Biomedical subjects

Evans Coutinho

Publications and source records attributed to Evans Coutinho.

15 recordsLinked to original sources

PubMed2006

Synthesis, anti-tuberculosis activity, and 3D-QSAR study of 4-(adamantan-1-yl)-2-substituted quinolines.

Structural optimization of the previously identified 4-(adamantan-1-yl)-2-quinolinecarbohydrazide (AQCH, MIC=6.25 microg/mL, 99% inhibition, Mycobacterium tuberculosis H37Rv) has led to two series of 4-(adamantan-1-yl)-2-substituted quinolines (Series 1-2). All new derivatives were evaluated in vitro for antimycobacterial activities against drug-sensitive M. tuberculosis H37Rv strain. Several 4-adamantan-1-yl-quinoline-2-carboxylic acid N'-alkylhydrazides (Series 1) described herein showed promising inhibitory activity. In particular, analogs 7, 9, 20, and 21 displayed MIC of 3.125 microg/mL. Further investigation of AQCH by its reaction with various aliphatic, aromatic, and heteroaromatic aldehydes led to the synthesis of 4-adamantan-1-yl-quinoline-2-carboxylic acid alkylidene hydrazides (Series 2). Analogs 42-44 and 48 have produced promising antimycobacterial activities (99% inhibition) at 3.125 microg/mL against drug-sensitive M. tuberculosis H37Rv strain. The most potent analog 35 of the series produced 99% inhibition at 1.00 microg/mL against drug-sensitive strain, and MIC of 3.125 microg/mL against isoniazid-resistant TB strain. To understand the relationship between structure and activity, a 3D-QSAR analysis has been carried out by three methods-comparative molecular field analysis (CoMFA), CoMFA with inclusion of a hydropathy field (HINT), and comparative molecular similarity indices analysis (CoMSIA). Several statistically significant CoMFA, CoMFA with HINT, and CoMSIA models were generated. Prediction of the activity of a test set of molecules was the best for the CoMFA model generated with database alignment. Based on the CoMFA contours, we have tried to explain the structure-activity relationships of the compounds reported herein.

Adamantane↗

PubMed2006

Synthesis, anti-tuberculosis activity, and 3D-QSAR study of ring-substituted-2/4-quinolinecarbaldehyde derivatives.

We have previously identified ring-substituted quinolines as a new structural class of anti-tuberculosis agents. In our ongoing efforts at structural optimization of this class, four series of ring-substituted-2/4-quinolinecarbaldehyde derivatives were synthesized. All twenty-four compounds were synthesized using short and convenient one to two high yielding steps. The newly synthesized compounds were tested in vitro against drug-sensitive Mycobacterium tuberculosis H37Hv strain. Several derivatives were found to be promising inhibitors of M. tuberculosis. For example, derivatives 4a-c (Series 2), 7a-d (Series 3), and 8a-b (Series 4) displayed >90% inhibition at 6.25 microg/mL in the primary assay. The most active compounds, N-(2-fluorophenyl)-N'-quinolin-2-ylmethylene-hydrazine (4a), N-(2-adamantan-1-yl-quinolin-4-ylmethylene)-N'-(4-fluorophenyl)hydrazine (7c), and N-(2-cyclohexyl-quinolin-4-ylmethylene)-N'-(2-fluorophenyl)hydrazine (8a), exhibited 99% inhibition at the lowest tested concentration of 3.125 microg/mL against drug-sensitive M. tuberculosis H37Rv strain. The similarity index based on steric and electrostatic features of the molecules was used, in conjunction with principal component analysis and linear discriminant analysis, successively to classify the molecules based on their activity into two classes. This classification method gives us confidence in predicting the activity class of any new unsynthesized molecule belonging to these series.

Antitubercular Agents↗

PubMed2006

Mechanism of action of L-arginine on the vitality of spermatozoa is primarily through increased biosynthesis of nitric oxide.

The ability of sperm to fertilize the egg is primarily dependent on sperm motility and membrane integrity. Nitric oxide (NO) plays a decisive role in regulating multiple functions within the male reproductive system. The aim of the present study is to determine the mechanism by which L-arginine confers a protective action on spermatozoa obtained from the goat epididymis. NO is synthesized from L-arginine by the enzyme nitric oxide-synthase (NOS) present in spermatozoa. A possible participation of NO and NOS in arginine action has been suggested.

Animals↗

PubMed2005

3D-QSAR study of ring-substituted quinoline class of anti-tuberculosis agents.

A 3D-QSAR analysis of a new class of ring-substituted quinolines with anti-tuberculosis activity has been carried out by three methods-Comparative Molecular Field Analysis (CoMFA), CoMFA with inclusion of a hydropathy field (HINT), and Comparative Molecular Similarity Indices Analysis (CoMSIA). The conformation of the molecules was generated using a simulated annealing protocol and they were superimposed using features common to the set with database alignment (SYBYL) and field fit methods. Several statistically significant CoMFA, CoMFA with HINT, and CoMSIA models were generated. Prediction of the activity of a set of test molecules was the best for the CoMFA model generated with database alignment. Based upon the information contained in the CoMFA model, we have identified some novel features that can be incorporated into the quinoline framework to improve the activity.

Antitubercular Agents↗

PubMed2005

Solution conformation of Substance P antagonists-[D-Arg1, D-Trp7,9, Leu11]-SP, [D-Arg1, D-Pro2, D-Trp7,9, Leu11]-SP and [D-Pro2, D-Trp7,9]-SP by CD, NMR and MD simulations.

Substance P (SP) is an important neuropeptide involved in pain transmission and induction of inflammation. Its antagonists are being extensively investigated for their non-narcotic analgesic and anti-inflammatory activity. With a view towards better understanding the structural requirements of these analogs for efficient interaction with the SP receptor, the conformation of three SP antagonists [D-Arg1, D-Trp7,9, Leu11]-SP, [D-Arg1, D-Pro2, D-Trp7,9, Leu11]-SP and [D-Pro2, D-Trp7,9]-SP has been studied by CD, NMR and molecular dynamics (MD) simulations. All three peptides exhibit a high dependence of structure on the solvent. The molecules tend to adopt beta-turns in solvents like DMSO and H2O and form helices in a hydrophobic environment. A direct relation between the helix forming potential of these antagonists with their receptor binding potency has been observed.

Circular Dichroism↗

PubMed2005

The amino-terminal domain of human signal transducers and activators of transcription 1: overexpression, purification and characterization.

The dual functional signal transducers and activators of transcription (STAT) proteins are latent cytoplasmic transcription factors that play crucial roles in host defense. Animals that lack these proteins are highly susceptible to microbial and viral infections and chemically induced primary tumours. We have over expressed the amino-terminal domain of human STAT1 (hSTAT1) in Escherichia coli and purified it by affinity chromatography and gel filtration chromatography. The entire process has been monitored by gel electrophoresis. The pure protein has been characterized by mass spectrometry and 2-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Our results indicate that the N-terminus of hSTAT1 exists as a dimer in solution.

Amino Acid Sequence↗

PubMed2004

Conformational study of fragments of envelope proteins (gp120: 254-274 and gp41: 519-541) of HIV-1 by NMR and MD simulations.

The envelope proteins, gp 120 and gp41 of HIV-1, play a crucial role in receptor (CD4+ lymphocytes) binding and membrane fusion. The fragment 254-274 of gp120 is conserved in all strains of HIV and, as a part of the full gp120 protein, behaves as 'immunosilent', but as an individual fragment it is 'immunoreactive'. When this fragment binds to its receptor, it activates the fusion domain of gp41 allowing viral entry into the host CD4+ cells. The conformation of fragment 254-274 of the gp120 domain and fragment 519-541 of the gp41 domain was studied by NMR and MD simulations. The studies were carried out in three varied media--water, DMSO-d6 and hexafluoroacetone (HFA). The fusogenic nature of the gp41 domain peptide was investigated by 31P NMR experiments with model bilayers prepared from dimyristoyl-L-alpha-phosphatidylcholine (DMPC). The solvent was seen to exert a major effect on the structure of the two peptides. Fragment (254-274) of gp120 in DMSO-d6 had a type I beta-turn around the tetrad Val9-Ser10-Thr11-Gln12 while in HFA a helical structure spanning the region Ile5 to Gln12 was seen with the remaining part of the peptide in a random coil structure. It is possible that the beta-turn may constitute an initiation site for the formation of the helix. In water at pH 4.5, the peptide adopted a beta-sheet. The NMR results for fragment 519-541 of gp41 are conclusive of a beta-sheet structure in DMSO-d6, a conformation which may help in insertion into the membrane, a notion also put forward by others. The 31P NMR studies of DMPC vesicles with this fragment show its fusogenic nature, promoting fusion of unilamellar vesicles to larger agglomerates like multilamellar ones.

Amino Acid Sequence↗

PubMed2004

Conformation of the cecropin-melittin hybrid, cecropin A(1-8)-melittin (1-18) antibacterial Peptide.

Cecropin A (1-8)-Melittin (1-18) is a synthetic cecropin A-melittin hybrid peptide with leishmanicidal activity. The primary sequence of the peptide is as follows: KWKLPKKIGIGAVLKVLTTGLPALIS-NH2. 1H and 13C 2D NMR techniques were used to deduce the conformational parameters of chemical shift, 3JNHalpha coupling constants, temperature coefficients of NH chemical shifts and the pattern of intra and inter-residue nOe's. NMR studies were carried out in water (pH 6.0) and hexafluoroacetone (HFA). The peptide was found in a beta-pleated structure in water, and in HFA it adopts a right-handed alpha-helix conformation. Solution structures generated using restrained molecular dynamics simulations were refined by Mardigras to R factors ranging from 0.5 to 0.6.

Acetone↗

PubMed2004

Substance P: structure, function, and therapeutics.

Extensive efforts since 1931, on the structural determination of the mammalian tachykinin SP by NMR, CD and IR have turned out to be inconclusive. Studies are now being concentrated on the structural properties and characteristics of various NK receptors (NK(1), NK(2) and NK(3)) with the help of genetics, cloning, receptor engineering, mutagenesis and modeling. This knowledge is now being fruitfully used in the development of non-peptide NK(1) receptor antagonists that essentially block the pharmacological effects of SP. It is now being realized that the simultaneous blockade of two or more receptors gives promising results in emesis, depression and pulmonary obstructive diseases. In addition to the synthetic compounds, the discovery of antagonists from natural origin has added a great value to this field. In this review we have made an attempt to present the structural characteristics of SP, its analogs and antagonists, the structural characteristics of the NK receptor, and structure activity relationships that have helped to improve the therapeutic utilities of SP antagonists.

Amino Acid Sequence↗

PubMed2003

An antiparallel beta-sheet and a beta-turn characterize the structure of antiviral HIV-1 peptide T140, as revealed by 2D NMR and MD Simulations.

The polyphemusins present in the hemocytes of the horsechoe crab and their structurally modified analogs have been shown to exhibit activity against HIV-1. Among the many variants, T22 ([Tyr(5,12), Lys(7)]-polyphemusin II), and its shorter and more potent analog, T140 [Arg(1)-Arg-2-Nal-Cys-Tyr(5)-Arg-Lys-D-Lys-Pro-Tyr(10)-Arg-Cit-Cys-Arg(14)] (Polyphemusin II-derived peptide), affect the HIV-cell fusion process and inhibit the T-cell line-tropic (T-tropic) HIV-1 infection. Conformational studies of polyphemusin II derived peptide have been carried out by (1)H and (13)C 2D-NMR and MD simulations in water and HFA (40%). The NMR parameters of chemical shift, temperature coefficients of the NH chemical shifts, (3)JNHalpha coupling constants and the pattern of nOe's were used to deduce the structural characteristics. Solution structures were generated using dihedral and distance restraints by MD simulations. The structures are characterized by a dominant family possessing an anti-parallel beta-pleated sheet that is constrained by the disulphide bridge between Cys4 and Cys13. The two strands of the beta-sheet are joined by a Type II' beta-turn spanning the residues Lys(7)-D-Lys(8)-Pro(9)-Tyr(10). This conformation is present in both water and HFA. The only difference in the two structures is that the beta-strands are more cohesive in HFA being firmly held by H-bonds. The solution structures generated from MD simulations were refined by MARDIGRAS to R-factors of 0.44 and 0.57 in water and HFA respectively. The conformation deduced for T140 is very similar to that reported for T22 and is thought to be associated with their anti HIV activity.

Animals↗

PubMed2002

CoMFA and CoMSIA studies of angiotensin (AT1) receptor antagonists.

Two 3D-QSAR methods--CoMFA and CoMSIA--were applied to a set of 38 angiotensin receptor (AT1) antagonists. The conformation and alignment of molecules were obtained by a novel method - consensus dynamics. The representation of biological activity, partial charge formalism, absolute orientation of the molecules in the grid, and grid spacing were also studied for their effect on the CoMFA models. The models were thoroughly validated through trials using scrambled activities and bootstrapping. The best CoMFA model had a cross-validated correlation coefficient ( q2) of 0.632, which improved with "region focusing" to 0.680. This model had a "predictive" r2 of 0.436 on a test series that was unique and with little representation in the training set. Although the "predictive" r2 of the best CoMSIA model, which included steric, electrostatic, and hydrogen bond acceptor fields was higher than that of the best CoMFA model, the other statistical parameters like q2, r2, F value, and s were unsatisfactory. The contour maps generated using the best CoMFA model were used to identify the structural features important for biological activity in these compounds.

Angiotensin II Type 1 Receptor Blockers↗

PubMed2002

Activity and conformation of a cyclic heptapeptide possessing the message sequence His-Phe-Arg-Trp of alpha-melanotropin.

Alpha-melanotropin (alpha-MSH, i.e. alpha-melanocyte stimulating hormone), tridecapeptide (Ac-Ser(1)-Tyr-Ser-Met-G1u(5)-His-Phe-Arg-Trp-Gly(10)-Lys-Pro-Val(13)-NH(2)), has been extensively studied to understand structure-activity relationships. The core sequence (His-Phe-Arg-Trp) is conserved in several species and is considered as the primary active site or "message sequence". Attempts have been made to design conformationally constrained cyclic analogs containing the message sequence to improve the activity. We had earlier reported that the cyclic analog--cyclo[Gly-His-D-Phe-Arg-Trp-Gly], a 18 membered ring system with two fused beta-turn structure, was less active than the corresponding linear peptide. It was suggested that ring size could be an important parameter in the activity of cyclic melanotropic analogs. To investigate the effect of ring size on biological activity, a cyclic heptapeptide, cyclo[Nle(1)-Gly-His-D-Phe-Arg(5)-Trp-Gly(7)], with 21 member ring system was synthesized. This peptide has three orders of magnitude higher biological activity than the cyclic hexapeptide. The conformational study of this cyclic heptapeptide in DMSO-d(6) by NMR and molecular dynamics simulations reveals a structure with two fused beta-turns running across the residues D-Phe(4)-Gly(7) (Type I) and Gly(7)-His(3) (Type II). These findings confirm that stabilization of beta-turns and a relatively larger ring size are essential determinants of activity for cyclic alpha-MSH analogs.

Animals↗

PubMed2002

Docking studies reveal a selective binding of D-penicillamine to the transactivator protein of human immunodeficiency virus type 1.

DOCK and Affinity studies were carried out to study the binding of D- and L-penicillamine to the transactivator protein (tat) of human immunodeficiency virus type 1 (HIV-1). These studies reveal a selective binding of D-penicillamine to the cysteine-rich region covering amino acid residues 20-38 of the tat protein. A careful analysis of the components of the binding energy of the D- and L-isomers reveals that the D-isomer has a more favorable van der Waals interaction resulting from an optimal placement of the dimethylthiomethyl side chain in the binding site. This observation matches the experimental data that D-penicillamine is a more potent inhibitor of tat-mediated transactivation than the L-isomer. The docking and experimental data offer an interesting approach to design structural molecules with potential application to block signal functions of the tat protein in HIV-1 pathogenesis.

Binding Sites↗

PubMed2002

Conformation of a model peptide of the tandem repeat decapeptide in mussel adhesive protein by NMR and MD simulations.

The conformation of a model peptide (Ala-Lys-Pro-Ser-Tyr-Hyp-Hyp-Thr-Tyr-Lys) of the tandem repeat decapeptide sequence of Mytilus edulis foot protein-1 (mefp-1) has been studied by 1H and 13C 2D-NMR in three diverse media-DMSO-d6, water (pH 3.5) and 40% hexafluoroacetone (HFA). Various NMR parameters that were used to deduce the secondary structure were chemical shift (1H and 13C) temperature coefficients of NH chemical shifts, 3J(NH alpha) coupling constants and the pattern of intra and inter-residue NOEs. Molecular dynamics simulations making integral use of the NMR data shows that the conformation of the peptide is conserved in all the three media. The structure in the three solvents is best defined as a left-handed polyproline II helix (PPII).

Amino Acid Sequence↗

PubMed2002

Conformational diversity of T-kinin in DMSO, water and HFA.

T-kinin (Ile-Ser-BK) is related to BK in its biological profile, but unlike BK, is more resistant to the action of ACE. A detailed NMR and molecular modeling study of T-kinin has been carried out in three diverse media: water (pH 4.0), DMSO-d(6) and HFA solution. In DMSO-d(6), T-kinin adopts a structure with two tandem beta-turns: the first at the mid segment tetrad Pro(4)-Pro(5)-Gly(6)-Phe(7) (type I) and the C-terminal end Ser(8)-Pro(9)-Phe(10)-Arg(11) harbors the second turn (also type I). While the first beta-turn is lost in presence of water, the second persists. In HFA, NMR reveals a alpha-helix like structure spanning residues Arg(3) to Arg(11). Structures with cis peptide bonds (XX-Pro) have been observed for T-kinin in DMSO-d(6) but not in water and HFA. Differences in the structures of BK and T-kinin in water may explain their susceptibility/resistance to the action of ACE.

Bradykinin↗