From SAR to comparative QSAR: role of hydrophobicity in the design of 4-hydroxy-5,6-dihydropyran-2-ones HIV-1 protease inhibitors

A robust, viable, and resource sparing HPLC-based logP method applied to common drugs

Reliable, experimentally determined partition coefficient P (logP) for most drugs are often unavailable in the literature. Many values are from in silico predictions and may not accurately reflect drug lipophilicity. In this study, a robust, viable, and resource sparing method to measure logP was developed using reverse phase high performance liquid chromatography (RP-HPLC). The logP of twelve common drugs was measured using calibration curves at pH 6 and 9 that were created using reference standards with well-established logP. The HPLC method reported here can be used for high throughput estimation of logP of commonly used drugs. LogP values here showed general agreement with the other few HPLC-based literature logP values available. Additionally, the HPLC-based logP values found here agreed partially with literature logP values found using other methodologies (±10%). However, there was no strong agreement since there are few experimentally determined literature logP values. This paper shows a facile method to estimate logP without using octanol or computational approaches. This method has excellent promise to provide reliable logP values of commonly used drugs available in literature. A larger pool of reliable logP values of commonly drugs has promise to improve quality of medicinal chemistry and pharmacokinetic (PK) models.

Hybrid-genetic algorithm based descriptor optimization and QSAR models for predicting the biological activity of Tipranavir analogs for HIV protease inhibition

The prediction of biological activity of a chemical compound from its structural features plays an important role in drug design. In this paper, we discuss the quantitative structure activity relationship (QSAR) prediction models developed on a dataset of 170 HIV protease enzyme inhibitors. Various chemical descriptors that encode hydrophobic, topological, geometrical and electronic properties are calculated to represent the structures of the molecules in the dataset. We use the hybrid-GA (genetic algorithm) optimization technique for descriptor space reduction. The linear multiple regression analysis (MLR), correlation-based feature selection (CFS), non-linear decision tree (DT), and artificial neural network (ANN) approaches are used as fitness functions. The selected descriptors represent the overall descriptor space and account well for the binding nature of the considered dataset. These selected features are also human interpretable and can be used to explain the interactions between a drug molecule and its receptor protein (HIV protease). The selected descriptors are then used for developing the QSAR prediction models by using the MLR, DT and ANN approaches. These models are discussed, analyzed and compared to validate and test their performance for this dataset. All three approaches yield the QSAR models with good prediction performance. The models developed by DT and ANN are comparable and have better prediction than the MLR model. For ANN model, weight analysis is carried out to analyze the role of various descriptors in activity prediction. All the prediction models point towards the involvement of hydrophobic interactions. These models can be useful for predicting the biological activity of new untested HIV protease inhibitors and virtual screening for identifying new lead compounds.

Small-sized human immunodeficiency virus type-1 protease inhibitors containing allophenylnorstatine to explore the S2' pocket

A series of HIV protease inhibitor based on the allophenylnorstatine structure with various P(2)' moieties were synthesized. Among these analogues, we discovered that a small allyl group would maintain potent enzyme inhibitory activity compared to the o-methylbenzyl moiety in clinical candidate 1 (KNI-764, also known as JE-2147, AG-1776, or SM-319777). Introduction of an anilinic amino group to 2 (KNI-727) improved water-solubility and anti-HIV-1 activity. X-ray crystallographic analysis of 13k (KNI-1689) with a beta-methallyl group at P(2)' position revealed hydrophobic interactions with Ala28, Ile84, and Ile50' similar to that of 1. The presence of an additional methyl group on the allyl group in compound 13k significantly increased anti-HIV activity over 1 while providing a rational drug design for structural minimization and improving membrane permeability.

Possible allosteric interactions of monoindazole-substituted P2 cyclic urea analogues with wild-type and mutant HIV-1 protease

Our ongoing efforts to understand the difference in the binding pattern of HIV-1 protease inhibitor (HIVPI) with the wild-type and mutant HIV-1 protease (HIVPR) and to provide mechanistic insight are continued further. We report here the results of a recent quantitative structure-activity relationship (QSAR) study on monoindazole-substituted P2 analogues of cyclic urea HIVPIs. The QSAR models revealed an inverted parabolic relationship between biological activity and calculated molar refractivity (CMR). That is, biological activity first decreases with increase in CMR and at a certain minimum point (inversion point) it suddenly changes and increases with further increase in CMR. CMR is a measure of volume-dependent-polarizability and is an indication of the polar interactions between ligand and receptor. The results seem to be best rationalized by larger molecules inducing a change in a receptor unit that allows for a new mode of interaction. Similar QSAR models were also observed for the biological activity of these molecules tested against a panel of mutant viruses including mutant strains with single amino acid substitution (I84V), double amino acid substitutions (I84V/V82F), and multiple amino acid changes corresponding to mutations observed in clinical isolates of patients treated with Ritonavir((R)). Interestingly the inversion points for these mutant strains were found larger than for wild-type. The subtle but significant difference in the inversion point indicates change in the shape and size of the binding pocket. Earlier QSAR studies have shown that the correlation of biological activity with an inverted parabola is an indicative of the 'allosteric interaction' of the ligands with the receptor. This report presents a detail analysis of these observations.

Synthesis and in vitro biological evaluation of valine-containing prodrugs derived from clinically used HIV-protease inhibitors

In an approach to improve the pharmacological properties and pharmacokinetic profiles of the current protease inhibitors (PIs) used in clinics, and consequently, their therapeutic potential, we performed the synthesis of PI-spacer-valine prodrugs (PI=saquinavir, nelfinavir and indinavir; spacer=-C(O)(CH(2))(5)NH-), and evaluated their in vitro stability with respect to hydrolysis, anti-HIV activity, cytotoxicity, and permeation through a monolayer of Caco-2 cells (used as a model of the intestinal barrier), as compared with their parent PI and first generation of valine-PIs (wherein valine was directly connected through its carboxyl to the PIs). The PI-spacer-valine conjugates were prepared in two steps, in good yields, by condensing an acid derivative of the appropriate protected valine-spacer moiety with the PI, followed by deprotection of the valine protecting group. With respect to hydrolysis, we found that the PI-spacer-valine prodrugs were chemically more stable than the first generation of PI-Val prodrugs. Their stabilities correlated with the low to very low in vitro anti-HIV activity measured for those prodrugs wherein the coupling of valine-spacer residue to the PIs was performed onto the peptidomimetic PI's hydroxyl. Prodrugs wherein the coupling of the valine-spacer residue was performed onto the non-peptidomimetic PI hydroxyl displayed a higher antiviral activity, indicating that these prodrugs are also to some extent anti-HIV drugs by themselves. While the direct conjugation of L-valine to the PIs constituted a most appealing alternative, which improved their absorptive diffusion across Caco-2 cell monolayers and reduced their recognition by efflux carriers, its conjugation to the PIs through the -C(O)(CH(2))(5)NH- spacer was found to inhibit their absorptive and secretory transepithelial transport. This was attributable to a drastic reduction of their passive permeation and/or active transport, indicating that the PI-spacer-valine conjugates are poor substrates of the aminoacid carrier system located at the brush border side of the Caco-2 cell monolayer.

β-Secretase inhibitors: Modification at the P4 position and improvement of inhibitory activity in cultured cells

Recently, we reported potent and small-sized beta-secretase (BACE1) inhibitors KMI-570 and KMI-684 in which we replaced carboxylic acid groups at the P(1)(') position of KMI-420 and KMI-429, respectively, with tetrazole derivatives as carboxylic acid bioisosteres. These modifications improved significantly BACE1 inhibitory activity and chemical stability. In this study, the acidic tetrazole ring of the P(4) position of KMI-420 and KMI-570, respectively, was replaced with various hydrogen bond acceptor groups. We found BACE1 inhibitor KMI-574 that exhibited potent inhibitory activity in cultured cells as well as in vitro enzymatic assay.

Modeling of activity of cyclic urea HIV-1 protease inhibitors using regularized-artificial neural networks

Artificial neural networks (ANNs) were used to model both inhibition of HIV-1 protease (K(i)) and inhibition of HIV replication (IC90) for 55 cyclic urea derivatives using constitutional and 2D descriptors. As a preliminary step, linear dependences were established by multiple linear regression (MLR) approaches, selecting the relevant descriptors by genetic algorithm (GA) feature selection. For ANN models non-linear GA feature selection was also applied. Non-linear modeling of K(i) overcame the results of the linear one using four properties, keeping in mind standard Pearson R correlation coefficients (0.931 vs. 0.862) and leave one out (LOO) cross-validation analysis (Q(LOO)2 = 0.703 vs. 0.510). On the other hand, IC90 modeling was insoluble by a linear approach: no predictive model was achieved; however, a non-linear relation was encountered according to statistic results (R = 0.891; Q(LOO)2 = 0.568). The best non-linear models suggested the influence of the presence of nitrogen atoms and the molecular volume distribution in the inhibitor structures on the HIV-1 protease inhibition as well as that the inhibition of HIV replication was dependent on the occurrence of five-member rings. Finally, inhibitors were well distributed regarding its activity levels in a Kohonen self-organizing map built using the input variables of the best non-linear models.

Hydrophobicity in the design of P2/P2′ tetrahydropyrimidinone HIV protease inhibitors

As part of an ongoing effort in understanding the role of hydrophobicity in the design of nonpeptidic HIV protease inhibitors, the QSAR study on P2/P2' tetrahydropyrimidinone is presented in this report. Our results suggest that the balance of hydrophobicity and a volume- dependent polarizability term plays a key role in the inhibition of the viral protease by these inhibitors. The size of the substituent of ligands at particular positions that induce steric fit is crucial. The role of hydrophobicity in the design of tetrahydropyrimidinone is discussed. It has been found that a sufficient spread in the data is required to observe the optimum value of ClogP for these inhibitors.