Comparative QSAR modeling of CCR5 receptor binding affinity of substituted 1-(3,3-diphenylpropyl)-piperidinyl amides and ureas

A structural-chemical explanation of fungal laccase activity

Fungal laccases (EC 1.10.3.2) are multi-copper oxidases that oxidize a wide variety of substrates. Despite extensive studies, the molecular basis for their diverse activity is unclear. Notably, there is no current way to rationally predict the activity of a laccase toward a given substrate. Such knowledge would greatly facilitate the rational design of new laccases for technological purposes. We report a study of three datasets of experimental K_m values and activities for Trametes versicolor and Cerrena unicolor laccase, using a range of protein modeling techniques. We identify diverse binding modes of the various substrates and confirm an important role of Asp-206 and His-458 (T. versicolor laccase numbering) in guiding substrate recognition. Importantly, we demonstrate that experimental K_m values correlate with binding affinities computed by MMGBSA. This confirms the common assumption that the protein-substrate affinity is a major contributor to observed K_m. From quantitative structure-activity relations (QSAR) we identify physicochemical properties that correlate with observed K_m and activities. In particular, the ionization potential, shape, and binding affinity of the substrate largely determine the enzyme’s K_m for the particular substrate. Our results suggest that K_m is not just a binding constant but also contains features of the enzymatic activity. In addition, we identify QSAR models with only a few descriptors showing that phenolic substrates employ optimal hydrophobic packing to reach the T1 site, but then require additional electronic properties to engage in the subsequent electron transfer. Our results advance our ability to model laccase activity and lend promise to future rational optimization of laccases toward phenolic substrates.

Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation

C-C chemokine receptor type 5 (CCR5) is the co-receptor of human immunodeficiency virus type 1 (HIV-1) and plays an important role in HIV-1 virus infection. Maraviroc has been proved to be effective for anti-HIV-1 by targeting CCR5. Understanding the detailed interaction mechanism between CCR5 and Maraviroc will be of great help to the rational design of a more potential inverse agonist to block HIV-1 infection. Here, we performed molecular dynamics (MD) simulation and accelerated MD simulation (aMD) to study the interaction mechanism between CCR5 and Maraviroc based on a recently reported crystal structure. The results of MD simulation demonstrate that Maraviroc can form stable hydrogen bonds with residues Tyr37(1.39), Tyr251(6.51) and Glu283(7.39). The results of aMD simulation indicate that the carboxamide moiety is more flexible than the tropane group of Maraviroc in the pocket of CCR5. The electrostatic potential analysis proves that Maraviroc can escape from the pocket of CCR5 along the negative electrostatic potential pathway during the dissociation process. The free energy calculation illustrates that there exist three binding pockets during the dissociation process of Maraviroc. Our results will be useful for understanding the interaction mechanism between CCR5 and Maraviroc as well as for the rational design of a more potent inverse agonist.

Designing hypothesis of substituted benzoxazinones as HIV-1 reverse transcriptase inhibitors: QSAR approach

A linear quantitative structure activity relationship (QSAR) model is presented for predicting human immunodeficiency virus-1 (HIV-1) reverse transcriptase enzyme inhibition. The 2D QSAR and 3D-QSAR models were developed by stepwise multiple linear regression, partial least square (PLS) regression and k-nearest neighbor-molecular field analysis, PLS regression, respectively using a database consisting of 33 recently discovered benzoxazinones. The primary findings of this study is that the number of hydrogen atoms, number of (-NH2) group connected with solitary single bond alters the inhibition of HIV-1 reverse transcriptase. Further, presence of electrostatic, hydrophobic and steric field descriptors significantly affects the ability of benzoxazinone derivatives to inhibit HIV-1 reverse transcriptase. The selected descriptors could serve as a primer for the design of novel and potent antagonists of HIV-1 reverse transcriptase.

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.

Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection

The HIV replication cycle offers multiple targets for chemotherapeutic intervention, including the viral exterior envelope glycoprotein, gp120; viral co-receptors CXCR4 and CCR5; transmembrane glycoprotein, gp41; integrase; reverse transcriptase; protease and so on. Most currently used anti-HIV drugs are reverse transcriptase inhibitors or protease inhibitors. The expanding application of simulation to drug design combined with experimental techniques have developed a large amount of novel inhibitors that interact specifically with targets besides transcriptase and protease. This review presents details of the anti-HIV inhibitors discovered with computer-aided approaches and provides an overview of the recent five-year achievements in the treatment of HIV infection and the application of computational methods to current drug design.

Quantitative structure-activity relationships studies of CCR5 inhibitors and toxicity of aromatic compounds using gene expression programming

Quantitative structure-activity relationship (QSAR) study of chemokine receptor 5 (CCR5) binding affinity of substituted 1-(3,3-diphenylpropyl)-piperidinyl amides and ureas and toxicity of aromatic compounds have been performed. The gene expression programming (GEP) was used to select variables and produce nonlinear QSAR models simultaneously using the selected variables. In our GEP implementation, a simple and convenient method was proposed to infer the K-expression from the number of arguments of the function in a gene, without building the expression tree. The results were compared to those obtained by artificial neural network (ANN) and support vector machine (SVM). It has been demonstrated that the GEP is a useful tool for QSAR modeling.

Current mathematical methods used in QSAR/QSPR studies

This paper gives an overview of the mathematical methods currently used in quantitative structure-activity/property relationship (QASR/QSPR) studies. Recently, the mathematical methods applied to the regression of QASR/QSPR models are developing very fast, and new methods, such as Gene Expression Programming (GEP), Project Pursuit Regression (PPR) and Local Lazy Regression (LLR) have appeared on the QASR/QSPR stage. At the same time, the earlier methods, including Multiple Linear Regression (MLR), Partial Least Squares (PLS), Neural Networks (NN), Support Vector Machine (SVM) and so on, are being upgraded to improve their performance in QASR/QSPR studies. These new and upgraded methods and algorithms are described in detail, and their advantages and disadvantages are evaluated and discussed, to show their application potential in QASR/QSPR studies in the future.

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.

3D-QSAR studies of substituted 1-(3, 3-diphenylpropyl)-piperidinyl amides and ureas as CCR5 receptor antagonists

3D-QSAR studies on the derivatives of 1-(3,3-diphenylpropyl)-piperidinyl amide and urea as CCR5 receptor antagonists were performed by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA) methods to rationalize the structural requirements responsible for the inhibitory activity of these compounds. The global minimum energy conformer of the template molecule, the most active and pharmacokinetically stable molecule of the series, was obtained by systematic search and used to build structures of the molecules in the dataset. The best predictions for the CCR5-receptor were obtained with the CoMFA standard model (q (2) = 0.787, r (2) = 0.962) and CoMSIA model combined steric, electrostatic and hydrophobic fields (q (2) = 0.809, r (2) = 0.951). The predictive ability of CoMFA and CoMSIA were determined using a test set of 12 compounds giving predictive correlation coefficients of 0.855 and 0.83, respectively, indicating good predictive power. Further, the robustness of the model was verified by bootstrapping analysis. The contour maps produced by the CoMFA and CoMSIA models were used to identify the structural features relevant to the biological activity in this series. Based on the CoMFA and CoMSIA analysis, we have identified some key features in the series that are responsible for CCR5 antagonistic activity which may be used to design more potent 1-(3,3-diphenylpropyl)-piperidinyl derivatives and predict their activity prior to synthesis.