Comparative molecular field analysis of a series of inhibitors of HIV-1 protease

Several protease inhibitors have reached the world market in the last fifteen years, dramatically improving the quality of life and life expectancy of millions of HIV-infected patients. In spite of the tremendous research efforts in this area, resistant HIV-1 variants are constantly decreasing the ability of the drugs to efficiently inhibit the enzyme. As a consequence, inhibitors with novel frameworks are necessary to circumvent resistance to chemotherapy. In the present work, we have created 3D QSAR models for a series of 82 HIV-1 protease inhibitors employing the comparative molecular field analysis (CoMFA) method. Significant correlation coefficients were obtained (q(2) = 0.82 and r(2) = 0.97), indicating the internal consistency of the best model, which was then used to evaluate an external test set containing 17 compounds. The predicted values were in good agreement with the experimental results, showing the robustness of the model and its substantial predictive power for untested compounds. The final QSAR model and the information gathered from the CoMFA contour maps should be useful for the design of novel anti-HIV agents with improved potency.

Acridone alkaloids as potent inhibitors of cathepsin V

Cathepsin V is a lysosomal cysteine peptidase highly expressed in thymus, testis and corneal epithelium. Eleven acridone alkaloids were isolated from Swinglea glutinosa (Bl.) Merr. (Rutaceae), with eight of them being identified as potent and reversible inhibitors of cathepsin V (IC(50) values ranging from 1.2 to 3.9 mu M). Detailed mechanistic characterization of the effects of these compounds on the cathepsin V-catalyzed reaction showed clear competitive inhibition with respect to substrate, with dissociation constants (K(i)) in the low micromolar range (2, K(i) = 1.2 mu M; 6, K(i) = 1.0 mu M; 7, K(i) = 0.2 mu M; and 11, K(i) = 1.7 mu M). Molecular modeling studies provided important insight into the structural basis for binding affinity and enzyme inhibition. Experimental and computational approaches, including biological evaluation, mode of action assessment and modeling studies were successfully employed in the discovery of a small series of acridone alkaloid derivatives as competitive inhibitors of catV. The most potent inhibitor (7) has a K(i) value of 200 nM. (C) 2011 Elsevier Ltd. All rights reserved.

Discovery of New Inhibitors of Schistosoma mansoni PNP by Pharmacophore-Based Virtual Screening

Schistosomiasis is considered the second most important tropical parasitic disease, with severe socioeconomic consequences for millions of people worldwide. Schistosoma monsoni, one of the causative agents of human schistosomiasis, is unable to synthesize purine nucleotides de novo, which makes the enzymes of the purine salvage pathway important targets for antischistosomal drug development. In the present work, we describe the development of a pharmacophore model for ligands of S. mansoni purine nucleoside phosphorylase (SmPNP) as well as a pharmacophore-based virtual screening approach, which resulted in the identification of three thioxothiazolidinones (1-3) with substantial in vitro inhibitory activity against SmPNP. Synthesis, biochemical evaluation, and structure activity relationship investigations led to the successful development of a small set of thioxothiazolidinone derivatives harboring a novel chemical scaffold as new competitive inhibitors of SmPNP at the low-micromolar range. Seven compounds were identified with IC(50) values below 100 mu M. The most potent inhibitors 7, 10, and 17 with 1050 of 2, 18, and 38 mu M, respectively, could represent new potential lead compounds for further development of the therapy of schistosomiasis.

Pharmacophore-based 3D QSAR studies on a series of high affinity 5-HT(1A) receptor ligands

5-HT(1A) receptor antagonists have been employed to treat depression, but the lack of structural information on this receptor hampers the design of specific and selective ligands. In this study, we have performed CoMFA studies on a training set of arylpiperazines (high affinity 5-HT(1A) receptor ligands) and to produce an effective alignment of the data set, a pharmacophore model was produced using Galahad. A statistically significant model was obtained, indicating a good internal consistency and predictive ability for untested compounds. The information gathered from our receptor-independent pharmacophore hypothesis is in good agreement with results from independent studies using different approaches. Therefore, this work provides important insights on the chemical and structural basis involved in the molecular recognition of these compounds. (C) 2010 Elsevier Masson SAS. All rights reserved.

Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: Kinetic and structural studies

Selectivity plays a crucial role in the design of enzyme inhibitors as novel antiparasitic agents, particularly in cases where the target enzyme is also present in the human host. Purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an attractive target for the discovery of potential antischistosomal agents. In the present work, kinetic studies were carried out in order to determine the inhibitory potency, mode of action and enzyme selectivity of a series of inhibitors of SmPNP. In addition, crystallographic studies provided important structural insights for rational inhibitor design, revealing consistent structural differences in the binding mode of the inhibitors in the active sites of the SmPNP and human PNP (HsPNP) structures. The molecular information gathered in this work should be useful for future medicinal chemistry efforts in the design of new inhibitors of SmPNP having increased affinity and selectivity. (C) 2010 Elsevier Ltd. All rights reserved.

Bendadaite, a new iron arsenate mineral of the arthurite group

Bendadaite, ideally Fe(2+)Fe(2)(3+)(AsO(4))(2)(OH)(2 center dot).4H(2)O, is a new member of the arthurite group It was found as a weathering product of arsenopyrite on a single hand specimen from the phosphate pegmatite Bendada. central Portugal (type locality) Co-type locality is the granite pegmatite of La via do Almerindo (Almerindo mine), Linopolis, Divmo das Laranjeiras county, Minas Gerais, Brazil Further localities are the Vein Negra mine, Copiapo province, Chile, mid-East, Bou Azzer district, Morocco, and Para Inferida yard, Fenugu Sibirt mine, Gonnosfanadiga, Medio Campidano Province, Sardinia. Italy Type bendadaite occurs as blackish green to dark brownish tufts (<0 1 mm long) and flattened radiating aggregates. in intimate association with an intermediate member of the scorodite-mansfieldite series It is monoclinic. space group P2(l/c). with a = 10 239(3) angstrom. b = 9 713(2) angstrom, c = 5 552(2) angstrom. beta = 94 11(2)degrees. = 550 7(2) angstrom(3). Z = 2 Electron-microprobe analysis yielded (wt %). CaO 0 04, MnO 0 03. CuO 006, ZnO 004. Fe(2)O(3) (total) 43 92, Al(2)O(3) 115. SnO(2) 0 10, As(2)O(5) 43 27. P(2)O(5) 1 86, SO(3) 0.03 The empirical formula is (Fe(0 52)(2+)Fe(0 32)(3+)rectangle(0 16))(Sigma 1 00)(Fe(1 89)(3+)Al(0 11))(Sigma 2 00)(As(1 87)P(0 13))(Sigma 2 00)O(8)(OH)(2 00) 4H(2)O based. CM 2(As,P) and assuming ideal 80, 2(OH), 4H2O and complete occupancy of the ferric on site by Fe(3+) and Al Optically, bendadaite is biaxial, positive, 2V(est) = 85+/-4 degrees, 2V(eale) = 88 degrees, with alpha 1 734(3). 13 1 759(3), 7 1 787(4) Pleochrosim is medium strong X pale reddish brown. Y yellowish brown, Z dark yellowish brown. absorption Z > V > X, optical dispersion weak, r > v. Optical axis plane Is parallel to (010), with X approximately parallel to a and Z nearly parallel to c Bendadaite has vitreous to sub-adamantine luster, is translucent and non-fluorescent It is brittle, shows irregular fracture and a good cleavage parallel to 1010} 3 15 0 10 g/cm(3), 3 193 g/cm3 (for the empirical formula) The five strongest powder diffraction lines [d in angstrom (I)(hkl] are 10 22 (10)(100), 7 036 (8)(110), 4 250 (5)(11 I), 2 865 (4)(311), 4 833 (3)(020,011) The d spacings are very similar to those of its Zn analogue, ojelaite The crystal structure of bendadaite was solved and refined using a crystal from the co-type locality with the composition (Fe(0 95)(2+)rectangle(0 05))(Sigma 1 00)(Fe(1 80)(3+)Al(0 20))Sigma(2 00)(As(1 48)P(0 52))(Sigma 2 00)O(8)) (OH)(2) 4H(2)O (R = 16%) and confirms an arthurite-type atomic arrangement

Comparison of roving-window and search-window techniques for characterising landscape morphometry

Brazil`s State of Sao Paulo Research Foundation

A criterion for unitary similarity of upper triangular matrices in general position

Each square complex matrix is unitarily similar to an upper triangular matrix with diagonal entries in any prescribed order. Let A = [a(ij)] and B = [b(ij)] be upper triangular n x n matrices that are not similar to direct sums of square matrices of smaller sizes, or are in general position and have the same main diagonal. We prove that A and B are unitarily similar if and only if parallel to h(A(k))parallel to = parallel to h(B(k))parallel to for all h is an element of C vertical bar x vertical bar and k = 1, ..., n, where A(k) := [a(ij)](i.j=1)(k) and B(k) := [b(ij)](i.j=1)(k) are the leading principal k x k submatrices of A and B, and parallel to . parallel to is the Frobenius norm. (C) 2011 Elsevier Inc. All rights reserved.

Absolute configuration reassignment of two chromanes from Peperomia obtusifolia (Piperaceae) using VCD and DFT calculations

Previous analysis of the ECD spectra of two prenylated benzopyrans isolated from Peperomia obtusifolia, by means of the helicity rule for the chromane chromophore, resulted in the incorrect assignment of their absolute configuration, (5) instead of (R) for a deduced P-helicity of the chromane ring for the (+)-enantiomers. This was discovered by the application of DFT calculations and VCD spectroscopy. Experimental and calculated (B3LYP/6-31G(d)) VCD and IR spectra were compared, and a definitive absolute configuration of (+)-1 and (+)-2 is reassigned directly in solution as (R). The assumption of equatorial positioning of bulky groups, shown here to be invalid for the title molecules, is the underlying cause of the previous incorrect assignment of absolute configuration. Moreover, TDDFT (B3LYP/6-311++G(2d,2p)//B3LYP/6-31G(d)) calculations of ECD spectra have shown that both P- and M-helicity of the heterocyclic ring, for a given absolute configuration, lead to the same sign for the (1)L(b) ECD band, thus bringing into question the validity of the empirical ECD helicity rule for chromane molecules. (C) 2010 Elsevier Ltd. All rights reserved.

Chemoenzymatic synthesis of boron-containing chiral amines and amides

The first application of lipases as catalysts to obtain optically active boron-containing amines and amides is described. We studied several reaction conditions to achieve the kinetic resolution of boron-containing amines via enantioselective acylation mediated by Candida antarctica lipase B (CAL-B). Excellent enantioselectivity (E>200) and high enantiomeric excess (up to >99%) of both the remaining amines and amides were obtained. (C) 2010 Elsevier Ltd. All rights reserved.

Geranylation of benzoic acid derivatives by enzymatic extracts from Piper crassinervium (Piperaceae)

The ability to carry out geranylations on aromatic substrates using enzymatic extracts from the leaves of Piper crassinervium (Piperaceae) was evaluated. A literature analysis pointed out its importance as a source of prenylated bioactive molecules. The screening performed on aromatic acceptors (benzoic acids, phenols and phenylpropanoids) including geranyl diphosphate as prenyl donor, showed the biotransformation of the 3,4-dihydroxybenzoic acid by the crude extract, and the p-hydroxybenzoic acid by both the microsomal fraction and the crude extract, after treating leaves with glucose. The analysis of the products allowed the identification of C- and O-geranylated derivatives, and the protease (subtilisin and pepsin) inhibition performed on the O-geranylated compounds showed weak inhibition. Electrophoretic profiles indicated the presence of bands/spots among 56-58 kDa and pI 6-7, which are compatible with prenyltransferases. These findings show that P. crassinervium could be considered as a source of extracts with geranyltransferase activity to perform biotransformations on aromatic substrates. (C) 2010 Elsevier Ltd. All rights reserved.

Effects of milk supplementation with skim milk powder, whey protein concentrate and sodium caseinate on acidification kinetics, rheological properties and structure of nonfat stirred yogurt

Milk supplementation with milk proteins in four different levels was used to investigate the effect on acidification and textural properties of yogurt. Commercial skim milk powder was diluted in distilled water, and the supplements were added to give different enriched-milk bases; these were heat treated at 90 degrees C for 5 min. These mixtures were incubated with the bacterial cultures for fermentation in a water bath, at 42 degrees C, until pH 4.50 was reached. Chemical changes during fermentation were followed by measuring the pH. Protein concentration measurements, microbial counts of Lactobacillus bulgaricus and Streptococcus thermophilus, and textural properties (G`, G ``, yield stress and firmness) were determined after 24 h of storage at 4 degrees C. Yogurt made with milk supplemented with sodium caseinate resulted in significant properties changes, which were decrease in fermentation time, and increase in yield stress, storage modulus, and firmness, with increases in supplement level. Microstructure also differed from that of yogurt produced with milk supplemented with skim milk powder or sodium caseinate. (C) 2009 Elsevier Ltd. All rights reserved.

Lipase-Catalyzed Highly Enantioselective Kinetic Resolution of Boron-Containing Chiral Alcohols

The first application of enzymes as catalysts to obtain optically pure boron compounds is described. The kinetic resolution of boron-containing chiral alcohols via enantioselective transesterification catalyzed by lipases was studied. Aromatic, allylic, and aliphatic secondary alcohols containing a boronate ester or boronic acid group were resolved by lipase from Candida antartica (CALB), and excellent E values (E > 200) and high enantiomeric excesses (up to >99%) of both remaining substrates and acetylated product were obtained.

Absolute Configuration and Selective Trypanocidal Activity of Gaudichaudianic Acid Enantiomers

Gaudichaudianic acid, a prenylated chromene isolated from Piper gaudichaudianum, has been described as a potent trypanocidal compound against the Y-strain of Trypanosoma cruzi. We herein describe its isolation as a racemic mixture followed by enantiomeric resolution using chiral HPLC and determination of the absolute configuration of the enantiomers as (+)-S and (-)-R by means of a combination of electronic and vibrational circular dichroism using density functional theory calculations. Investigation of the EtOAc extract of the roots, stems, and leaves from both adult specimens and seedlings of P. gaudichaudianum revealed that gaudichaudianic acid is biosynthesized as a racemic mixture from the seedling stage onward. Moreover, gaudichaudianic acid was found exclusively in the roots of seedlings, while it is present in all organs of the adult plant. Trypanocidal assays indicated that the (+)-enantiomer was more active than its antipode. Interestingly, mixtures of enantiomers stowed a synergistic effect, with the racemic mixture being the most active.

Solvatochromism in Binary Mixtures: First Report on a Solvation Free Energy Relationship between Solvent Exchange Equilibrium Constants and the Properties of the Medium

We have employed UV-vis spectroscopy in order to investigate details of the solvation of six solvatochromic indicators, hereafter designated as ""probes"", namely, 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (RB); 4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePM; 1-methylquinolinium-8-olate, QB; 2-bromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr, 2,6-dichloro-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (WB); and 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr,, respectively. These can be divided into three pairs, each includes two probes of similar pK(a) in water and different lipophilicity. Solvation has been studied in binary mixtures, BMs, of water, W, with 12 protic organic solvents, S, including mono- and bifunctional alcohols (2-alkoxyethanoles, unsaturated and chlorinated alcohols). Each medium was treated as a mixture of S, W, and a complex solvent, S-W, formed by hydrogen bonding. Values of lambda(max) (of the probe intramolecular charge transfer) were converted into empirical polarity scales, E(T)(probe) in kcal/mol, whose values were correlated with the effective mole fraction of water in the medium, chi w(effective). This correlation furnished three equilibrium constants for the exchange of solvents in the probe solvation shell; phi(W/S) (W substitutes S): phi(S-W/W) (S-W substitutes W), and phi(S-W/S) (S-W substitutes S), respectively. The values of these constants depend on the physicochemical properties of the probe and the medium. We tested, for the first time, the applicability of a new solvation free energy relationship: phi = constant + a alpha(BM) + b beta(BM) + s(pi*(BM) + d delta) + p log P(BM), where a, b, s, and p are regression coefficients alpha(BM), beta(BM), and pi*(BM) are solvatochromic parameters of the BM, delta is a correction term for pi*, and log P is an empirical scale of lipophilicity. Correlations were carried out with two-, three-, and four-medium descriptors. In all cases, three descriptors gave satisfactory correlations; use of four parameters gave only a marginal increase of the goodness of fit. For phi(W/S), the most important descriptor was found to be the lipophilicity of the medium; for phi(S-W/W) and phi(S-W/S), solvent basicity is either statistically relevant or is the most important descriptor. These responses are different from those of E(T)(probe) of many solvatochromic indicators in pure solvents, where the importance of solvent basicity is usually marginal, and can be neglected.