An ant algorithm for the conformational analysis of flexible molecules

Originally, the ant system was developed for optimization in discrete search spaces such as the traveling salesman problem. We detail our adaptation of the algorithm to optimization in the continuous search space of conformational analysis. The parameters of the algorithm were tuned using a simple test molecule, undecane, and a drug molecule, imatinib. The algorithm is further tested on four more drug or drug-like molecules, on vitamin A and on alanine tetrapeptide.

In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine)

Ideally, an anti-HIV drug should (1) be highly active against wild-type and mutant HIV without allowing breakthrough; (2) have high oral bioavailability and long elimination half-life, allowing once-daily oral treatment at low doses; (3) have minimal adverse effects; and (4) be easy to synthesize and formulate. R278474, a new diarylpyrimidine (DAPY) non-nucleoside reverse transcriptase inhibitor (NNRTI), appears to meet these criteria and to be suitable for high compliance oral treatment of HIV-1 infection. The discovery of R278474 was the result of a coordinated multidisciplinary effort involving medicinal chemists, virologists, crystallographers, molecular modelers, toxicologists, analytical chemists, pharmacists, and many others.

Design, Synthesis, and SAR of a Novel Pyrazinone Series with Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitory Activity

A series of novel pyrazinones designed as non-nucleoside reverse transcriptase inhibitors (NNRTIs) was synthesized and their anti-HIV structure-activity relationship (SAR) was studied.

On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data

There are several indications that a given compound or a set of related compounds can bind in different modes to a specific binding site of a protein. This is especially evident from X-ray crystallographic structures of ligand-protein complexes. The availability of multiple binding modes of a ligand in a binding site may present an advantage in drug design when simultaneously optimizing several criteria. In the case of the design of anti-HIV compounds we observed that the more active compounds that are also resilient against mutation of the non-nucleoside binding site of HIV1-reverse transcriptase make use of more binding modes than the less active and resilient compounds.

Correlations between Factors Determining the Pharmacokinetics and Antiviral Activity of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors of the Diaryltriazine and Diarylpyrimidine Classes of Compounds

OBJECTIVE

To investigate the important factors that determine the bioavailability and the antiviral activity of the diaryltriazine (DATA) and diarylpyrimidine (DAPY) non-nucleoside reverse transcriptase inhibitors (NNRTIs) of HIV-1 in animal species and humans using cell-based assays, physicochemical and computed parameters.

METHODS

This naturalistic study included 15 parameters ranging from molecular mechanics calculations to phase I clinical trials. The calculated parameters were solvent-accessible surface area (SASA), polar surface area and Gibbs free energy of solvation. Physicochemical parameters comprised lipophilicity (octanol/water partition coefficient [cLogP]), ionisation constant (pKa), solubility and aggregate radius. Cell-based assays included human colonic adenocarcinoma cell (Caco-2) permeability (transepithelial transport), drug metabolism and antiviral activity (negative logarithm of the molar effective concentration inhibiting viral replication by 50% [pEC50]). Exposure was tested in rats, dogs and human volunteers.

RESULTS

Of the 15 parameters, eight correlated consistently among one another. Exposure (area under the plasma concentration-time curve [AUC]) in humans correlated positively with that in rats (r = 1.00), with transepithelial transport (r = 0.83), lipophilicity (r = 0.60), ionisability (r = 0.89), hydrodynamic radius of aggregates (r = 0.66) and with antiviral activity (r = 0.61). Exposure in humans was also seen to correlate negatively with SASA (r = -0.89). No consistent correlation was found between exposure in dogs and the eight parameters. Of the 14 DATA/DAPY molecules, 11 form aggregates with radii between 34 and 100 nm.

CONCLUSIONS

We observed correlations between exposure in humans with exposure in rats, transepithelial transport (Caco-2 cells), ionisability, lipophilicity, aggregate radius and SASA in the class of DATA/DAPY NNRTI compounds. The lipophilic DATA/DAPY compounds form aggregates. It can be assumed that absorption in the intestinal tract and endocytosis in infected cells of these lipophilic compounds are governed by the common phenomenon of aggregate formation. As the lymphatic system offers a pathway for intestinal uptake of aggregates, this may offer a therapeutic advantage in the treatment of HIV-1 infection. Although it was not the objective of the study, we found that the rat was a better in vivo model than the dog for the prediction of systemic exposure in this particular set of compounds.

Long-term outcome of patients with multiple (> or = 3) noninfected transvenous leads: a clinical and echocardiographic study

To prospectively assess the incidence and clinical significance of thromboembolic complications in patients with multiple (> or = 3) noninfected transvenous leads; 48 consecutive patients were evaluated. Half of the patients had two ventricular leads and one atrial lead, 15 patients had two atrial leads and one ventricular lead, while 9 patients had two ventricular and two atrial leads. No additional care was provided except for aspirin (80 mg bid) and annually performed echo-Doppler studies. Clinical follow-up included signs and symptoms of subclavian and/or axillary vein thrombosis, the presence of right congestive heart failure, the number of hospital admissions, and death. Echo-Doppler studies assessed the presence of an enlarged right atrium or ventricle, right atrial or ventricular spontaneous contrast, and the presence of tricuspid regurgitation. During a total follow-up of 7.4 +/- 2.2 years there were no differences in the incidence of clinical variables as compared to age-matched controls with DDD pacemakers. The most common complication was transient venous thrombosis (mostly presenting as venous prominence 1-2 weeks after implantation), which was seen in 17% of the study group versus 15% in controls (NS). Cumulative mortality was not different in both groups (13% in the study group vs 15% in controls). No differences were present with respect to hospital admissions (1.1 +/- 0.27/year in the study group vs 1.2 +/- 0.30/year in the controls). In patients with multiple ventricular leads, tricuspid regurgitation on echo-Doppler studies was more frequent (24%) as compared to controls (4%); however, clinical signs of right heart failure were equally distributed. Thus, patients with multiple (> or = 3) noninfected leads have no clinical adverse outcome during long-term follow-up.