Navigating the chemical space of dipeptidyl peptidase-4 inhibitors.

This study represents the first large-scale study on the chemical space of inhibitors of dipeptidyl peptidase-4 (DPP4), which is a potential therapeutic protein target for the treatment of diabetes mellitus. Herein, a large set of 2,937 compounds evaluated for their ability to inhibit DPP4 was compiled from the literature. Molecular descriptors were generated from the geometrically optimized low-energy conformers of these compounds at the semiempirical AM1 level. The origins of DPP4 inhibitory activity were elucidated from computed molecular descriptors that accounted for the unique physicochemical properties inherently present in the active and inactive sets of compounds as defined by their respective half maximal inhibitory concentration values of less than 1 µM and greater than 10 µM, respectively. Decision tree analysis revealed the importance of molecular weight, total energy of a molecule, topological polar surface area, lowest unoccupied molecular orbital, and number of hydrogen-bond donors, which correspond to molecular size, energy, surface polarity, electron acceptors, and hydrogen bond donors, respectively. The prediction model was subjected to rigorous independent testing via three external sets. Scaffold and chemical fragment analysis was also performed on these active and inactive sets of compounds to shed light on the distinguishing features of the functional moieties. Docking of representative active DPP4 inhibitors was also performed to unravel key interacting residues. The results of this study are anticipated to be useful in guiding the rational design of novel and robust DPP4 inhibitors for the treatment of diabetes.

Probing the origins of 17ß-hydroxysteroid dehydrogenase type 1 inhibitory activity via QSAR and molecular docking.

It is generally known that proliferation of human breast cancer cells is stimulated by excess estrogen namely 17ß-estradiol. Therefore, reduction of 17ß-estradiol production by inhibiting 17ß-hydroxysteroid dehydrogenase type 1 (17ß-HSD1) is an interesting route for breast cancer treatment particularly during adjuvant therapy. This study investigated the structure-activity relationship of 17ß-HSD1 inhibitors as to gain insights and understanding on the origins of 17ß-HSD1 inhibitory activities. To meet this goal, multiple linear regression model was constructed and correspondingly the results revealed good predictivity (N = 31, R(2) = 0.9438, Q(2) = 0.8530). The model suggested that low molecular weight and energy were preferred as 17ß-HSD1 inhibitors. Additionally, high molecular flexibility and high number of hydrogen bond donors were also shown to be important that is in correspondence to previously reported pharmacophore model of 17ß-HSD1 inhibitors. Furthermore, molecular docking of inhibitors to 17ß-HSD1 followed by anchor analysis suggested that three different pockets comprising of hydrogen bonding sites 1 and 2 as well as van der Waals contacts contributed to protein-ligand interactions. Post-docking analysis of potent compound 9 with 17ß-HSD1 suggested that the binding modality was similar to the binding of substrate (i.e. estradiol) and its analog (i.e. equilin). Such information is useful in guiding the further design of novel and robust 17ß-HSD1 inhibitors.

Predictive QSAR modeling of aldose reductase inhibitors using Monte Carlo feature selection.

This study explores the chemical space and quantitative structure-activity relationship (QSAR) of a set of 60 sulfonylpyridazinones with aldose reductase inhibitory activity. The physicochemical properties of the investigated compounds were described by a total of 3230 descriptors comprising of 6 quantum chemical descriptors and 3224 molecular descriptors. A subset of 5 descriptors was selected from the aforementioned pool by means of Monte Carlo (MC) feature selection coupled to multiple linear regression (MLR). Predictive QSAR models were then constructed by MLR, support vector machine and artificial neural network, which afforded good predictive performance as deduced from internal and external validation. The investigated models are capable of accounting for the origins of aldose reductase inhibitory activity and could be utilized in predicting this property in screening for novel and robust compounds.

Insights into antioxidant activity of 1-adamantylthiopyridine analogs using multiple linear regression.

A data set of 1-adamantylthiopyridine analogs (1-19) with antioxidant activity, comprising of 2,2-diphenyl-1-picrylhydrazyl (DPPH) and superoxide dismutase (SOD) activities, was used for constructing quantitative structure-activity relationship (QSAR) models. Molecular structures were geometrically optimized at B3LYP/6-31g(d) level and subjected for further molecular descriptor calculation using Dragon software. Multiple linear regression (MLR) was employed for the development of QSAR models using 3 significant descriptors (i.e. Mor29e, F04[N-N] and GATS5v) for predicting the DPPH activity and 2 essential descriptors (i.e. EEig06r and Mor06v) for predicting the SOD activity. Such molecular descriptors accounted for the effects and positions of substituent groups (R) on the 1-adamantylthiopyridine ring. The results showed that high atomic electronegativity of polar substituent group (R = CO2H) afforded high DPPH activity, while substituent with high atomic van der Waals volumes such as R = Br gave high SOD activity. Leave-one-out cross-validation (LOO-CV) and external test set were used for model validation. Correlation coefficient (QCV) and root mean squared error (RMSECV) of the LOO-CV set for predicting DPPH activity were 0.5784 and 8.3440, respectively, while QExt and RMSEExt of external test set corresponded to 0.7353 and 4.2721, respectively. Furthermore, QCV and RMSECV values of the LOO-CV set for predicting SOD activity were 0.7549 and 5.6380, respectively. The QSAR model's equation was then used in predicting the SOD activity of tested compounds and these were subsequently verified experimentally. It was observed that the experimental activity was more potent than the predicted activity. Structure-activity relationships of significant descriptors governing antioxidant activity are also discussed. The QSAR models investigated herein are anticipated to be useful in the rational design and development of novel compounds with antioxidant activity.

Exploring the chemical space of aromatase inhibitors.

Aromatase, a rate-limiting enzyme catalyzing the conversion of androgen to estrogen, is overexpressed in human breast cancer tissue. Aromatase inhibitors (AIs) have been used for the treatment of estrogen-dependent breast cancer in post-menopausal women by blocking the biosynthesis of estrogen. The undesirable side effects in current AIs have called for continued pursuit for novel candidates with aromatase inhibitory properties. This study explores the chemical space of all known AIs as a function of their physicochemical properties by means of univariate (i.e., statistical and histogram analysis) and multivariate (i.e., decision tree and principal component analysis) approaches in order to understand the origins of aromatase inhibitory activity. Such a non-redundant set of AIs spans a total of 973 compounds encompassing both steroidal and non-steroidal inhibitors. Substructure analysis of the molecular fragments provided pertinent information on the structural features important for ligands providing high and low aromatase inhibition. Analyses were performed on data sets stratified according to their structural scaffolds (i.e., steroids and non-steroids) and bioactivities (i.e., actives and inactives). These analyses have uncover a set of rules characteristic to active and inactive AIs as well as revealing the constituents giving rise to potent aromatase inhibition.

Machine learning approaches for discerning intercorrelation of hematological parameters and glucose level for identification of diabetes mellitus.

BACKGROUND: The aim of this study is to explore the relationship between hematological parameters and glycemic status in the establishment of quantitative population-health relationship (QPHR) model for identifying individuals with or without diabetes mellitus (DM). METHODS: A cross-sectional investigation of 190 participants residing in Nakhon Pathom, Thailand in January-March, 2013 was used in this study. Individuals were classified into 3 groups based on their blood glucose levels (normal, Pre-DM and DM). Hematological (white blood cell (WBC), red blood cell (RBC), hemoglobin (Hb) and hematocrite (Hct)) and glucose parameters were used as input variables while the glycemic status was used as output variable. Support vector machine (SVM) and artificial neural network (ANN) are machine learning approaches that were employed for identifying the glycemic status while association analysis (AA) was utilized in discovery of health parameters that frequently occur together. RESULTS: Relationship amongst hematological parameters and glucose level indicated that the glycemic status (normal, Pre-DM and DM) was well correlated with WBC, RBC, Hb and Hct. SVM and ANN achieved accuracy of more than 98 % in classifying the glycemic status. Furthermore, AA analysis provided association rules for defining individuals with or without DM. Interestingly, rules for the Pre-DM group are associated with high levels of WBC, RBC, Hb and Hct. Conclusion This study presents the utilization of machine learning approaches for identification of DM status as well as in the discovery of frequently occurring parameters. Such predictive models provided high classification accuracy as well as pertinent rules in defining DM.