Reverse pharmacognosy: another way to harness the generosity of nature.

A huge amount of data has been generated by decades of pharmacognosy supported by the rapid evolution of chemical, biological and computational techniques. How can we cope with this overwhelming mass of information? Reverse pharmacognosy was introduced with this aim in view. It proceeds from natural molecules to organisms that contain them via biological assays in order to identify an activity. In silico techniques and particularly inverse screening are key technologies to achieve this goal efficiently. Reverse pharmacognosy allows us to identify which molecule(s) from an organism is(are) responsible for the biological activity and the biological pathway(s) involved. An exciting outcome of this approach is that it not only provides evidence of the therapeutic properties of plants used in traditional medicine for instance, but may also position other plants containing the same active compounds for the same usage, thus increasing the curative arsenal e.g. development of new botanicals. This is particularly interesting in countries where western medicines are still not affordable. At the molecular level, in organisms, families of metabolites are synthesized and seldom have a single structure. Hence, when a natural compound has an interesting activity, it may be desirable to check whether there are more active and/or less toxic derivatives in organisms containing the hit - this corresponds to a kind of "natural combinatorial" chemistry. At a time when the pharmaceutical industry is lacking drug candidates in clinical trials, drug repositioning - i.e. exploiting existing knowledge for innovation - has never been so critical. Reverse pharmacognosy can contribute to addressing certain issues in current drug discovery - such as the lack of clinical candidates, toxicity... - by exploiting existing data from pharmacognosy. This review will focus on recent advances in computer science applied to natural substance research that consolidate the new concept of reverse pharmacognosy.

Ligand-escape pathways from the ligand-binding domain of PPARgamma receptor as probed by molecular dynamics simulations.

Conformational rearrangements of peroxysome proliferator activated receptor (PPARgamma) ligand-binding domain (LBD) that accompany the release and binding of ligands are not well understood. To determine the major events associated with the escape of the partial agonist GW0072, molecular dynamic (MD) simulations were performed using two different methods: reversed targeted molecular dynamics (TMD(-1)) and time-dependent distance restraints (TDR) using as restraints either the root mean square deviation from a reference structure (TMD(-1)) or the distance between the geometrical centers of the binding pocket and of the ligand (TDR). Both methods do not assume any a priori route for ligand extraction. To avoid artifacts, different initial simulation conditions were used and particular attention was paid for giving time to the protein to relax during the extraction process by running 10-12 ns simulations within explicit water. Two distinct exit gates A and B were found, independently of initial conditions and method. During the exit process no interaction between GW0072 and the transactivation AF-2 helix was observed. Our results suggest that the ligand uses the intrinsic flexibility of the protein to move within the receptor. Paths A and B are very similar to those found for other nuclear receptors, suggesting that these routes are a common characteristics of nuclear receptors that are used by different kinds of ligands. Finally, the knowledge of entry/exit pathways of a receptor should be very useful in discriminating between different ligands that could have been favorably docked in the binding pocket by introducing docking along these pathways into computational drug design protocols.

Study of the attachment of Na+ on glucose and on some of its methylated derivatives.

The mechanism of attachment of Na(+) on glucose, methyl-alpha-D-glucose, methyl-beta-D-glucose, 3-O-methylglucose, tetra-O-methylglucose, and also on galactose and methyl-beta-D-galactose, was studied. For this we measured the ion yields for the complex [sugar-Na(+)] formed by ionisation by matrix-assisted laser desorption/ionisation (MALDI) and ionspray. These data were compared with the relative volatilities and hydrophobicities of the sugars, measured by evaporative light scattering and reversed-phase liquid chromatography, respectively. Some formation enthalpies for the complexes [sugar-Na(+)], starting from the sugar and the cation, were obtained by ab initio calculations. No simple correlations could be observed between the ion yields and the parameters studied, so that the cationisation mechanism of the sugars remains unclear.

alpha-, beta-, and gamma-Cyclodextrin dimers. Molecular modeling studies by molecular mechanics and molecular dynamics simulations.

The alpha-, beta-, and gamma-cyclodextrin (CyD) dimers have been studied by molecular mechanics (MM) and molecular dynamics (MD) calculations, and the relative stability of dimers and the involved molecular interactions have been determined. Three possible orientations were considered for the alpha-, beta-, and gamma-CyD dimers: the head-to-head, the head-to-tail, and the tail-to-tail. In vacuo MM calculations were used to obtain the most stable arrangements, and MD simulations were performed over all energy minima obtained for each dimer. Results from MD always show head-to-head orientation as the most stable as a result of the larger number of intermolecular hydrogen bonds present.

Attachment of alkali cations on beta-D-glucopyranose: matrix-assisted laser desorption/ionization time-of-flight studies and ab initio calculations.

In matrix-assisted laser desorption/ionization mass spectrometry, carbohydrates ionize by attachment of an alkali cation, and the ion yield varies with the nature of the cation. In an attempt to contribute to the understanding of the mechanisms involved, we have conducted matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) experiments on the simple glucose molecule with the alkali cations Li+, Na+ and K+, and have also performed ab initio calculations. The calculations show that, for the most stable carbohydrate-cation geometry, the carbohydrate ring is twisted and the cation is coordinated to four oxygen atoms. Calculations also show that in these complexes the positions of the three cations are very similar, and the smaller the cation, the closer it is to the oxygen atoms. Finally, the calculated formation enthalpies of the different complexes agree with the experimental results obtained for the order of stability of these complexes.

3D-QSAR CoMFA study on imidazolinergic I(2) ligands: a significant model through a combined exploration of structural diversity and methodology.

Displaying an unprecedented structural diversity, 119 I(2) ligands, and their pK(i) values, were collected and submitted to a comparative molecular fields analysis (CoMFA) study. They were discerned into three structural subsets (A, B, C), to explore the I(2) 3D-QSARs from finite structural systems (A, B, C) to more complex ones (AB, AC, BC, ABC). In addition, various key steps of the CoMFA methology were explored. The applied method used two pharmacophore templates and seven molecular field combinations (electrostatic, lipophilic, steric), as well as eight alignment methods (two point-by-point and six similarity-based variations). That way, 644 CoMFA models were obtained and further selected according to their predictive ability through two filters. The first filter was mainly based on the q(2), which internally evaluates the predictive ability from the training set. For the second filter, the predictive ability was externally evaluated through the prediction of test sets. Finally, one model was extracted from the whole data as the best. Indeed, it combines three features of upmost importance for the further design of ligands endowed with high I(2) affinity: structural diversity (n = 73), robustness (N = 9, r(2) = 0.96, s = 0. 28, F = 148), and a great fully assessed predictive ability (q(2) = 0.50, r(2)(test set) = 0.81, n(test set) = 46). On the basis of structural data and CoMFA isocontours, some elements of the I(2) tridimensional pharmacophore are also suggested.

A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA.

The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)3-N+(CH3)3 and -(CH2)6-I)) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to oligonucleotides with the aim of being used for specific in situ detection of biomolecular interactions. Both photophysical measurements and molecular calculations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 x 10(-5) and 2 x 10(-4), respectively. However, upon binding to double-stranded DNA, large spectroscopic changes result and the quantum yield of fluorescence is enhanced by four orders of magnitude, reaching values up to phi F = 0.2 and 0.3, respectively, as a result of an intercalation mechanism between DNA base pairs. A modulation of the quantum yield is observed as a function of the base sequence. The two derivatives also bind with single-stranded oligonucleotides, but the fluorescence quantum yield is not so great as that when bound to double-stranded samples. Typical fluorescence quantum yields of 7 x 10(-3) to 3 x 10(-2) are observed when the dyes interact with short oligonucleotides, whereas the fluorescence quantum yield remains below 10(-2) when interacting with single-stranded oligonucleotides. This slight but significant quantum-yield increase is interpreted as a folding of the single strand around the dye, which reduces the internal rotation of the two heterocycles around the central methine bridge that links the two moieties of the dye. From these properties, it is proposed to link monomer covalently to oligonucleotides for the subsequent detection of target sequences within cells.

Pharmacophoric search and 3D-QSAR comparative molecular field analysis studies on agonists of melatonin sheep receptors.

Conformational analysis was used to characterize the agonist pharmacophore for melatonin sheep brain receptor recognition and activation. The molecular geometry shared by all conformations of the selected active ligands was determined. Assuming that all the compounds interact at the same binding site at the receptor level, 2-iodomelatonin pharmacophoric conformation served as a template for the superimposition of 64 structurally heterogeneous agonists constituting the training set used to perform a three-dimensional quantitative structure-activity relationship study via the comparative molecular field analysis method. A statistically significant model was obtained for the totality of the compounds (n = 64, q2 = 0.62, N = 6, r2 = 0.96, s = 0.28, F = 249) with steric, electrostatic, and lipophilic relative contributions of 28%, 35%, and 37%, respectively. The predictive power of the proposed model was discerned by successfully testing the 78 agonist ligands constituting the test set. The model so obtained and validated brings important structural insights to aid the design of novel melatoninergic agonist ligands prior to their synthesis.

3-amino-3,4-dihydro-2H-1-benzopyran derivatives as 5-HT1A receptor ligands and potential anxiolytic agents. 2. Synthesis and quantitative structure-activity relationship studies of spiro[pyrrolidine- and piperidine-2,3'(2'H)-benzopyrans].

In continuation of our work on 3-amino-3,4-dihydro-2H-1-benzopyran derivatives with high affinity for 5-HT1A receptors, we have prepared rigid spirobenzopyran analogues designed from the pharmacophore models of Mellin and selected via a quantitative structure-activity relationship approach mainly based on similarity indices. A series of spiro[pyrrolidine- and piperidine-2,3'(2'H)-benzopyrans] with various substitutions on the aromatic ring as well as on the extracyclic spiranic nitrogen atom were then synthesized and evaluated for their serotonergic and dopaminergic activities. Good correlation between the predicted and the experimental binding values was observed with an average difference of 0.2 unit on log(IC50). Affinities for the 5-HT1A receptors were in the nanomolar range for the best compounds ((+)-11a,23) with a high selectivity versus other 5-HT (5-HT1B, 5-HT2, 5-HT3) or dopamine (D1, D2) receptor subtypes. As for the 3-amino-3,4-dihydro-2H-1-benzopyran series, the dextrorotatory enantiomer (+)-11a showed better affinity and selectivity for 5-HT1A receptors than its levorotatory analogue (-)-11a. Compound (+)-11a proved in vitro to be a full agonist and in vivo to be active in various comportmental tests predictive of psychotropic activity, such as the forced swim test and the tail suspension test, and is currently under complementary investigations.