Biomedical subjects

J J Perez

Publications and source records attributed to J J Perez.

At least 19 recordsLinked to original sources

PubMed2005

Genetic heterogeneity of BCR/ABL+ adult B-cell precursor acute lymphoblastic leukemia: impact on the clinical, biological and immunophenotypical disease characteristics.

Philadelphia-positive (Ph(+)) B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a genetically heterogeneous disease with a very poor prognosis. In this study, we analyzed the frequency of supernumerary Ph, trisomy 8, monosomy 7, and del(9p21) by FISH and its relationship with the characteristics of the disease, in 46 BCR/ABL(+) adult BCP-ALL patients. The frequency of supernumerary Ph, trisomy 8, monosomy 7 and del(9p21) was 30%, 20%, 15%, and 24%, respectively. Although all patients displayed a BII/common phenotype, supernumerary Ph and trisomy 8 were associated with higher expression of CD19 and CD22 and of CD19, CD34, CD45, and HLA-DR, respectively; in turn, cases with monosomy 7 showed lower CD19, CD22, CD34, and cCD79a and del(9p21)(+) blasts were CD13(-) and CD33(-). Overall, similar clinical and hematological features were observed at presentation, independently of the underlying genetic abnormalities. However, relapse-free survival (RFS) was significantly shorter in cases with supernumerary Ph, trisomy 8, and del(9p21), the latter being the most powerful independent prognostic factor for RFS.

Adult↗

PubMed2005

Immunomodulatory effects of a set of amygdalin analogues on human keratinocyte cells.

Peptide T (PT) is an octapeptide shown to resolve psoriatic lesions. Our previous investigations suggest that keratinocytes play an important role in conditioning the therapeutic effects of the PT in psoriasis. However, peptides are not good therapeutic agents, because they exhibit poor absorption, are easily metabolized and are immunogenic. Using computational methods, the natural product amygdalin was identified as peptidomimetic of PT. However, amygdalin exhibits a toxic profile due to its cyanide group. To overcome this deleterious effect, we synthesized analogues lacking the cyanide group. Human keratinocytes were treated with PT or with three different peptidomimetics of PT. To study its effects on the expression of HSP-70, TGF-beta, alpha-v integrin, ICAM-1 and cytokines, we analysed the protein levels by Western blot and ELISA. Our results show that the different peptidomimetics of PT tested exhibit a similar biological behaviour in regard to the overexpression of HSP-70, TGF-beta and alpha-v integrin than the native peptide. TNF-alpha is overexpressed by PT and SVT-03018; between the other two analogs, SVT-03016 do not produce any significant change in regard to the control, while SVT-03017 shows only a moderate increase in regard to control. SVT-03018 provokes a remarkable upregulation of IL-10, stronger than SVT-03016, SVT-03017 and PT. All the other three analogues reduce comparably to the PT, the expression of ICAM-1 and do not increase the release of proinflammatory cytokines. The results highlighted that the three analogues of amygdalin with the cyanide group removed exhibit the same biological effects of PT. Therefore, they can be considered peptidomimetics, suggesting their possible use in the treatment of psoriasis.

Amygdalin↗

PubMed2001

Toward the design of chemical libraries for mass screening biased against mutagenic compounds.

The ability to develop a chemical into a drug depends on multiple factors. Beyond potency and selectivity, ADME/PK and the toxicological profile of the compound play a significant role in its evaluation as a candidate for development. Those factors are being brought into bear earlier in the discovery process and even into the design of libraries for screening. The purpose of our study is the comparative analysis of simple physical characteristics of compounds that have been reported to be mutagens and nonmutagenic ones. The analysis of differences can lead to the development of knowledge-based biases in the libraries designed for massive screening. For each of four Salmonella strains, TA-98, TA-100, TA-1535, and TA-1537, an analysis of the statistical significance of the deviance of the averages for a number of global properties was carried out. The properties studied included parameters, such as topological indices, and bit strings representing the presence or absence of certain chemical moieties. The results suggest that mutagens display a larger number of hydrogen bond acceptor centers for most strains. Moreover, the use of bit strings points to the importance of certain molecular fragments, such a nitro groups, for the outcome of a mutagenicity study. Development of multivariate models based on global molecular properties or bit strings point to a small advantage of the latter for the prediction of mutagenicity. The benefits of the bit strings are in accord with the use of fragment-based approaches for the prediction of carcinogenicity and mutagenicity in methods described in the literature.

Combinatorial Chemistry Techniques↗

PubMed2001

Study of the conformational profile of the cyclohexane analogs of L-phenylalanine.

The conformational profile of the conformationally constrained cyclohexane analogs of phenylalanine (1-amino-2-phenylcyclohexanecarboxylic acids, c6Phe) was assessed using computational methods. For this purpose, the conformational space of the N-acetyl methylamide derivatives of the stereoisomers (2S,3R)c6Phe and (2S,3S)c6Phe was explored by computing their respective Ramachandran maps, and low-energy minima were characterized at molecular mechanics level by means of the AMBER program, using the parm94 force field set of parameters. In order to assess the performance of the molecular mechanics calculations, each of the low-energy conformations was also investigated further at the ab initio level. Accordingly, the molecular mechanics geometries were used as starting conformations to perform full geometry optimizations at the Hartree-Fock level, using a 6-31G(d) basis set. Analysis of the results revealed that the cyclohexane structure directly induces some restrictions on the backbone, and constrains the orientation of the aromatic side-chain to two narrow regions for each stereoisomer. The conformational profile of these amino acids is then explained on the grounds of the interaction between the rigidly held phenyl ring and the main chain NH and CO groups. The results obtained are in good accordance with the experimental observations.

Cyclohexanes↗

PubMed2000

Docking of peptide-T onto the D1 domain of the CD4 receptor.

Peptide T (pepT) is a segment of the human immunodeficiency virus (HIV) envelope protein gp120. The peptide competitively binds to the CD4 receptor of a subset of peripheral T lymphocytes and inhibits binding of gp120. Previous studies of this laboratory allowed the assessment of a bioactive form of the peptide and a pharmacophore for the peptide-receptor interaction. In the present study the proposed bioactive form of pepT and its (4-8) segment, the smallest pepT fragment shown to retain full activity, were docked onto the D1 domain of the CD4 receptor. The bioactive conformation of the peptides complements well a cleft on the surface of the CD4 receptor, shown to be the attachment site of gp120 from site directed mutagenesis experiments. These studies provide an improved description of the ligand-receptor pharmacophore.

Amygdalin↗

PubMed1999

Structural basis of the dynamic mechanism of ligand binding to cyclooxygenase.

Molecular modeling studies performed on the two cyclooxygenase (COX) isozymes suggest that the cavity at the mouth of the active site on the membrane domain that may act as an actual binding site of COX ligands. Actual docking of different inhibitors at this site provides a structural basis to explain the dynamics of COX inhibition.

Animals↗

PubMed1999

Study of the conformational profile of selected unnatural amino acid residues derived from L-phenylalanine.

The present work reports the results of a conformational study performed on seven unnatural amino acid residues and on its natural precursor, investigated by means of computational methods at the molecular mechanics level. Amino acid residues selected for the present study are derivatives of L-phenylalanine substituted at the alpha and/or beta carbons. This series is composed of different linear analogs, including alpha-methyl, beta-methyl and beta-phenyl substituted with different stereochemistry. Analysis of the Ramachandran maps of the corresponding dipeptides in vacuo reveals their conformational preferences, to be used as guidance for the synthesis of constrained peptide analogs with desired conformational propensities. The available conformational space for every dipeptide is also analysed.

Dipeptides↗

PubMed1999

Molecular dynamics study of kaliotoxin in water.

Kaliotoxin (KTX), a potassium channel blocker found in the venom of the scorpion Androctonous Mauretanicus is a 38 residue polypeptide with a well defined structure consisting of a alpha-helix and a three strand antiparallel beta-sheet interconnected by three disulfide bonds. Although the 3D structure has been determined by NMR, there is a number of features, mainly concerning the conformation and flexibility of the side chains, but also the long range order in the peptide and its fluctuations, that may have escaped the experimental study. These questions are now being addressed using molecular dynamics (MD) simulations. Accordingly, the present work reports the analysis of a 430 ps molecular dynamics trajectory of the polypeptide soaked with 4700 TIP3 water molecules inside a 56 A box. MD calculations were performed with periodic boundary conditions. Analysis of the conformational space sampled by each of the residues along the trajectory, suggests a special behavior of Pro17 and Lys19 both located on the helix. Furthermore, analysis of the relative movements of the secondary structure elements indicates that the alpha-helix and beta-sheets fluctuate in a correlated motion, preserving the tertiary structure of the polypeptide along the trajectory. Finally, analysis of the charge distribution was also examined. The direction of the dipole moment, computed from the center of masses appears to be an interesting feature of the structure probably related to the biological function of the molecule.

Computer Simulation↗

PubMed1999

Molecular modeling study of the differential ligand-receptor interaction at the mu, delta and kappa opioid receptors.

3D models of the opioid receptors mu, delta and kappa were constructed using BUNDLE, an in-house program to build de novo models of G-protein coupled receptors at the atomic level. Once the three opioid receptors were constructed and before any energy refinement, models were assessed for their compatibility with the results available from point-site mutations carried out on these receptors. In a subsequent step, three selective antagonists to each of three receptors (naltrindole, naltrexone and nor-binaltorphamine) were docked onto each of the three receptors and subsequently energy minimized. The nine resulting complexes were checked for their ability to explain known results of structure-activity studies. Once the models were validated, analysis of the distances between different residues of the receptors and the ligands were computed. This analysis permitted us to identify key residues tentatively involved in direct interaction with the ligand.

Amino Acid Sequence↗

PubMed1999

Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods.

Ras farnesyltransferase catalyzes the carboxyl-terminal farnesylation of Ras as well as other proteins involved in signal transduction processes. Previous studies demonstrated that its inhibition suppresses the activity of Ras transformed phenotypes in cultured cells, causing tumor regression in animal models. This observation led to the consideration of farnesyltransferase as a target for cancer therapy. In the present work we report the results of a computational study aimed at assessing the bioactive conformation of the peptide Cys-Val-Phe-Met, known to be the minimum peptide sequence that inhibits farnesyltransferase. For this purpose the conformational preferences of four analogs of the peptide were assessed by means of thorough searches of their respective conformational spaces, using a simulated annealing protocol as sampling technique. Specifically, two active analogs: Cys-Val-Tic-Met and Cys-Val-psi(CH2NH)Tic-Met and two inactive analogs: Cys-Val-Tic-psi(CH2NH)Met and Cys-Val-Aic-Met were selected for the present study. Low energy conformations of the four analogs were classified according to their structural motifs. The putative bioactive conformation of the minimum farnesyltransferase recognition motif was assessed by cross-comparison of the different classes of conformations obtained for the two active and the two inactive analogs. The putative bioactive conformation is characterized by two structural motifs: i) a C14 pseudo-ring stabilized by a hydrogen bond between the amino group of Cys1 and the carboxylate group of Met4 and a C11 pseudo-ring involving the residues Cys1 and Tic3. In addition, the thiol group of Cys1 side chain of the bioactive conformation points to the carboxylate moiety of Met4.

Algorithms↗

PubMed1998

Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies.

The geometrical features of the proposed bioactive conformation of peptide T assessed by computational methods in a previous study, together with available structure-activity studies on peptide T, led us to propose a pharmacophore for the CD4-peptide T interaction. Subsequent, data base searching permitted us to identify amygdalin as a peptide T peptidomimetic.

Amygdalin↗

PubMed1998

Incontinence after lateral internal sphincterotomy: anatomic and functional evaluation.

PURPOSE: This study was designed to evaluate the anatomic and functional consequences of lateral internal sphincterotomy in patients who developed anal incontinence and in matched controls. METHODS: The study includes 13 patients with anal incontinence after lateral internal sphincterotomy and 13 controls who underwent the same operation and were continent and satisfied with the results of the procedure. Patients underwent clinical evaluation, anorectal manometry, pudendal nerve terminal motor latency testing, and endoanal ultrasonography. RESULTS: Sphincterotomies were longer in incontinent patients (75 vs. 57 percent), but the resting pressure and length of the high-pressure zone were not different between groups. Surprisingly, maximum voluntary contraction was higher in incontinent patients than in continent controls (136 vs. 100 mmHg). Rectal sensation and pudendal nerve terminal motor latency were similar in both groups. The defect in the internal sphincter was wider in incontinent patients than in continent controls (17.3 vs. 14.4 mm), but these differences were not statistically significant. The thickness of the internal sphincter measured by endoanal ultrasound was identical in both groups, but the external sphincter was thinner in incontinent patients both at the site of the sphincterotomy (6.8 vs. 8.1 mm) and in the posterior midline (7.1 vs. 8.6 mm). CONCLUSIONS: Anal incontinence after lateral internal sphincterotomy is directly related to the length of the sphincterotomy. Whether secondary to preoperative sphincter abnormality or the result of lateral internal sphincterotomy, the external sphincter is thinner in incontinent patients than in continent controls.

Adult↗

PubMed1998

New insights into the conformational requirements of B2 bradykinin antagonism.

The conformational profiles of a selected group of a new series of small linear and cyclic penta- and hexapeptides, inspired on the C-terminal segment of second-generation bradykinin (BK) antagonists, were independently computed in order to assess the chemical and geometrical requirements necessary for BK antagonism. Specifically, four cyclic peptides: cyclo-(Gly-Thi-D-Tic-Oic-Arg), cyclo-(Gly-Ala-D-Tic-Oic-Arg), cyclo-(Abu-Ala-Ser-D-Tic-Oic-Arg), cyclo-(Abu-D-Phe-Ala-D-Tic-Oic-Arg), and a linear peptide: Thi-Ser-D-Tic-Oic-Arg were selected for the present study. The first three BK analogs are capable to antagonize kinin-induced rabbit jugular vein and rabbit aorta smooth muscle contraction, while last two show no detectable affinity for the BK B2 receptor. The conformational space of the five peptides was thoroughly explored using simulated annealing (SA) in an iterative fashion as sampling technique. The bioactive conformation was assessed by pairwise cross comparisons between each of the unique low energy conformations found for each of the different peptides studied within a 5 kcal/mol threshold in respect to the global minimum. The conformational profile of the highly potent BK antagonist HOE-140, computed in an independent study, was also used in conjunction with the bioactive form assessed in the present study, to propose a pharmacophore that includes the stereochemical requirements for B2 BK antagonism.

Amino Acid Sequence↗

PubMed1998

BUNDLE: a program for building the transmembrane domains of G-protein-coupled receptors.

The only information available at present about the structural features of G-protein-coupled receptors (GPCRs) comes from low resolution electron density maps of rhodopsin obtained from electron microscopy studies on 2D crystals. Despite their low resolution, maps can be used to extract information about transmembrane helix relative positions and their tilt. This information, together with a reliable algorithm to assess the residues involved in each of the membrane spanning regions, can be used to construct a 3D model of the transmembrane domains of rhodopsin at atomic resolution. In the present work, we describe an automated procedure applicable to generate such a model and, in general, to construct a 3D model of any given GPCR with the only assumption that it adopts the same helix arrangement as in rhodopsin. The present approach avoids uncertainties associated with other procedures available for constructing models of GPCRs based on a template, since sequence identity among GPCRs of different families in most of the cases is not significant. The steps involved in the construction of the model are: (i) locate the centers of the helices according to the low-resolution electron density map; (ii) compute the tilt of each helix based on the elliptical shape observed by each helix in the map; (iii) define a local coordinate system for each of the helices; (iv) bring them together in an antiparallel orientation; (v) rotate each helix through the helical axis in such a way that its hydrophobic moment points in the same direction of the bisector formed between three consecutive helices in the bundle; (vi) rotate each helix through an axis perpendicular to the helical one to assign a proper tilt; and (vii) translate each helix to its center deduced from the projection map.

Amino Acid Sequence↗

PubMed1998

A proposed bioactive conformation of peptide T.

The conformational profiles of Peptide T, (5-8)Peptide T, [Abu5](4-8)Peptide T and (4-8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo beta-turn involving the side chain of Thr5 and the carbonyl oxygen of Tyr7 forming a C12 ring.

Amino Acid Sequence↗

PubMed1998

Conformational analysis of the highly potent bradykinin antagonist Hoe-140 by means of two different computational methods.

The AMBER 4.0 force field was used to perform the characterization of the conformational profile of the highly potent bradykinin antagonist Hoe-140 (D-Arg0-Arg1-Pro2-Hyp3-Gly4-Thi5-Ser6-D-++ +Tic7-Oic8-Arg9). The structural features of the peptide were assessed using two different computational methods, both capable to provide a good sampling of the low-energy conformations of the molecule. Specifically, the conformational space of the peptide was explored: i) computing molecular dynamics trajectories in cycles of high (900 K) and low (300 K) temperature and ii) using simulated annealing (SA) in an iterative fashion. Analysis of the structures characterized indicates that most of the low-energy conformations of the peptide exhibit a betaII'-turn motif at its C-terminus, in agreement with previous experimental and theoretical studies. On the other hand, about a 50% of the low-energy conformations characterized also exhibit different beta-turn type motifs at the N-terminus, whereas the rest of the conformations can be described as bends. Finally, in order to get new insights into the structural requirements necessary to design more potent and selective antagonists of bradykinin, present results were compared with those previously reported by this laboratory on the conformational preferences of the native nonapeptide and its DPhe7 analog.

Bradykinin↗

PubMed1997

Comparative molecular modeling study of the three-dimensional structures of prostaglandin endoperoxide H2 synthase 1 and 2 (COX-1 and COX-2).

To understand the structural features that dictate the selectivity of diverse nonsteroidal antiinflammatory drugs for the two isoforms of the human prostaglandin H2 synthase (PGHS), the three-dimensional (3D) structure of human COX-2 was assessed by means of sequence homology modeling. The ovine COX-1 structure, solved by X-ray diffraction methods and sharing a 61% sequence identity with human COX-2, was used as template. Both structures were energy minimized using the AMBER 4.0 force field with a dielectric constant of 4r. (S)-Flurbiprofen, a nonselective COX inhibitor, and SC-558, a COX-2-selective ligand, were docked at the cyclooxygenase binding site in both isozymes, evidencing the role of different residues in the ligand-protein interaction. The 3D structures of the constructed four ligand-enzyme complexes were refined by energy minimization. Molecular dynamics simulations were also carried out, to understand more deeply the structural origins of the selectivity. Distances calculated during the dynamics process between the different ligands and the interacting residues of the two PGHS isozymes provided evidence of the flexible nature of the cyclooxygenase active site, permitting the identification of different conserved and nonconserved residues as responsible for ligand selectivity.

Amino Acid Sequence↗

PubMed1997

Conformational study of vasoactive intestinal peptide by computational methods.

The conformational profile of vasoactive intestinal peptide (VIP) was characterized using computational methods. The strategy devised included a close examination of the conformational profile of the first 11 residues fragment followed by a study that considered the compatibility of the different conformations found with a continuation of the polypeptide chain in a alpha-helical conformation. Accordingly, a detailed analysis of the conformational preferences of the N-terminal fragment of VIP(1-11) was carried out within the framework of the molecular mechanics approach, using simulated annealing in an iterative fashion as the sampling technique. In a second step, low-energy structures of the fragment were fused to the remainder of the VIP chain in the form of two noninteracting alpha-helices, according to a model of the structure of the peptide proposed from NMR studies. After investigation for compatibility of each of the low-energy structures of VIP(1-11) with the two helical regions by energy minimization, only 5 of 35 structures were discarded. Analysis of the structures characterized indicates that most of the conformations of VIP(1-11), including the global minimum, can be described as bent conformations. Conformations exhibiting alpha-turns and beta-turns, previously proposed by NMR studies were also characterized. The conformational analysis also suggests that the common structural features found in VIP(1-11) should also be present in VIP. Finally, because of the sequence homology between VIP and Peptide T, and the fact that both are ligands of the CD4 receptor, both sets of low-energy conformations were compared for similarity. The relevance of these results as guidance of the design of new peptide analogs targeted to the CD4 receptor is also discussed.

CD4 Antigens↗