Shape and pharmacophore-based virtual screening to identify potential cytochrome P450 sterol 14α-demethylase inhibitors.

Sterol 14α-demethylase (CYP51) is a cytochrome P450 heme thiolate containing enzyme involved in biosynthesis of membrane sterols, including sterol in animals, ergosterol in fungi, and a variety of C24-modified sterols in plants and protozoa. Several clinical drugs have been developed to reduce the impact of fungal diseases, but their clinical uses have been limited by the emergence of drug resistance and insufficiencies in their antifungal activity. Therefore, in order to identify potential CYP51 inhibitors, we have implemented a virtual screening (VS) protocol by using both phase shape and pharmacophore model (AHHRR) against Asinex, ChemBridge and Maybridge databases. A filtering protocol, including Lipinski filter, number of rotatable bonds and different precisions of molecular docking was applied in hits selection. The results indicated that both shape-based and pharmacophore-based screening yielded the best result with potential inhibitors. The searched compounds were also evaluated with ADME properties, which show excellent pharmacokinetic properties under the acceptable range. We identified potential CYP51 inhibitors for further investigation, they could also be employed to design ligands with enhanced inhibitory potencies and to predict the potencies of analogs to guide synthesis/or prepare synthetic antifungal analogs against CYP51.

Exploring the selectivity of a ligand complex with CDK2/CDK1: a molecular dynamics simulation approach.

Cyclin-dependent kinases (CDKs) are core components of the cell cycle machinery that govern the transition between phases during cell cycle progression. Abnormalities in CDKs activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Their inhibitors have entered in clinical trials to treat cancer. Very recently, Heathcote et al. (J. Med. Chem. 2010, 53:8508-8522) have found a ligand BS194 that has a high affinity with CDK2 (IC(50) = 3 nM) but shows low affinity with CDK1 (IC(50) = 30 nM). To understand the selectivity, we used homology modeling, molecular docking, molecular dynamics, and free-energy calculation to analyze the interactions. A rational three-dimensional model of the CDK1/BS194 complex is built. We found that Leu83 is a key residue that recognizes BS194 more effectively with CDK2 with good binding free energies rather than CDK1. Energetic analysis reveals that van der Waals interaction and non-polar contributions to solvent are favorable in the formation of complexes and amine group of the ligand, which plays a crucial role for binding selectivity between CDK2 and CDK1.

Pharmacophore modelling and atom-based 3D-QSAR studies on N-methyl pyrimidones as HIV-1 integrase inhibitors.

Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to N-methyl pyrimidones as HIV-1 integrase inhibitors. Based on the ligand-based pharmacophore model, we got 5-point pharmacophore model AADDR, with two hydrogen bond acceptors (A), two hydrogen bond donors (D) and one aromatic ring (R). The generated pharmacophore-based alignment was used to derive a predictive atom-based 3D-QSAR model for the training set (r(2) = 0.92, SD = 0.16, F = 84.8, N = 40) and for test set (Q(2) = 0.71, RMSE = 0.06, Pearson R = 0.90, N = 10). From these results, AADDR pharmacophore feature was selected as best common pharmacophore hypothesis, and atom-based 3D-QSAR results also support the outcome by means of favourable and unfavourable regions of hydrophobic and electron-withdrawing groups for the most potent compound 30. These results can be useful for further design of new and potent HIV-1 IN inhibitors.

A fluorescence-displacement assay using molecularly imprinted polymers for the visual, rapid, and sensitive detection of the algal metabolites, geosmin and 2-methylisoborneol.

A visual, rapid, and sensitive method for the detection of two algal metabolites, geosmin (GSM) and 2-methylisoborneol (2-MIB) using a competitive displacement technique based on molecular imprinted polymers (MIPs) and fluorescent tags was developed. In this method, fluorescent tags that bind to synthetic receptor sites of MIPs were designed and synthesised. In the presence of target analytes (geosmin and 2-methylisoborneol respectively), the tags are displaced leading to fluorescence signals. The MIPs were derived from the polymerisation of functional monomers and crosslinkers in the presence of suitable templates. Good to high binding capacities and selectivities were obtained with the MIPs. The displacement of fluorescent-tagged substrates from the respective MIPs by the target analytes enabled the quantitative detection of geosmin at concentrations as low as 0.38 µM (69 µg L-1), while the LOD for 2-methylisoborneol is 0.29 µM (48 µg L-1) without any cross-reactivity, non-specific (false-positive) binding, and matrix complications. Qualitative detection of geosmin and 2-methylisoborneol is also possible via visualisation of fluorescence using a hand held UV lamp, with LOD for geosmin and 2-methylisoborneol at 0.44 µM (80 µg L-1) and 0.35 µM (60 µg L-1), respectively. The sensitivity of the system can be improved with a pre-concentration step using the respective MIPs as a sorbent.

Insight into the binding mode between N-methyl pyrimidones and prototype foamy virus integrase-DNA complex by QM-polarized ligand docking and molecular dynamics simulations.

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the viral replication cycle as it catalyzes the insertion of the reverse transcribed viral DNA into host chromosome. The structure of prototype foamy virus (PFV) IN has structural and functional homology with HIV-1 IN (no full-length structure available). In this study, we have used PFV IN-DNA complex as a surrogate model for HIV-1 IN-DNA complex to investigate the binding modes of N-methyl pyrimidones (NMPs) by QM-polarized ligand docking (QPLD), binding free energy calculations and molecular dynamics simulations. The O,O,O donor atom triad of NMPs show metal chelation with divalent Mg(2+) ions in the active site of PFV IN, in perfect agreement with the proposed mechanism of IN strand transfer inhibitors (INSTIs). The results also show that the benzyl group of compounds fit into a pocket to displace the 3'-terminal adenosine of viral DNA from the IN active site making it unavailable for the nucleophile to attack the target DNA in the strand transfer (ST) reaction. The halobenzyl moiety show hydrophobic interactions with conserved PFV IN Tyr212 and Pro214 residues, corresponding to HIV-1 IN Tyr143 and Pro145, respectively. Molecular dynamics (MD) simulations gave important insights into the structural and chemical basis involved in ST inhibition. Based on MD results, hydrogen bond with Tyr212, coordinate bonds with Mg(2+) ions, and hydrophobic interactions play an important role in the stabilization of compounds. Our results provide additional insight into the possible mechanism of action and binding mode of NMPs, and might have implications for rational design of specific HIV-1 INSTIs with improved affinity and selectivity.

Combined ligand and structure-based approaches on HIV-1 integrase strand transfer inhibitors.

HIV-1 integrase (IN) is an essential enzyme in the viral replication cycle and represents a promising target for anti-HIV drug design. In the present study, pharmacophore modeling and atom-based 3D-QSAR studies were carried out on a series of compounds belonging to dihydroxy isoindole derivatives as HIV-1 IN strand transfer inhibitors. The best pharmacophore model generated consists of six features AADHRR: two hydrogen bond acceptors (A), a hydrogen bond donor (D), a hydrophobic group (H) and two aromatic rings (R). Based on the best pharmacophore model, a statistically valid atom-based 3D-QSAR model was developed. The obtained atom-based 3D-QSAR model has an excellent correlation coefficient value (R(2)=0.87) and also exhibited good predictive power (Q(2)=0.72). The best pharmacophore model was further validated through enrichment calculations and it shows strong predictive power with a high performance in identifying active ligands from the total hits (actives+decoys). QM-polarized ligand docking and molecular dynamics simulations of selected active compounds in the active site of prototype foamy virus intasome gave important insights into the chemical and structural basis involved in the molecular recognition process. The O,O,O donor atom triad of compounds show metal chelation with divalent Mg(2+) ions bound to the three catalytic amino acids in the enzyme's active site and π-stacking interaction with the viral DNA residue DA17. The results might have implications for rational design of specific HIV-1 integrase strand transfer inhibitors with improved affinity and selectivity.

Blocking the interaction between HIV-1 integrase and human LEDGF/p75: mutational studies, virtual screening and molecular dynamics simulations.

HIV-1 integrase (IN) mediates integration of viral cDNA into the host cell genome, an essential step in the retroviral life cycle. The human lens epithelium-derived growth factor (LEDGF/p75) is a co-factor of HIV-1 IN that plays a crucial role in viral integration. Because of its crucial role in early steps of HIV replication, the IN-LEDGF/p75 interaction represents an attractive target for anti-HIV drug discovery. In this study, the IN-LEDGF/p75 interaction was studied by in silico mutational studies and molecular dynamics simulations. The results showed that all of the key residues in the LEDGF/p75 binding pocket of IN protein are important for stabilization of the complex. Structure-based virtual screening against HIV-1 IN using the ChemBridge database was performed through three different protocols of docking simulations with varying precisions and computational intensities. Six compounds based on the docking score, binding affinity and pharmacokinetic parameters were selected and an analysis of the interactions with key amino acid residues of IN was carried out. Subsequently, molecular dynamics simulations of these compounds in the LEDGF/p75 binding site of IN were carried out in order to study the stability of complexes and their hydrogen bonding interactions. IN residues Glu170, His171, and Thr174 in chain A as well as Gln95 and Thr125 in chain B were discovered to play important roles in the binding of compounds. These findings could be helpful for blocking IN-LEDGF/p75 interaction, and provide a method for avoiding viral resistance and cross-resistance.