Comparative molecular field analysis (CoMFA) and docking studies of non-nucleoside HIV-1 RT inhibitors (NNIs)

Identifying Anti-prion Chemical Compounds Using a Newly Established Yeast High-Throughput Screening System

Prion-like protein aggregation underlies the pathology of a group of fatal neurodegenerative diseases in humans, including Alzheimer's disease (AD), Parkinson's disease, amyotrophic lateral sclerosis, and transmissible spongiform encephalopathy. At present, few high-throughput screening (HTS) systems are available for anti-prion small-molecule identification. Here we describe an innovative phenotypic HTS system in yeast that allows for efficient identification of chemical compounds that eliminate the yeast prion [SWI⁺]. We show that some identified anti-[SWI⁺] compounds can destabilize other non-[SWI⁺] prions, and their antagonizing effects can be prion- and/or variant specific. Intriguingly, among the identified hits are several previously identified anti-PrP^Sc compounds and a couple of US Food and Drug Administration-approved drugs for AD treatment, validating the efficacy of this HTS system. Moreover, a few hits can reduce proteotoxicity induced by expression of several pathogenic mammalian proteins. Thus, we have established a useful HTS system for identifying compounds that can potentially antagonize prionization and human proteinopathies.

Phylogenetic analysis, structure modeling and docking study of HCV NS3 protease for the identification of potent inhibitors

The nonstructural protein 3 (NS3) helicase of HCV is believed to be a plausible target for the identification and designing of potent antiviral drugs. NS3 protein is involved in a positive sense single-stranded viral replication as well as it also cleaves viral poly protein into diverse mature proteins at different time spans. Structural exploration of NS3 revealed that HCV helicase could also act as translocase. In order to identify potential inhibitors for HCV-3a, the current study has been designed. Serum samples from the Pakistani HCV positive patients were collected, sequenced and after purification included in the present study. Phylogenetic analysis on the samples clustered around it in the same group with those from India. Using homology modeling technique, we determined 3D structure of NS3 gene of HCV-3a and employed further in docking studies to discover potent inhibitor against it. As a result of docking Compound 1, with IC50 value of 0.015 and -14.4 kcal/mol energy, ranked as a most pungent inhibitor among all the studied inhibitors. Compound 1 also exhibited good hydrogen bond interactions with the modeled protein. The finding of present study could be used as a lead in future to design an effective dual inhibitor against HCV-3a.

CH-π hydrogen bonds in biological macromolecules

This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

Conformation depends on 4D-QSAR analysis using EC-GA method: pharmacophore identification and bioactivity prediction of TIBOs as non-nucleoside reverse transcriptase inhibitors

The electron conformational and genetic algorithm methods (EC-GA) were integrated for the identification of the pharmacophore group and predicting the anti HIV-1 activity of tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepinone (TIBO) derivatives. To reveal the pharmacophore group, each conformation of all compounds was arranged by electron conformational matrices of congruity. Multiple comparisons of these matrices, within given tolerances for high active and low active TIBO derivatives, allow the identification of the pharmacophore group that refers to the electron conformational submatrix of activity. The effects of conformations, internal and external validation were investigated by four different models based on an ensemble of conformers and a single conformer, both with and without a test set. Model 1 using an ensemble of conformers for the training (39 compounds) and test sets (13 compounds), obtained by the optimum seven parameters, gave satisfactory results (R²(training) = 0.878, R²(test)= 0.910, q² = 0.840, q²(ext1) = 0.926 and q²(ext2) = 0.900).

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.

Three-dimensional quantitative structure-activity relationship studies on UGT1A9-mediated 3-O-glucuronidation of natural flavonols using a pharmacophore-based comparative molecular field analysis model

Glucuronidation is often recognized as one of the rate-determining factors that limit the bioavailability of flavonols. Hence, design and synthesis of more bioavailable flavonols would benefit from the establishment of predictive models of glucuronidation using kinetic parameters [e.g., K(m), V(max), intrinsic clearance (CL(int)) = V(max)/K(m)] derived for flavonols. This article aims to construct position (3-OH)-specific comparative molecular field analysis (CoMFA) models to describe UDP-glucuronosyltransferase (UGT) 1A9-mediated glucuronidation of flavonols, which can be used to design poor UGT1A9 substrates. The kinetics of recombinant UGT1A9-mediated 3-O-glucuronidation of 30 flavonols was characterized, and kinetic parameters (K(m), V(max), CL(int)) were obtained. The observed K(m), V(max), and CL(int) values of 3-O-glucuronidation ranged from 0.04 to 0.68 μM, 0.04 to 12.95 nmol/mg/min, and 0.06 to 109.60 ml/mg/min, respectively. To model UGT1A9-mediated glucuronidation, 30 flavonols were split into the training (23 compounds) and test (7 compounds) sets. These flavonols were then aligned by mapping the flavonols to specific common feature pharmacophores, which were used to construct CoMFA models of V(max) and CL(int), respectively. The derived CoMFA models possessed good internal and external consistency and showed statistical significance and substantive predictive abilities (V(max) model: q(2) = 0.738, r(2) = 0.976, r(pred)(2) = 0.735; CL(int) model: q(2) = 0.561, r(2) = 0.938, r(pred)(2) = 0.630). The contour maps derived from CoMFA modeling clearly indicate structural characteristics associated with rapid or slow 3-O-glucuronidation. In conclusion, the approach of coupling CoMFA analysis with a pharmacophore-based structural alignment is viable for constructing a predictive model for regiospecific glucuronidation rates of flavonols by UGT1A9.

Predicting anti-HIV activity of PETT derivatives: CoMFA approach

HIV-1 (Human Immunodeficiency Virus Type-1) is the pathogenic retrovirus and causative agent of AIDS. HIV-1 RT is one of the key enzymes in the duplication of HIV-1. Inhibitors of HIV-1 RT are classified as NNRTIs and NRTIs. NNRTIs bind in a region not associated with the active site of the enzyme. Within the NNRTIs category, there is a set of inhibitors commonly referred to as phenyl ethyl thiazolyl thiourea (PETT) derivatives. The present 3D QSAR study attempts to explore the structural requirements of phenyl ethyl thiazolyl thiourea (PETT) derivatives for anti-HIV activity. Based on the structures and biodata of previous PETT analogs, 3D-QSAR (CoMFA) study has been performed with a training set consisting of 60 molecules, which resulted in a reliable computational model with q(2)=0.657, S(PRESS)=0.957, r(2)=0.938, and standard error of estimation (SEE)=0.270 with the number of partial least square (PLS) components being 5. It is shown that the steric and electrostatic properties predicted by CoMFA contours can be related to the anti-HIV activity. The predictive ability of the resultant model was evaluated using a test set comprised of 11 molecules and the predicted r(2)=0.893. This model is a more significant guide to trace the features that really matter especially with respect to the design of novel compounds.

CH···π Interaction for Rhenium-Based Rectangles: An Interaction That Is Rarely Designed into a Host−Guest Pair

Alkoxy- and thiolato-bridged Re(I) molecular rectangles [{(CO)3Re(mu-ER)2Re(CO)3}2(mu-bpy)2] (ER = SC4H9, 1a; SC8H17, 1b; OC4H9, 2a; OC12H25, 2b; bpy = 4,4'-bipyridine) exhibit strong interactions with several planar aromatic molecules. The nature of their binding was studied by spectral techniques and verified by X-ray diffraction analysis. Standard absorption and fluorescence titrations showed that a relatively strong 1:1 interaction occurs between aromatic guests such as pyrene and these rectangles. The results of a single-crystal X-ray diffraction analysis show that the recognition of 1 with a pyrene molecule is mainly due to CH...pi interactions and the face of the guest pyrene is located over the edges of the bpy linkers of 1. This is a fairly novel example of an interaction that is rarely designed into a host-guest pair. Furthermore, the interaction of 1 with Ag+ results in the self-organization of supramolecular arrays, as revealed by solid-state data.

Design, Synthesis, Biological Evaluation, and Molecular Modeling Studies of TIBO-Like Cyclic Sulfones as Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors

TIBO- and TBO-like sulfone derivatives 1 and 2 were designed, synthesized, and tested for their ability to block the replication cycle of HIV-1 in infected cells. The anti-HIV-1 activities of sulfones 3, which were intermediates in the syntheses of 1 and 2, were also evaluated. Surprisingly, the sulfone analogues of TIBO R82913 (compounds 1) were inactive, whereas interesting results were obtained for truncated derivatives 2. Compound 2 w was the most potent among this series in cell-based assays (EC50=0.07 microM, CC50>200 microM, SI>2857). It was twofold less potent than R82913, but more selective. An X-ray crystallographic analysis was carried out to establish the absolute configuration of 2 w and its enantiomer 2 x, which were obtained by semipreparative HPLC of 2 v, one of the most potent racemates. Compounds 1-3 were proven to target HIV-1 RT. In fact, representative derivatives inhibited recombinant HIV-1 RT in vitro at concentrations similar to those active in cell-based assays. 3D QSAR studies and docking simulations were developed on TIBO- and TBO-like sulfone derivatives to rationalize their anti-HIV-1 potencies and to predict the activity of novel untested sulfone derivatives. Predictive 3D QSAR models were obtained with a receptor-based alignment by docking of TIBO- and TBO-like derivatives into the NNBS of RT.

CoMFA 3D-QSAR analysis of HIV-1 RT nonnucleoside inhibitors, TIBO derivatives based on docking conformation and alignment

HIV-1 RT is one of the key enzymes in the duplication of HIV-1. Inhibitors of HIV-1 RT are classified as nonnucleoside RT inhibitors (NNRTIs) and nucleoside analogues. NNRTIs bind in a region not associated with the active site of the enzyme. Within the NNRTI category, there is a set of inhibitors commonly referred to as TIBO inhibitors. Fifty TIBO inhibitors were used in the work to build 3-D QSAR models. The two known crystal structures of complexes are used to investigate and validate the docking protocol. The results show that the docking simulations reproduce the crystal complexes very well with RMSDs of approximately 1 A and approximately 0.6 A for 1REV and 1COU, respectively. The alignment of molecules and "active" conformation selection are the key to a successful 3D-QSAR model by CoMFA. The flexible docking (Autodock3) was used on determination of "active" conformation and molecular alignment, and CoMFA and CoMSIA were used to develop 3D-QSAR models of 50 TIBOs in the work. The 3D-QSAR models demonstrate a good ability to predict the activity of studied compounds (r2 = 0.972, 0.944, q2 = 0.704, 0.776). It is shown that the steric and electrostatic properties predicted by CoMFA contours can be related to the binding structure of the complex. The results demonstrate that the combination of ligand-based and receptor-based modeling is a powerful approach to build 3D-QSAR models.

Structure-Based Validation of the 3D-QSAR Technique MaP

For three target proteins with different binding pocket characteristics (size and shape, hydrophobicity, hydrogen-bonding) a structure-based validation of the translationally and rotationally invariant 3D-QSAR technique MaP is performed (MaP: Mapping Property distributions of molecular surfaces). The structure-based validation procedure comprises two steps: first, QSAR models are derived without using the information of the target protein. Second, the models are back-projected into the crystal structure of the binding pockets and interpreted. It is demonstrated that MaP is able to identify characteristics important for ligand binding in the cases studied here. Moreover, it is demonstrated that MaP is a versatile 3D-QSAR technique since good, predictive models could be obtained for all three data sets showing distinct characteristics.

2-(2,6-Dihalophenyl)-3-(pyrimidin-2-yl)-1,3-thiazolidin-4-ones as non-nucleoside HIV-1 reverse transcriptase inhibitors

Several 1,3-thiazolidin-4-ones bearing a 2,6-dihalophenyl group at C-2 and a substituted pyrimidin-2-yl ring at the N-3 were synthesised and evaluated as anti-HIV agents. The results of the in vitro tests showed that some of them were highly effective inhibitors of human immunodeficiency virus type-1 (HIV-1) replication at 10-40 nM concentrations with minimal cytotoxicity. Structure-activity relationship studies revealed that the nature of the substituents at the 2 and 3 positions of the thiazolidinone nucleus had a significant impact on the in vitro anti-HIV activity of this class of potent antiretroviral agents. The compounds had significantly reduced activity against the characteristic NNRTI-resistant virus mutants (bearing the K103N and Y181C RT mutations), thereby acting as non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors (NNRTIs).

Flexible docking of pyridinone derivatives into the non-nucleoside inhibitor binding site of HIV-1 reverse transcriptase

Potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) of the pyridinone derivative type were docked into nine NNRTIs binding pockets of HIV-1 reverse transcriptase (RT) structures. The docking results indicate that pyridinone analogues adopt a butterfly conformation and share the same binding mode as the crystal inhibitors in the pocket geometries of nevirapine, 1051U91, 9-Cl-TIBO, Cl-alpha-APA, efavirenz, UC-781, and S-1153. The results are in agreement with the data concerning mutational and structure-activity relationships available for pyridinone analogues and aid in the understanding, at the molecular level, of the biological response of published hybrid pyridinone molecules. Strategies to design further pyridinone derivatives active against RT containing mutations are discussed.

Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS

Tetrahydroimidazo-[4,5,l-jk][1,4]-benzodiazepin-2-(1H)-one (TIBO) derivatives are important nonnucleoside human immunodeficiency virus-1 reverse transcriptase inhibitors (NNRTI). Several TIBO derivatives have shown high potency to inhibit reverse transcriptase (RT) and one (Tivirapine) has entered into clinical trials. The free energy of binding (FEB) is a numerical way to express the binding affinity of a ligand to its receptor and has been applied in screening candidates in rational drug design. In this work, the FEB of 42 TIBOs in RT was studied. Relative FEB is expressed in the form of a linear combination of vdW, electrostatic, solvation, and nonpolar solvation energy terms. The predicted FEB activity of the TIBOs studied has a good correlation (r(2) = 0.8680, q(2) = 0.8298) with respect to the experimental activity (pIC(50)). Based on the data reported here, the Finite Difference Poisson Boltzmann with a Gaussian Smooth Dielectric Constant Function method (PB/GS) solvation energy term is very important in predicting the binding affinity of TIBOs in RT. In summary, the Dock-Molecular Mechanics (MM)-PB/GS method is a promising technique in predicting ligand/receptor binding affinity and it can be used to screen relatively large sets of molecules in a reasonable amount of computer time.

Validation tools for variable subset regression

Variable selection is applied frequently in QSAR research. Since the selection process influences the characteristics of the finally chosen model, thorough validation of the selection technique is very important. Here, a validation protocol is presented briefly and two of the tools which are part of this protocol are introduced in more detail. The first tool, which is based on permutation testing, allows to assess the inflation of internal figures of merit (such as the cross-validated prediction error). The other tool, based on noise addition, can be used to determine the complexity and with it the stability of models generated by variable selection. The obtained statistical information is important in deciding whether or not to trust the predictive abilities of a specific model. The graphical output of the validation tools is easily accessible and provides a reliable impression of model performance. Among others, the tools were employed to study the influence of leave-one-out and leave-multiple-out cross-validation on model characteristics. Here, it was confirmed that leave-multiple-out cross-validation yields more stable models. To study the performance of the entire validation protocol, it was applied to eight different QSAR data sets with default settings. In all cases internal and external model performance was good, indicating that the protocol serves its purpose quite well.

Anti-HIV agents: design and discovery of new potent RT inhibitors

This paper reports our work in the field of nonnucleoside RT inhibitors (NNRTIs). On the basis of extensive studies on 1H,3H-thiazolo[3,4-a]benzimidazole derivatives (TBZs) followed by structure-activity relationship (SAR) considerations and molecular modeling, the design and synthesis of a series of 2,3-diaryl-1,3-thiazolidin-4-ones have been performed. Some derivatives proved to be highly effective in inhibiting human immunodeficiency virus type-1 (HIV-1) replication at nanomolar concentrations with minimal toxicity, acting as reverse transcriptase (RT) inhibitors. Computational studies were used in order to probe the binding of our ligands to HIV-1-RT.

Synthesis and anti-HIV activity of 2,3-diaryl-1,3-thiazolidin-4-ones

Several 1,3-thiazolidin-4-ones bearing a 2,6-dihalophenyl group at C-2 and a variously substituted phenyl ring at N-3 have been synthesized and tested as anti-HIV agents. The results of the in vitro tests showed that some of them proved to be effective inhibitors of HIV-1 replication.

Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase

The docking of small molecules to proteins has played an important role in the understanding of drug/receptor interactions. An important drug/receptor interaction is between non-nucleoside inhibitors of HIV-1 RT and the non-nucleoside binding pocket. We report the results of docking calculations in which we have docked known and proposed non-nucleoside reverse transcriptase inhibitors to the type 1 virus. The proposed NNRTIs dock in a similar position and orientation as known inhibitors. In addition, we observe a linear correlation between the calculated interaction energy and EC50 for the inhibitors, suggesting that the docked structure orientation and the interaction energies are reasonable. Two hydrogen bonds between nevirapine and RT (3HVT and 1VRT) are observed and are reproduced across different docking schemes. Since we used two different HIV-1 RT crystal structures (3HVT and 1VRT), which are at different levels of resolution (2.9 and 2.2 A, respectively), we propose that structures with resolutions better than 3 A can be used to produce reasonable docking results.

Design, synthesis, structure-activity relationships, and molecular modeling studies of 2,3-diaryl-1,3-thiazolidin-4-ones as potent anti-HIV agents

Starting from 1H,3H-thiazolo[3,4-a]benzimidazoles (TBZs), we performed the design, synthesis, and the structure-activity relationship studies of a series of 2,3-diaryl-1,3-thiazolidin-4-ones. Some derivatives proved to be highly effective in inhibiting HIV-1 replication at nanomolar concentrations with minimal cytotoxicity, thereby acting as nonnucleoside HIV-1 RT inhibitors (NNRTIs). Computational studies were used to delineate the ligand-RT interactions and to probe the binding of the ligands to HIV-1 RT.

Synthesis and anti-hIV activity of 1-(2,6-difluorophenyl)-1H,3H-thiazolo[3,4-a]benzimidazole structurally-related 1,2-substituted benzimidazoles

The synthesis of 1,2-substituted benzimidazoles is reported. These novel derivatives share chemical similarities with 1-aryl-1H,3H-thiazolo[3,4-a]benzimidazoles, a class of HIV-1 NNRTIs studied widely. All compounds prepared were tested in MT-4 cells to explore their potential anti-HIV activity and were found to be less potent than 1-(2,6-difluorophenyl)-1H,3H-thiazolo[3,4-a]benzimidazole (TBZ).

Synthesis and anti-HIV activity of 2,3-diaryl-1,3-thiazolidin-4-(thi)one derivatives

Several 2,3-diaryl-1,3-thiazolidine-4-thione derivatives and 2,3-diaryl-1,3-thiazolidin-4-ones bearing a methyl group at C-5 position have been synthesized and tested as anti-HIV agents. The results of the in vitro tests showed that some of them proved to be effective inhibitors of HIV-1 replication.

Discovery of 2,3-diaryl-1,3-thiazolidin-4-ones as potent anti-HIV-1 agents

Design, synthesis and anti-HIV activity of a series of 2,3-diaryl-1,3-thiazolidin-4-ones are reported. Some derivatives proved to be highly effective in inhibiting HIV-1 replication at nanomolar concentrations thereby acting as non-nucleoside HIV-1 RT inhibitors (NNRTIs). SAR studies evidenced that the nature of the substituents at the 2 and 3 positions of the thiazolidinone nucleus largely influenced the in vitro anti-HIV activity of this new class of potent antiviral agents.

Synthesis, biological activity, pharmacokinetic properties and molecular modelling studies of novel 1H,3H-oxazolo[3,4-a]benzimidazoles: non-nucleoside HIV-1 reverse transcriptase inhibitors

New 1H,3H-oxazolo[3,4-albenzimidazoles (OBZs) were synthesized as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) to extend the structure-activity relationships observed for an early series of related 1H,3H-thiazolo[3,4-a]benzimidazole derivatives (TBZs). The new compounds showed inhibitory activity against the replication of various HIV-1 strains, including NNRTI-resistant strains. Testing of a representative OBZ derivative in an HPLC assay on biological fluids, indicated that the sulphur substitution appreciably improved the metabolic stability of the TBZ compound. In addition, molecular modelling studies demonstrated that OBZs, TBZs and other NNRTIs have similar structural properties, that is a butterfly-like conformation, which is a key structural requirement for reverse transcriptase inhibition.

QSAR modeling with the electrotopological state: TIBO derivatives

Quantitative structure-activity relationships (QSAR), based on the atom level E-state indices and calculated molecular properties (log P, MR), have been developed for the affinity of a large set of TIBO derivatives against HIV-1 reverse transcriptase (HIV-1 RT) utilizing multiple linear regression techniques. A model with five descriptors, including four atom level E-state indices (carbon atoms 2, 4, 8, and 9) and calculated log P, showed good statistics both in the regression (r2 = 0.85 and s = 0.52) and leave-one-out cross-validation (q2 = 0.80 and s(PRESS) = 0.56) for the training set of 41 compounds. The statistics for the prediction of anti-HIV activity in the test set of 24 TIBO derivatives were r2 = 0.80 and s = 0.64, respectively. The model descriptors indicate the importance of lipophilic and electronic contributions toward HIV-1 RT inhibition of TIBO derivatives used in this study.