphthalen-2-ones, 2,6-bis(benzylidene)cyclohexanones, and 3,5-bis(benzylidene)-4-piperidones possess significant potencies toward L1210, Molt 4/C8, and CEM cell lines. The objective of the current 3D QSAR study is to discover some of the structural parameters which govern cytotoxic potencies. The CoMFA models with steric and electrostatic fields provided satisfactory statistical data [(r2cv = 0.485, r2ncv = 0.834, r2pred = 0.591), (r2cv = 0.532, r2ncv = 0.850, r2pred = 0.729), and (r2cv = 0.561, r2ncv = 0.864, r2pred = 0.666)] in regard to the cytotoxic potencies observed toward L1210, Molt 4/C8, and CEM cell lines, respectively. The CoMSIA model with steric, electrostatic, hydrophobic, and H-bond donor fields exhibited r2cv = 0.513, r2ncv = 0.833, and r2pred = 0.562 for cytotoxic activity toward L1210 cells, while the best CoMSIA models were obtained by a combination of steric, electrostatic, and hydrophobic fields which yielded statistically significant data [(r2cv = 0.531, r2ncv = 0.828, r2pred = 0.652) and (r2cv = 0.560, r2ncv = 0.841, r2pred = 0.729)] to explain the cytotoxicity toward Molt 4/C8 and CEM cells, respectively. The information obtained from the CoMFA and CoMSIA 3D contour maps can be used in the design of more potent cytotoxins.     

Structural investigations of anthranilimide derivatives by CoMFA and CoMSIA 3D-QSAR studies reveal novel insight into their structures toward glycogen phosphorylase inhibition

In the present work, three-dimensional quantitative structure–activity relationship (3-D QSAR) studies on a set of 70 anthranilimide compounds has been performed using docking-based as well as substructure-based molecular alignments. This resulted in the selection of more statistically relevant substructure-based alignment for further studies. Further, molecular models with good predictive power were derived using CoMFA (r ^2?=?0.997; Q ^2?=?0.578) and CoMSIA (r ^2?=?0.976; Q ^2?=?0.506), for predicting the biological activity of new compounds. The so-developed contour plots identified several key features of the compounds explaining wide activity ranges. Based on the information derived from the CoMFA contour maps, novel leads were proposed which showed better predicted activity with respect to the already reported systems. Thus, the present study not only offers a highly significant predictive QSAR model for anthranilimide derivatives as glycogen phosphorylase (GP) inhibitors which can eventually assist and complement the rational drug-design attempts, but also proposes a highly predictive pharmacophore model as a guide for further development of selective and more potent GP inhibitors as anti-diabetic agents.     

A new concise synthesis of arcyriacyanin A and its unique inhibitory activity against a panel of human cancer cell line

The nucleophilic addition reaction of N-tosyl-4-oxo-4,5,6,7-tetrahydroindole (12) with the lithium salt of 1-methoxyindole (5), followed by dehydration with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) gave the derivative of 2,4'-bi-1H-indole (9) which provides a new concise synthetic method of an indole pigment of the slime mould, arcyriacyanin A. The compound was first demonstrated here to have unique inhibitory activity to a panel of human cancer cell lines and to inhibit protein kinase C and protein tyrosine kinase.     

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models for a series of thiazolone derivatives as novel inhibitors bound to the allosteric site of hepatitis C virus (HCV) NS5B polymerase were developed based on CoMFA and CoMSIA analyses. Two different conformations of the template molecule and the combinations of different CoMSIA field/fields were considered to build predictive CoMFA and CoMSIA models. The CoMFA and CoMSIA models with best predictive ability were obtained by the use of the template conformation from X-ray crystal structures. The best CoMFA and CoMSIA models gave q (2) values of 0.621 and 0.685, and r (2) values of 0.950 and 0.940, respectively for the 51 compounds in the training set. The predictive ability of the two models was also validated by using a test set of 16 compounds which gave r (pred) (2) values of 0.685 and 0.822, respectively. The information obtained from the CoMFA and CoMSIA 3D contour maps enables the interpretation of their structure-activity relationship and was also used to the design of several new inhibitors with improved activity.     

Palladium(II) N-heterocyclic carbene complexes: synthesis,structures and cytotoxicity potential studies against breast cancer cell line

Abstract

Mononuclear trans-Pd(II)–NHC complexes (where NHC?=?N-heterocyclic carbene) bearing asymmetrically substituted NHC-ligand have been synthesized via transmetalation reaction between Ag(I)–NHC complexes and [Pd(NCCH₃)₂Cl₂]. The NHC precursors are accessible in two steps by N-n-alkyl reactions of benzimidazole. The resultant benzimidazolium salts were deprotonated with Ag₂O by in situ deprotonation to facilitate the formation of mononuclear Ag(I)–NHC complexes. Single-crystal structural study for Pd(II)–NHC shows that the palladium(II) ion exhibits a square-planar geometry of two NHC ligands and two chloride ions. The cytotoxicity study was investigated against breast cancer cell line (MCF-7). The Ag(I)–NHC complexes exhibit better activities than their corresponding Pd(II)–NHC complexes, whereas all benzimidazolium salts are inactive toward MCF-7 cancer cell line.     

Design,synthesis of novel quinazolin-4-one derivatives and biological evaluation against human MCF-7 breast cancer cell line

A new series of 6,8-dibromo-2-(4-chlorophenyl)quinazolin-4(3H)-one derivatives VI–XIII were synthesized. Their chemical structures were confirmed by spectral and elemental analysis. The cytotoxic effect of the newly synthesized compounds was tested in vitro against human breast cancer cell line (MCF-7). Most of the tested compounds have shown promising cytotoxic activity. Compounds X and XIIIb exerted a powerful cytotoxic effect against MCF-7 with a very low IC50 (0.0015 and 0.0047 µmol/ml), while compounds VI, VII, VIII, XIIb, XI, XIIIc and IX exerted a moderate cytotoxic effect (IC50 0.01523, 0.0213, 0.031, 0.0478, 0.049, 0.068 and 0.079 µmol/ml respectively), compared to doxorubicin (0.0025 µmol/ml). Exploring their apoptotic effect; interestingly,all compounds activated apoptotic cascade in MCF-7. Compounds VI, XIIIb, XIIb, XI, XIIa, VII, V and VIII showed potent effect even much more than doxorubicin by 12.87–5.91 folds, while compounds XIIIc, IX, XIIIa, XIIc and X showed moderate increase in CASP3 activity by 4.96–3.22 folds relative to untreated cells more or less similar to doxorubicin (5.57 folds).     

New gold(III) chlorophenyl terpyridine complex: Biomolecular interactions and anticancer activity against human oral squamous cell carcinoma

In this work we synthesized new monofunctional gold(III) complex [Au(Cl-Ph-tpy)Cl]Cl₂ (Cl-Ph-tpy = 4′-[4-chlorophenyl]-2,2′:6′, 2″-terpyridine). This complex was characterized by UV–Vis, NMR, IR, and ESI-MS spectrometry. The kinetic study of the substitution reactions of the Au-Cl-Ph-tpy complex with biomolecules showed that the rate constants depend on the nature of the entering nucleophile. Based on the calculated values of entropy (∆H^≠ > 0) and enthalpy (∆S^≠ < 0) the proposed substitution mechanism is associative. Additionally, the relative stability and thermodynamic properties of Au-Cl-Ph-tpy complex were compared with the analogue Au-tpy complex by the B3LYP/def2-svp method. DNA/BSA binding studies showed that Au-Cl-Ph-tpy complex interacts with CT DNA through the intercalation and moderately quenches the fluorescence of tryptophan residues in serum albumin (BSA). Molecular docking confirmed results obtained by spectroscopic experiments and suggested site I (subdomain IIA) for binding of Au complex to BSA. We demonstrated that the Au chlorophenyl terpyridine complex possessed significant in vitro cytotoxic activity against human oral squamous carcinoma cells (CAL-27), induced apoptosis, inhibited proliferation of CAL-27 cells, and induced cell cycle disturbance. Treatment of CAL-27 cells with the Au complex enhanced expression of cyclin-dependent kinase inhibitors p21 and p27, resulting in cell cycle arrest in the G1 phase, reduced the percentage of CAL-27 cells in S phase and decreased expression of Ki-67. Additionally, Au complex reduced expression of phosphorylated STAT3 and downstream regulated molecules associated with cancer stemness, NANOG, and Sox2 protein.     

Psoralen derivatives and longwave ultraviolet irradiation are active in vitro against human melanoma cell line

Cutaneous malignant melanoma is a very serious form of skin cancer that arises from melanocytes. Currently there is no effective treatment for metastatic melanoma so intense clinical trials are evaluating new drugs for this human malignancy. Psoralens are a group of compounds that bind to DNA in rapidly dividing cells and with ultraviolet light in the A band (UVA) cause DNA crosslinking, thereby preventing cellular division. They are used in the treatment of psoriasis and cutaneous T-cell lymphoma among other skin and blood diseases. We have investigated the cytotoxic potential of three psoralen derivatives plus UVA exposure (PUVA) on a established cell line of human melanoma. Cells were treated with different concentrations of 8-methoxypsoralen (8-MOP), 4,5',8-trimethylpsoralen (TMP) and 7-methylpyridopsoralen (MPP), for 1 h and after exposure to UVA light (0.3 J/cm(2)) were allowed to recover over a 24-72 h period. Viability was assessed by the microculture 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay. Cisplatin, one of the most important drugs in the chemotherapy of melanoma, was included for comparative studies. All the psoralen derivatives tested were markedly cytotoxic in a dose and post-exposure-time dependent manner. The IC(50) values for 72 h of post-exposure time were as follows: MPP=0.05+/-0.01, TMP=0.13+/-0.003 and 8-MOP=10.79+/-1.85 micromol/L. Regardless of the limitations of the in vitro model, our results suggested that the lower IC(50) values of TMP and MPP might be of clinical importance.     

Photodynamic studies of metallo 5,10,15,20-tetrakis(4-methoxyphenyl) porphyrin: photochemical characterization and biological consequences in a human carcinoma cell line.

The photodynamic activities of the free-base 5,10,15,20-tetrakis(4-methoxyphenyl)porphyrin (TMP) and their metal complexes with zinc(II) (ZnTMP), copper(II) (CuTMP) and cadmium(II) (CdTMP) have been compared in two systems: reverse micelle of n-heptane/sodium bis(2-ethylhexyl)sulfosuccinate/water bearing photooxidizable substrates and Hep-2 human larynx carcinoma cell line. The quantum yields of singlet molecular oxygen, O2(1 delta g), production (phi delta) of TMP, ZnTMP and CdTMP in tetrahydrofuran, were determined yielding values of 0.65, 0.73 and 0.73, respectively, while O2(1 delta g) formation was not detected for CuTMP. In the reverse micellar system, the amino acid L-tryptophan (Trp) was used as biological substrate to analyze the O2(1 delta g)-mediated photooxidation. The observed rate constants for Trp photooxidation (kobsTrp) were proportional to the sensitizer quantum yield of O2(1 delta g). A value of approximately 2 x 10(7) s-1 M-1 was found for the second-order rate constant of Trp (krTry) in this system. The response of Hep-2 cells to cytotoxicity photoinduced by these agents in a biological medium was studied. The Hep-2 cultures were treated with 1 microM of porphyrin for 24 h at 37 degrees C and the cells exposed to visible light. The cell survival at different light exposure levels was dependent on phi delta. Under these conditions, the cytotoxic effect increases in the order: Cu-TMP < TMP < ZnTMP approximately CdTMP, correlating with the production of O2(1 delta g). A similar behavior was observed in both the chemical and biological media indicating that the O2(1 delta g) mediation appears to be mainly responsible for the cell inactivation.     

NMR and X-ray studies of the chromonic lyomesophases formed by some xanthone derivatives

Optical microscopy, NMR and X-ray measurements are presented for four chromonic lyomesogens derived from 9-xanthone. The measurements provide details about the mesogen-water binary phase diagrams of the four compounds as well as quantitative information about the ordering and structural parameters of the mesophases. All four systems exhibit peritectic phase diagrams with a nematic (N) phase at low mesogen concentration and a hexagonal (H) phase at high concentration. The results are consistent with previously suggested models for chromonic lyomesophases in which columnar aggregates are formed by stacked mesogenic molecules. In the N phase these columns are parallel to the director but are otherwise randomly distributed in the bulk solvent, while in the H phase they form a two dimensional hexagonal array.     

Highly predictive CoMFA and CoMSIA models for two series of stromelysin-1 (MMP-3) inhibitors elucidate S1' and S1-S2' binding modes

Three-dimensional quantitative structure-activity relationship models have been derived using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for two training sets of arylsulfonyl isoquinoline-based and thazine/thiazepine-based matrix metalloproteinase inhibitors (MMPIs). The crystal structure of stromelysin-1 (MMP-3) was used to pinpoint areas on the ligands and receptors where steric and electrostatic effects (for CoMFA) and steric, electrostatic, hydrogen-bond donor, hydrogen-bond acceptor, and hydrophobic effects (for CoMSIA) correlate with an increase or decrease in experimental biological activity. The most predictive CoMFA and CoMSIA models were obtained using training-series subsets that sampled a wide range of activities, together with docking and scoring, inertial alignment, investigation of various partial charge formalisms, and manual adjustment of each compound within the active site. The models developed in this study are in agreement with experimentally observed MMP-3 structure-activity relationship data and offer new insights into binding modes involving the partly solvent-exposed S1-S2' subpocket and certain zinc-chelating groups.     

Design,synthesis and cytotoxic activity of vitamin E bearing selenium compounds against human breast cancer cell line (MCF-7)

A new series of vitamin E/selenated pyridine, vitamin E/selenated pyridazine, vitamin E/selenated coumarine and vitamin E/selenated nicotine moieties were synthesized and their cytotoxic activity is investigated using the human breast cancer cell line. The newly synthesized compounds were characterized using spectroscopic tools (IR, ¹H NMR, ¹³C NMR, and mass spectroscopy) as well as microanalysis. Our study reveals that compound vitamin E/selenated nicotine moiety has the highest cytotoxic effect than the other synthesized compounds.