Combinatorial Chemistry & High Throughput Screening - Volume 19, Issue 6, 2016

Tubulin is a potent molecular target for development of anticancer agents. In this report, the binding of non-steroidal anti-inflammatory drugs as tubulin inhibitors potential are investigated by extensive computational techniques, such as, molecular docking, molecular dynamics simulations and binding free energy calculations. The results suggest that a potent indomethacin derivative inhibits the tubulin polymerization by interacting on the colchicine-site binding. This potential chemotherapeutic agent showed high stability in the molecular dynamics simulations, when complexed on the same binding site of colchicine, a potent and toxic, tubulin inhibitor. Then, our results can be useful designing new compounds for cancer treatments.

New synthesized compounds, particularly those with biological activity, are potential drug candidates. This article describes experimental studies performed to estimate lipophilicity parameters of new 3-(4-substituted benzyl)-5-phenylhydantoins. Lipophilicity, as one of the most important molecular characteristics for the activity, was determined using the reversed-phase liquid chromatography (RP-18 stationary phase and methanol-water mobile phase). Molecular structures were used to generate in silico data which were used to estimate pharmacokinetic properties of the investigated compounds. The results show that generally, the investigated compounds attain good bioavailability properties. A more detailed analysis shows that the presence of a nitro, methoxy and tert-butyl group in the molecule is indicated as unfavorable for the oral bioavailability of hydantoins. Multivariate exploratory analysis was used in order to visualize grouping patterns among molecular descriptors as well as among the investigated compounds. Molecular docking study performed for two hydantoins with the highest bioavailability scores shows high binding affinity to tyrosine kinase receptor IGF-1R. The results achieved can be useful as a template for future development and further derivation or modification to obtain more potent and selective antitumor agents.

In the present work, molecular modeling studies have been reported on a series of diazine indole acetic acid derivatives to analyze the structure-activity relationship studies of CRTH2 using fragment (Topomer CoMFA and HQSAR) and field (CoMFA and CoMSIA) based QSAR methods. Twenty-six compounds were used as a training set to establish the model, and six compounds were used as a test set to validate the model. The generated models exhibited good statistical results such as correlation coefficient (r2) and the cross-validated correlation coefficient (q2). Topomer CoMFA analysis yielded the q2 of 0.610 and r2 of 0.981. HQSAR model generated using bond and connectivity as fragment distinction and 3-6 as fragment size has the q2 value of 0.707 and conventional r2 value of 0.892 with five components. CoMFA model was assessed by cross-validated q2 value of 0.543 and r2 value of 0.901 with steric and electrostatic fields. CoMSIA model generated using steric, hydrophobic and donor fields with q2 value of 0.550 and r2 value of 0.888 was found to be the optimal model among the various models generated. The contour maps were generated to analyze the important structural features that regulate their inhibitory potency. From the result of contour maps we have suggested the critical sites for chemical modification which will be useful in designing potent compounds with improved activity.

An early prediction of physicochemical properties is highly desirable during drug discovery to find out a viable lead candidate. Although there are several methods available to determine partition coefficient (log P), distribution coefficient (log D) and ionization constant (pKa), none of them involves simple and fixed, miniaturized protocols for diverse set of compounds. Therefore, it is necessary to establish simple, uniform and medium-throughput protocols requiring small sample quantities for the determination of these physicochemical properties. Log P and log D were determined by shake flask method, wherein, the compound was partitioned between presaturated noctanol and water phase (water/PBS pH 7.4) and the concentration of compound in each phase was determined by HPLC. The pKa determination made use of UV spectrophotometric analysis in a 96-well microtiter plate containing a series of aqueous buffers ranging from pH 1.0 to 13.0. The medium-throughput miniaturized protocols described herein, for determination of log P, log D and pKa, are straightforward to set up and require very small quantities of sample (< 5 mg for all three properties). All established protocols were validated using diverse set of compounds.

β-secretase (BACE1) is an aspartyl protease, which is considered as a novel vital target in Alzheimer's disease therapy. We collected a data set of 294 BACE1 inhibitors, and built six classification models to discriminate active and weakly active inhibitors using Kohonen’s Self-Organizing Map (SOM) method and Support Vector Machine (SVM) method. Each molecular descriptor was calculated using the program ADRIANA.Code. We adopted two different methods: random method and Self-Organizing Map method, for training/test set split. The descriptors were selected by F-score and stepwise linear regression analysis. The best SVM model Model2C has a good prediction performance on test set with prediction accuracy, sensitivity (SE), specificity (SP) and Matthews correlation coefficient (MCC) of 89.02%, 90%, 88%, 0.78, respectively. Model 1A is the best SOM model, whose accuracy and MCC of the test set were 94.57% and 0.98, respectively. The lone pair electronegativity and polarizability related descriptors importantly contributed to bioactivity of BACE1 inhibitor. The Extended-Connectivity Finger-Prints_4 (ECFP_4) analysis found some vitally key substructural features, which could be helpful for further drug design research. The SOM and SVM models built in this study can be obtained from the authors by email or other contacts.

The important factor which differentiates gemini surfactants from conventional monomeric surfactants is the spacer group. The molecular connectivity method was used to study the effect of the spacer group on critical micelle concentration of cationic gemini surfactants. Two models were derived employing only Kier and Hall molecular connectivity indices. The relationships were developed for a set of 17 gemini surfactants with various spacer groups only. These models can be used to design the structure of the spacer group and in consequence novel cationic gemini surfactants more active in micelle formation.

Aims: A series of acylated coumarin derivatives have been evaluated for their in silico ADMET properties and in vitro antibacterial activities. Methods and Results: In silico analysis confirmed their physicochemical properties in conformation with various layout filters and further their ADMET properties were predicted. Antibacterial activities were evaluated by Resazurin based microbroth dilution assay against standard Gram positive bacteria: Staphylococcus aureus (MTCC No. 3160) and Bacillus cereus (MTCC No. 10085). When used alone, these derivatives showed higher MIC values. However, in combination with standard drugs they exhibited synergistic effects according to fractional inhibitory concentration index. The synergistic effect was further confirmed by time kill curves. Their cytotoxity was evaluated by haemolytic assay and they were found to be non-toxic upto a concentrations of 500 μg ml-1. Conclusion: The data support the potential use of acylated coumarin derivatives as next generation adjuvants as evaluated by their in silico ADMET analysis and in vitro antibacterial and cytotoxicity evaluation. Further research involving these combinations is warranted. Significance and Impact of the Study: This study suggests that acylated coumarin derivatives act as antibacterial adjuvants in combination with standard drugs and have potential to be used in pharmaceutical preparations.

P-glycoprotein (P-gp) is well known to cause multidrug resistance (MDR) in cancer cells. This MDR leads to cancer recurrence which is a major obstacle in cancer treatment. High P-gp expression has been observed in the population of cancer stem cells (CSCs) having self-renewal potential. Early detection and inhibition of these CSCs is directly beneficial to cancer treatment. In this study coumarin derivatives are used to inhibit efflux process and thereby enhance bioavailability of various drugs like paclitaxel (PTX). This drug is most commonly used for the treatment of cancers of breast, ovary, head and neck. Coumarin derivatives can be used to reduce the growth of breast cancer stem cells through P-gp mediated efflux inhibition and paclitaxel bioavailability enhancement. With the use of computational approaches including molecular docking simulation and pharmacophore study, few coumarin derivatives have been found to be more potential inhibitors of P-gp mediated efflux. Based on high affinity inhibitors, new coumarin derivatives have been designed and docked at active site cavity of P-gps. Some newly designed coumarin derivatives were found to be more potent due to their higher binding affinity towards target protein. The finding that newly designed coumarins can be exploited for inhibition of P-gp mediated efflux in order to enhance paclitaxel bioavailability and can inhibit breast cancer stem cell growth is significant for designing potent anticancer drugs.

Local anesthetics are the most widely consumed drugs in the practice of medicine which provide a loss of sensation in a certain body part without loss of consciousness or impairment of central control of essential functions. Lidocaine (I) is the most commonly local anaesthetic drug which is widely used in all species due to its fabulous diffusing and penetrating properties as well as prompt onset of surgical analgesia. In this study, new aminobenzothiazole (with many useful biological and pharmacological properties) analogues were synthesized by changing of amine moiety of I. Both acute and chronic pain properties of new compounds (II-VI) were studied by using the tail immersion and formalin tests on mice and the outcomes were compared with control and lidocaine groups. According to the results, aminobenzothiazole derivatives are better candidates than diethylamine group for replacement on amine moiety of I. Also, derivatives with electron-withdrawing groups on this amine (V and VI) could decrease pain better than electron-donating ones (II and III) (specially on position 6 of this amine, II and V) which may be of concern for blockade of specific sodium channels by these new compounds.