A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach.     

Synthesis and photochemistry of beta,beta'-di(2-furyl)-substituted o-divinylbenzenes: intra- and/or intermolecular cycloaddition as an effect of annelation

New heteroaryl-substituted o-divinylbenzenes, 2,2'-(1,2-phenylenedivinylene)difuran (9), 2,2'-(1,2-phenylenedivinylene)bisbenzo[b]furan (10), and 2,2'-(1,2-phenylenedivinylene)bisnaphtho[2,1-b]furan (11), were prepared and irradiated at various concentrations; intramolecular photocycloaddition and intermolecular [2+2] twofold photoaddition reactions took place to give bicyclo[3.2.1]octadiene derivatives 12-14 and cyclophane derivatives 15-17, respectively. Compound 11 was the most selective of these o-divinylbenzenes, which, owing to pi-pi intra- or intermolecular complexation, gave only the exo-bicyclo[3.2.1]octadiene derivative 14 at low concentrations, and only the cyclophane derivative 17 at high concentrations.     

Preparation via Diastereoselective Hydrogenation,Absolute Conformation and Configuration of Exogeneous Anabolic Zeranol ((3S, 7R)-3,4,5,6,7,8,9,10,11,12-Decahydro-7,14,16-trihydroxy-3-methy-1H-2-benzoxacyclotetradecin-1-one)

Hydrogenation of the ketone group in di-O-benzylderivative ( 8 ) of the known macrocyclic lactone zeralenone ( 7 ) using a novel chiral borane complex 3 . BH₃, prepared in situ, proceeded at lower temperatures with moderate diastereoselectivity (～40%, d. e. at ?60°). Unsaturated diastereomers 9 and 10 were separated, and 9 converted into zeranol ( 11 ), a known anabolic agent. Restricted conformational mobility at lower temperatures is assumed for the intermediate 8 on the basis of the temperature-dependent CD spectra of its acetyl congeners 18 and 19 . X-Ray structure analysis of 7-O-acetylderivative ( 13 ) of 11 revealed the (R)-configuration at C(7). Two crystallographically independent H₂O molecules are involved in the H-bonds, one of them (O(21)) rises the helices of the molecules of 13 along b. Small positive torsional angle [C(16)-]C(161)-C(1) [=O] (+19.3°), transoid(E) conformation of the lactone group, and nearly achiral arrangement of the C(11)-C(12) bond (torsional angle [C(11)-]C(12)-C(121)[C(161)] is ?93°) are the main conformational features that differentiate the macrocylic RAL (resorcinic-acid lactone) derivatives from the 6-membered lactone derivative 20 , studied earlier by CD. Consequently, the rules developed for the CD effects within conjugation band (around 270 nm), and n→π* band (around 255 nm) of the latter compound, cannot be applied the macrocyclic lactones.     

Correlation of the absolute conformation of sec alcohols derived from macrocyclic lactones of resorcylic acid and their stereoselective transacetylation in organic solvents by Pseudomonas fluorescens lipase

Transacetylation of diastereomeric pairs of sec. alcohols, derived from macrocyclic lactones of resorcylic acid; 7,β-trans-zearalenols (1,2, full names., (3S,7R and 3S,7S) trans- 3,4,5,6,9,10-octahydro-7,14,16-trihydroxy-3-methyl-1H-2-benzoxacyclotetradecine-1-ones), 7,β-cis-zearalenols (5,6),and 7,β-zearanols (9,10,full names., (3S,7R and 3S,7S) 3,4,5,6,9,10,11,12-decahydro-714,16-trihydroxy-3-methyl-1H-2-benzoxacyclotetradecine-1-ones) by vinylacetate, catalysed by Pseudomonas sp. and Pseudomonas fluorescens lipase in n-heptane and acetonitrile has been studied. It is highly stereoselective; diastereomeric excess of 7β-O-acetates was usually near 100%. K_M, V_max and specificity constant V_max/K_M do not significantly differ for 7β-stereoisomers 2, 6 and 10. However, they notably change on going from n-heptane to acetonitrile, and the specificity constant drops by factor ca 10-100. The enzyme-bound water is assumed to be partly released in the latter solvent, thus diminishing the interaction with the hydrophilic region of the substrates, and affecting the activity. but not the stereoselectivity of lipases. To correlate the structural and conformational properties of these substrates with unexpectedly high diastereoselectivity of enzymatic transacetylation, the solid state structures of 7β-isomers 2, 4, 6, 10 and 12 have been determined by X-ray analysis. The X-ray structure analysis has revealed that the 7 and 7β isomers possess notably different and in some cases almost mirror-image related absolute conformations around the reactive center. The importance of conformational chirality in the hydrophobic region of these substrates for stereoselection in transacylation by microbial lipases is discussed.     

Bis­(ethyl­enedi­amine‐N,N′)(pyrimidine‐2‐carboxyl­ato‐N1,O)­cobalt(III) bis­(tri­fluoro­methane­sulfonate) dihydrate

In the title compound, the coordination geometry of the Co^III atom is only slightly distorted from regular octahedral, and the racemic nature of the material was confirmed by X‐ray structure analysis.     

Circular Dichroism of Some 2-(Phenylmethyl)pyridine Derivatives

The absolute configuration of the 2-(phenylmethyl)pyridine derivatives 1 – 9 had been established by X-ray diffraction and chemical correlation. Their CD spectra have been studied in different solvents for the free and protonated forms. It has now been found that, from the sign of the strong CD couplet between 270 and 220 nm, which was observable for all these compounds besides 7 and 9 , their absolute configuration can be determined much quicker.     

Classification of auxin plant hormones by interaction property similarity indices

Although auxins were the first type of plant hormone to be identified, little is known about the molecular mechanism of this important class of plant hormones. We present a classification of a set of about 50 compounds with measured auxin activities, according to their interaction properties. Four classes of compounds were defined: strongly active, weakly active with weak antiauxin behaviour, inactive and inhibitory. All compounds were modeled in two low-energy conformations, P and T, so as to obtain the best match to the planar and tilted conformations, respectively, of indole 3-acetic acid. Each set of conformers was superimposed separately using several different alignment schemes. Molecular interaction energy fields were computed for each molecule with five different chemical probes and then compared by computing similarity indices. Similarity analysis showed that the classes are on average distinguishable, with better differentiation achieved for the T conformers than the P conformers. This indicates that the T conformation might be the active one. Further, a screening was developed which could distinguish compounds with auxin activity from inactive compounds and most antiauxins using the T conformers. The classifications rationalize ambiguities in activity data found in the literature and should be of value in predicting the activities of new plant growth substances and herbicides.     

2D and 3D supramolecular assemblies of double cyclopalladated azobenzenes realized by C-H?Cl-Pd, π?π and C-H?π interactions

The double cyclopalladated complex with azobenzene, μ-[(E)-1,2-diphenyldiazene-C^2,8, N^1,2]-di-[chloro(dimethylsulfoxide)palladium(II)]; (DMSO)PdCl(μ-C₆H₄NNC₆H₄)(DMSO)PdCl (1) and its analogous complex with DMF as ancillary ligand, (DMF)PdCl(μ-C₆H₄NNC₆H₄)(DMF)PdCl; μ-[(E)-1,2-diphenyldiazene-C^2,8,N^1,2]-di-[chloro(dimethylformamide)palladium(II)] (2a) were synthesized and the function of cyclopalladated moiety in molecular assembling in the solid state is illustrated by their crystal packings. The polymorphism of 2a and 2b is discussed. The crystal structures reveal assemblies with molecular components self-organized by C-H?Cl-Pd hydrogen bonds, π?π, and C-H?π interactions. The double cyclopalladated complexes of azobenzene, with two Pd-Cl moieties participating in the hydrogen bond formation and π-conjugated system involved in the π?π or C-H?π interactions, represent a new class of building blocks for construction of solid state supramolecular assemblies.     

Synthesis, structure, and biological evaluation of C-2 sulfonamido pyrimidine nucleosides

The C-2 sulfonamido pyrimidine nucleosides were prepared by opening the 2,2′- or 2,3′-bond in anhydronucleosides under nucleophilic attack of sulfonamide anions. Reaction of the sodium salt of p-toluenesulfonamide or 2-(aminosulfonyl)-N,N-dimethylnicotinamide with 2,2′-anhydro-1-(β-d-arabinofuranosyl)cytosine gave the C-2 sulfonamido derivatives in excellent yields. Ring opening of the less reactive 2,2′-anhydrouridine and 2,3′-anhydrothymidine could be accomplished with DBU/CH₃CN activation of p-toluenesulfonamide, giving moderate yields for C-2 sulfonamido derivatives. The action of acetic acid or ZnBr₂/CH₂Cl₂ on 5-methyl-N²-tosyl-1-(2-deoxy-5-O-trityl-β-d-threo-pentofuranosyl)isocytosine led to the cleavage of both the protection group and the nucleoside bond, yielding 5-methyl-N²-tosylisocytosine as the major product. Structures of the prepared C-2 sulfonamido nucleosides were confirmed by the 1D and 2D NMR experiments, and X-ray structural analysis of 4-imino-N²-tosylamino-1-(β-d-arabinofuranosyl)pyrimidine. Both methods confirmed β-configuration and anti-conformation of the 2-sulfonamido nucleosides. The investigated compounds displayed moderate inhibition of tumor cell growth in vitro, as determined by the MTT assay using six different human tumor cell lines.