Exploring QSAR on 3-aminopyrazoles as antitumor agents for their inhibitory activity of CDK2/cyclin A

Synthesis, in vitro inhibition effect of novel phthalocyanine complexes as carbonic anhydrase and paraoxonase enzyme inhibitors

The preparation and assessment of carbonic anhydrase and paraoxonase enzyme inhibition properties of 3-(2-(5-amino-4-(4-bromophenyl)-3-methyl-1H-pyrazol-1-yl)ethoxy)phthalonitrile (2) and its nitrogen-containing non-peripheral phthalocyanine derivatives (3 and 4) are reported for the first time. The new phthalonitrile and its phthalocyanine derivatives have been elucidated by FT-IR spectroscopy, 1H-NMR, [Formula: see text]C-NMR, mass and UV-vis spectroscopy. The results demonstrated that all synthesized compounds moderately inhibited carbonic anhydrase and paraoxonase enzymes. Among the compounds, the most active ones were found to be compound 4 for PON (Ki : 0.14 [Formula: see text]M), compound 3 for hCA I (Ki : 22.52 [Formula: see text]M) and compound 1 for hCA II (Ki : 13.62 [Formula: see text]M).

Recent advances on CDK inhibitors: An insight by means of in silico methods

The cyclin dependent kinases (CDKs) are a small family of serine/threonine protein kinases that can act as a potential therapeutic target in several proliferative diseases, including cancer. This short review is a survey on the more recent research progresses in the field achieved by using in silico methods. All the "armamentarium" available to the medicinal chemists (docking protocols and molecular dynamics, fragment-based, de novo design, virtual screening, and QSAR) has been employed to the discovery of new, potent, and selective inhibitors of cyclin dependent kinases. The results cited herein can be useful to understand the nature of the inhibitor-target interactions, and furnish an insight on the structural/molecular requirements necessary to achieve the required selectivity against cyclin dependent kinases over other types of kinases.

Towards cheminformatics-based estimation of drug therapeutic index: Predicting the protective index of anticonvulsants using a new quantitative structure-index relationship approach

The overall efficacy and safety profile of a new drug is partially evaluated by the therapeutic index in clinical studies and by the protective index (PI) in preclinical studies. In-silico predictive methods may facilitate the assessment of these indicators. Although QSAR and QSTR models can be used for predicting PI, their predictive capability has not been evaluated. To test this capability, we developed QSAR and QSTR models for predicting the activity and toxicity of anticonvulsants at accuracy levels above the literature-reported threshold (LT) of good QSAR models as tested by both the internal 5-fold cross validation and external validation method. These models showed significantly compromised PI predictive capability due to the cumulative errors of the QSAR and QSTR models. Therefore, in this investigation a new quantitative structure-index relationship (QSIR) model was devised and it showed improved PI predictive capability that superseded the LT of good QSAR models. The QSAR, QSTR and QSIR models were developed using support vector regression (SVR) method with the parameters optimized by using the greedy search method. The molecular descriptors relevant to the prediction of anticonvulsant activities, toxicities and PIs were analyzed by a recursive feature elimination method. The selected molecular descriptors are primarily associated with the drug-like, pharmacological and toxicological features and those used in the published anticonvulsant QSAR and QSTR models. This study suggested that QSIR is useful for estimating the therapeutic index of drug candidates.

An in silico exploration of the interaction mechanism of pyrazolo[1,5-a]pyrimidine type CDK2 inhibitors

CDK2, which interacts with cyclin A and cyclin E, is an important member of the CDK family. Having been proved to be associated with many diseases for its vital role in cell cycle, CDK2 is a promising target of anti-cancer drugs dealing with cell cycle disorders. In the present work, a total of 111 pyrazolo[1,5-a]pyrimidines (PHTPPs) as CDK2/cyclin A inhibitors were studied to conduct three-dimensional quantitative structure-activity (3D-QSAR) analyses. The optimal comparative molecular similarity indices analysis (CoMSIA) model shows that Q(2) = 0.516, Rncv(2) = 0.912, Rpre(2) = 0.914, Rm(2) = 0.843, SEP = 0.812, SEE = 0.347 with 10 components using steric, hydrophobic and H-bond donor field descriptors, indicating its effective internal and external predictive capacity. The contour maps further indicate that (1) bulky substituents in R1 are beneficial while H-bond donor groups at this position are detrimental; (2) hydrophobic contributions in the R2 area are favorable; (3) large and hydrophilic groups are well tolerated at the R3 position (a close H-bond donor moiety is favorable while a distal H-bond donor moiety in this area is disfavored); (4) bulky and hydrophobic features in the R4 region are beneficial for the biological activities and (5) the 7-N-aryl substitution is crucial to boost the inhibitory activities of the PHTPP inhibitors. Finally, docking and MD simulations demostrate that PHTPP derivatives are stabilized in a 'flying bat' conformation mainly through the H-bond interactions and hydrophobic contacts. Comparative studies indicate that PHTPP derivatives fit well within the ATP binding cleft in CDK2, with the core heterocyclic ring overlapping significantly with the adenine group of ATP despite a small deflection. In comparison to numerous other inhibitors binding to the ATP pocket, PHTPP analogues follow the binding fashion of purine inhibitors of this kinase. It is anticipated that the binding mechanism and structural features of PHTPP inhibitors studied in the present work will benefit the discovery of more potent CDK2 inhibitors, and the valid pyrazolo[1,5-a]pyrimidine-7-N-yl inhibitors will soon emerge from the large number of screening programmes to enter in clinical studies.

Exploring structural requirements of 1-N-substituted thiocarbamoyl-3-phenyl-2-pyrazolines as antiamoebic agents using comparative QSAR modelling

Amoebiasis is a potentially lethal disease and causes 70,000 deaths per year. To find structural requirements for more active antiamoebic agents than metronidazole, comparative QSAR modelling was done on thirty 1-N-substituted thiocarbamoyl-3-phenyl-2-pyrazolines. The best model was obtained by using PLS technique with R(A)(2) and R(CV)(2) value of 88.50% and 82.90%, respectively. Amoebicidal activity may increase when Wang-Ford charges at atom numbers 6 and 12 have large positive values. Number of six-membered ring and sum of Kier-Hall electrotopological states may also increase amoebicidal activity when these have large positive values. Increasing value of rotatable bond fraction, approximate surface area and mean atomic polarizability scaled on carbon atom may be detrimental for antiamoebic activity. Decrease in values of electrostatic potential charges at atom numbers 1 and 12 may be conducive for activity. Electrophilic attacks may be favourable at these positions.

Predictive comparative QSAR modelling of (phenylpiperazinyl-alkyl) oxindoles as selective 5-HT1A antagonists by stepwise regression, PCRA, FA-MLR and PLS techniques

5-Hydroxytryptamine, a neurotransmitter released by 5-HT neurons in raphe nuclei and 5-HT(1A) receptors are involved in the pain mechanism of migraine, prevention of postpartum haemorrhage, CNS effects like sleep, anxiety and thermoregulation. Comparative QSAR study was done on thirtytwo (phenylpiperazinyl-alkyl) oxindoles using stepwise regression, PCRA, FA-MLR and PLS techniques to find structurally significant models. ETSA indices at atom numbers 19, 20 and 22, RTSA indices at atom numbers 6, 10 and 20, charge at atom number 19 and presence of chlorine at the atom number 6 may be conducive for the receptor inhibition. Electrophilic attack at atom number 21 may be unfavourable but nucleophilic attack at atom numbers 8 and 14 may be beneficial for % 5-HT(1A) inhibition.

Structural finding of R/S-3,4-dihydro-2,2-dimethyl-6-halo-4-(substituted phenylaminocarbonylamino)-2H-1-benzopyrans as selective pancreatic β-cells KATP-pβ channel openers

R/S-3,4-Dihydro-2,2-dimethyl-6-halo-4-(substituted phenylaminocarbonyl-amino)-2H-1-benzopyrans are pancreatic β-cells potassium (KATP-pβ) channel openers with inhibitory effect on insulin secretion. To find the more active and effective benzopyrans as selective potassium (KATP-pβ) channel openers towards the pancreatic tissues, quantitative structure–activity relationships (QSAR) study was performed using E-state and R-state indices along with Wang–Ford charges, n-octanol/water partition coefficient, molar refractivity, and indicator parameters. QSAR models were developed by statistical techniques, e.g., multiple linear regression (MLR), principle component regression analysis (PCRA), and partial least squares (PLS) analysis. The generated equations were validated by the leave-one-out cross-validation method. The models show the importance of ETSA indices of atom numbers 16, 17, 18, 19, 21 as well as 22. The positive coefficient of S16, S17, S18, S19, S21, and S22 indicate that with the increase of the value of E-state indices, desired activity decreases. RTSA index is also important for the biological activity, and the atom numbers 16, 17, 18, 19, 20 and 22 are involved in van der Waals interactions. RTSA index also possesses negative impact on the inhibition of residual insulin secretion. Wang–Ford charges of some particular atoms are also important for the inhibition. Increase of n-octanol/water partition coefficients of compounds inhibit insulin secretion, and the presence of chlorine atom at m- and p- positions of the phenyl ring B is necessary for the inhibition of residual insulin secretion.Key words: benzopyran derivatives, potassium channel openers, PCRA, PLS, QSAR.