Quantitative structure-activity relationship studies of [(biphenyloxy)propyl]isoxazole derivatives. Inhibitors of human rhinovirus 2 replication

Selective inhibitors of picornavirus replication

Picornaviruses cover a large family of pathogens that have a major impact on human but also on veterinary health. Although most infections in man subside mildly or asymptomatically, picornaviruses can also be responsible for severe, potentially life-threatening disease. To date, no therapy has been approved for the treatment of picornavirus infections. However, efforts to develop an antiviral that is effective in treating picornavirus-associated diseases are ongoing. In 2007, Schering-Plough, under license of ViroPharma, completed a phase II clinical trial with Pleconaril, a drug that was originally rejected by the FDA after a New Drug Application in 2001. Rupintrivir, a rhinovirus protease inhibitor developed at Pfizer, reached clinical trials but was recently halted from further development. Finally, Biota's HRV drug BTA-798 is scheduled for phase II trials in 2008. Several key steps in the picornaviral replication cycle, involving structural as well as non-structural proteins, have been identified as valuable targets for inhibition. The current review aims to highlight the most important developments during the past decades in the search for antivirals against picornaviruses.

New pleconaril and [(biphenyloxy)propyl]isoxazole derivatives with substitutions in the central ring exhibit antiviral activity against pleconaril-resistant coxsackievirus B3

Amino acid 1092 (AA1092) in capsid protein 1 of coxsackievirus B3 (CVB3) is located in close vicinity to the central phenoxy group of capsid binders (i.e. pleconaril). Whereas isoleucine is associated with drug susceptibility, leucine and methionine confer resistance to pleconaril. In the present study, novel analogues with different substitutions in the central phenoxy group were synthesized to study their influence on anti-CVB3 activity with the aim to overcome pleconaril resistance. Two [(biphenyloxy)propyl]isoxazoles and pleconaril were synthesized without methyl groups in the central phenoxy ring using Suzuki coupling reaction and tested for antiviral activity against the pleconaril-resistant CVB3 Nancy. Furthermore, pleconaril with 3-methyl, 3-methoxy, 3-bromine, 2,3-dimethyl in the central ring as well as the external rings in meta position were synthesized for structure-activity relationship analysis with CVB3 variants containing leucine, methionine or isoleucine at position 1092, other coxsackieviruses B (CVB) as well as several rhinoviruses. The results demonstrate a high impact of substituents in the central ring of capsid inhibitors for anti-enteroviral activity. Pleconaril resistance of CVB3 based on Leu1092 or Met1092 was overcome by unsubstituted analogues or by monosubstitution with 3-methyl as well as 3-bromine in the central phenyl. The 3-bromine derivative inhibited a broad spectrum of CVB and rhinoviruses.

New descriptors of amino acids and their application to peptide QSAR study

A new set of descriptors was derived from a matrix of three structural variables of the natural amino acid, including van der Waal's volume, net charge index and hydrophobic parameter of side residues. They were selected from many properties of amino acid residues, which have been validated being the key factors to influence the interaction between peptides and its protein receptor. They were then applied to structure characterization and QSAR analysis on bitter tasting di-peptide, agiotensin-converting enzyme inhibitor and bactericidal peptides by using multiple linear regression (MLR) method. The leave one out cross validation values (Q(2)) were 0.921, 0.943 and 0.773. The multiple correlation coefficients (R(2)) were 0.948, 0.970 and 0.926, the root mean square (RMS) error for estimated error were 0.165, 0.154 and 0.41, respectively for bitter tasting di-peptide, angiotensin-converting enzyme inhibitor and bactericidal peptides. Test sets of peptides were used to validate the quantitative model, and it was shown that all these QSAR models had good predictability for outside samples. The results showed that, in comparison with the conventional descriptors, the new set of descriptors is a useful structure characterization method for peptide QSAR analysis, which has multiple advantages, such as definite physical and chemical meaning, easy to get, and good structural characterization ability.

The effect of nitroaromatics' composition on their toxicity in vivo: novel, efficient non-additive 1D QSAR analysis

Novel 1D QSAR approach that allows analysis of non-additive effects of molecular fragments on toxicity has been proposed. Twenty-eight nitroaromatic compounds including some well-known explosives have been chosen for this study. The 50% lethal dose concentration for rats (LD50) was used as the estimation of toxicity in vivo to develop 1D QSAR models on the framework of Simplex representation of molecular structure. The results of 1D QSAR analysis show that even the information about the composition of molecules provides the main trends of toxicity changes. The necessity of consideration of substituents' mutual impacts for the development of adequate QSAR models of nitroaromatics' toxicity was demonstrated. Statistic characteristics for all the developed partial least squares QSAR models, except the additive ones are quite satisfactory (R2=0.81-0.92; Q2=0.64-0.83; R2 test=0.84-0.87). A successful performance of such models is due to their non-additivity i.e. possibility of taking into account the mutual influence of substituents in benzene ring which plays the governing role for toxicity change and could be mediated through the different C-H fragments of the ring. The correspondence between observed and predicted by these models toxicity values is good. This allowing combine advantages of such approaches and develop adequate consensus model that can be used as a toxicity virtual screening tool.

The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study

The present study applies the Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) for (i) evaluation of the influence of the characteristics of 28 nitroaromatic compounds (some of which belong to a widely known class of explosives) as to their toxicity; (ii) prediction of toxicity for new nitroaromatic derivatives; (iii) analysis of the effects of substituents in nitroaromatic compounds on their toxicity in vivo. The 50% lethal dose concentration for rats (LD50) was used to develop the QSAR models based on simplex representation of molecular structure. The preliminary 1D QSAR results show that even the information on the composition of molecules reveals the main tendencies of changes in toxicity. The statistic characteristics for partial least squares 2D QSAR models are quite satisfactory (R2 = 0.96-0.98; Q2 = 0.91-0.93; R2 (test) = 0.89-0.92), which allows us to carry out the prediction of activity for 41 novel compounds designed by the application of new combinations of substituents represented in the training set. The comprehensive analysis of toxicity changes as a function of substituent position and nature was carried out. Molecular fragments that promote and interfere with toxicity were defined on the basis of the obtained models. It was shown that the mutual influence of substituents in the benzene ring plays a crucial role regarding toxicity. The influence of different substituents on toxicity can be mediated via different C-H fragments of the aromatic ring.

Quantitative structure-affinity relationship of 5-HT1A receptor ligands by the classification tree method

The influence of molecular structure of 346 ligands on their affinity for 5-HT1A receptors was investigated. It was shown that the effectiveness of the proposed novel approach for interpretation of decision tree models compared favourably with the PLS method. In the context of the proposed approach, molecular fragments and their values of the relative influence on the affinity for 5-HT1A receptors were defined.