Structure-based secondary structure-independent approach to design protein ligands: Application to the design of Kv1.2 potassium channel blockers

We have developed a structure-based approach to the design of protein ligands. This approach is based on the transfer of a functional binding motif of amino acids, often referred as to the "hot spot", on a host protein able to reproduce the functional topology of these residues. The scaffolds were identified by a systematic in silico search in the Protein Data Bank for proteins possessing a group of residues in a topology similar to that adopted by the functional motif in a reference ligand of known 3D structure. In contrast to previously reported studies, this search is independent of the particular secondary structure supporting the functional motif. To take into account the global properties of the host protein, two additional criteria were taken into account in the selection process: (1) Only those scaffolds sterically compatible with the positioning of the functional motif as observed in a reference complex model were retained. (2) Host proteins displaying electrostatic potentials, in the region of the transferred functional motif, similar to that of the reference ligand were selected. This approach was applied to the development of protein ligands of the Kv1.2 channel using BgK, a small protein isolated from the sea anemone Bunodosoma granulifera, as the reference ligand. Four proteins obtained by this approach were produced for experimental evaluation. The X-ray structure of one of these proteins was determined to check for similarity of the transferred functional motif with the structure it adopts in the reference ligand. Three of these protein ligands bind the Kv1.2 channel with inhibition constants of 0.5, 1.5, and 1.6 microM. Several mutants of these designed protein ligands gave binding results consistent with the presumed binding mode. These results show that protein ligands can be designed by transferring a binding motif on a protein host selected to reproduce the functional topology of this motif, irrespective to the secondary structure supporting the functional motif, if the host protein possesses steric and electrostatic properties compatible with the binding to the target. This result opens the way to the design of protein ligands by taking advantage of the considerable structural repertoire of the Protein Data Bank.

Dihydro-beta-agarofuran sesquiterpenes: a new class of reversal agents of the multidrug resistance phenotype mediated by P-glycoprotein in the protozoan parasite Leishmania

Leishmaniasis is the most important emerging and uncontrolled infectious disease and the second cause of death among parasitic diseases, after Malaria. One of the main problems concerning the control of infectious diseases is the increased resistance to usual drugs. Overexpression of P-glycoprotein (Pgp)-like transporters represents a very efficient mechanism to reduce the intracellular accumulation of drugs in cancer cells and parasitic protozoans, thus conferring a multidrug resistance (MDR) phenotype. Pgps are active pumps belonging to the ATP-binding cassette (ABC) superfamily of proteins. The inhibition of the activity of these proteins represents an interesting way to control drug resistance both in cancer and in infectious diseases. Most conventional mammalian Pgp-MDR modulators are ineffective in the modulation of Pgp activity in the protozoan parasite Leishmania. Consequently, there is a necessity to find effective modulators of Pgp-MDR for protozoan parasites. In this review we describe a rational strategy developed to find specific Pgp-MDR modulators in Leishmania, using natural and semisynthetic dihydro-beta-agarofuran sesquiterpenes from Celastraceae plants. A series of these compounds have been tested on a MDR Leishmania tropica line overexpressing a Pgp transporter to determine their ability to revert the resistance phenotype and to modulate intracellular drug accumulation. Almost all of these natural compounds showed potent reversal activity with different degrees of selectivity and a significant low toxicity. The three-dimensional quantitative structure-activity relationship using the comparative molecular similarity indices analysis (CoMSIA), was employed to characterize the requirements of these sesquiterpenes as modulators at Pgp-like transporter in Leishmania.

Multiple sclerosis gender issues: clinical practices of women neurologists

Substantially more women than men develop multiple sclerosis (MS), but information about the effects of MS and gender-specific issues such as pregnancy, breastfeeding, menstruation and hormone use is lacking. A survey study of neurologists' practice patterns was undertaken to elicit information about gender-specific topics and the use of disease-modifying MS therapies (DMT) including the interferons and glatiramer acetate (GA). A total of 147 surveys were returned. Half of respondents require patients to discontinue DMT during pregnancy, while 35% encourage discontinuation. Among those who allow patients to continue therapy, half consider GA to be safer during pregnancy than the interferons. Nearly 86% of respondents do not use DMT in patients who are breastfeeding. Among the 11% who actually prescribe during breastfeeding, most recommend GA. Neurologists generally leave the decision to breastfeed up to patients, and most refer patients to obstetrician/gynaecologists for counselling about contraception or hormone replacement therapy. The survey results described here provide insight into how neurologists manage reproductive health issues among women with MS.

The neuronal lipid membrane permeability was markedly increased by bupivacaine and mildly affected by lidocaine and ropivacaine

We investigated the local anesthetic action on ionic membrane conductance (membrane conductance) and selectivity in membranes formed with neuronal phospholipids in the absence and presence of cholesterol. In membranes without cholesterol, 1 mM bupivacaine and ropivacaine increased the membrane conductance approximately 4.5-fold; and 5 mM lidocaine, ropivacaine and bupivacaine increased the membrane conductance by 2.7-, 2.8- and 22.2-fold, respectively. In the presence of cholesterol, 5 mM ropivacaine had no effect, lidocaine decreased the membrane conductance by 2-fold, and bupivacaine increased the membrane conductance by 17-fold. Local anesthetics did not affect the ion selectivity in membranes without cholesterol, but they all decreased the Na(+) selectivity in membranes with cholesterol. Cholesterol reduced the lidocaine- and ropivacaine-induced membrane conductance increase by eliminating or reversing the Na(+) conductance increase and by lowering the Cl(-) conductance increase. In the absence of cholesterol, 5 mM bupivacaine increased both Na(+) conductance (38-fold) and Cl(-) conductance (19-fold), while in the presence of cholesterol it only increased Cl(-) conductance (26-fold). Of the local anesthetics studied, ropivacaine was the least membrane toxic while bupivacaine was the most toxic.

3-D-QSAR/CoMFA and recognition models of benzimidazole derivatives at the 5-HT(4) receptor

3-D-QSAR/CoMFA methodology and computational simulation of ligand recognition have been successfully applied to explain the binding affinities of a series of benzimidazole derivatives 1-24 acting at serotonin 5-HT(4)Rs. Both derived computational models have facilitated the identification of the structural elements of the ligands that are key to high 5-HT(4)R affinity. The results provide the tools for predicting the affinity of related compounds, and for guiding the design and synthesis of new ligands with predetermined affinities and selectivity.

Computational model of the complex between GR113808 and the 5-HT4 receptor guided by site-directed mutagenesis and the crystal structure of rhodopsin

A computational model of the transmembrane domain of the human 5-HT4 receptorcomplexed with the GR113808 antagonist was constructed from the crystal structure of rhodopsin and the putative residues of the ligand-binding site, experimentally determined by site-directed mutagenesis. The recognition mode of GR113808 consist of: (i) the ionic interaction between the protonated amine and Asp3.32; (ii) the hydrogen bond between the carbonylic oxygen and Ser5.43; (iii) the hydrogen bond between the ether oxygen and Asn6.55; (iv) the hydrogen bond between the C-H groups adjacent to the protonated piperidine nitrogen and the pi electrons of Phe6.51; and (v) the pi-sigma aromatic-aromatic interaction between the indole ring and Phe6.52. This computational model offers structural indications about the role of Asp3.32, Ser5.43, Phe6.51, Phe6.52, and Asn6.55 in the experimental binding affinities. Asp3.32Asn mutation does not affect the binding of GR113808 because the loss of binding affinity from an ion pair to a charged hydrogen bond is compensated by the larger energetical penalty of Asp to disrupt its side chain environment in the ligand-free form, and the larger interaction between Phe6.51 and the piperidine ring of the ligand in the mutant receptor. In the Phe6.52Val mutant the indole ring of the ligand replaces the interaction with Phe6.52 by a similarly intense interaction with Tyr5.38, with no significant effect in the binding of GR113808. The mutation of Asn6.55 to Leu replaces the hydrogen bond of the ether oxygen of the ligand from Asn6.55 to Cys5.42, with a decrease of binding affinity that approximately equals the free energy difference between the SH...O and NH...O hydrogen bonds. Because these residues are also present in the other members of the neurotransmitter family of G protein-coupled receptors, these findings will also serve for our understanding of the binding of related ligands to their cognate receptors.

Clinical and histologic effects of facial skin rejuvenation with pulsed- and continuous-wave flash-scanned CO(2) lasers

LEARNING OBJECTIVES

The reader is presumed to have some understanding of the use of lasers in skin resurfacing. After studying the article, the participant should be able to: Physicians may earn 1 hour of Category 1 CME credit by successfully completing the examination based on material covered in this article. The examination begins on page 409.

BACKGROUND

The selection of the ideal laser for facial resurfacing is debatable.

OBJECTIVE

The purpose of the study was to determine whether any clinical and histologic differences existed in short- and long-term results after treatment with the Coherent UltraPulse 5000G laser (a pulsed laser; PL) and the Sharplan Silk Touch laser (a continuous-wave laser [CWL] with a flash scanner).

METHODS

Eight patients underwent facial resurfacing treatment on different areas. In each case, one side was treated with the PL and the other with the CWL. The condition of the patients and the treated tissue were monitored periodically after treatment. Histologic assessment of punch biopsies was performed 3 months and 1 year after treatment with hematoxylin-eosin, Masson trichromic, and Verhoeff's stains.

RESULTS

The areas treated with the PL achieved earlier epithelialization with a good appearance. Longer-lasting erythema was observed on the side treated with the CWL. On a histologic level, although the PL-treated tissue epithelialized more quickly, at 3 months and 1 year the collagen was better compacted and better aligned in the CWL-treated tissue, and the macroscopic appearance of the CWL-treated areas was more enhanced.

CONCLUSIONS

The more active vascularization seen in the CWL-treated tissue, associated with the longer-lasting erythema and possibly greater collateral thermal injury, is possibly the reason for the better collagenization and remodeling of collagen and elastin fibers as compared with the results with the PL-treated tissue. This may explain the longer effect associated with CWL treatment. The clinician would do well to bear in mind the histologic findings as well as the macroscopic clinical results when assessing the long-term effects of laser skin resurfacing. (Aesthetic Surg J 2001;21:399-411.).

Patients' answers to a postoperative questionnaire related to laser resurfacing

To date there is no information that evaluates, from the patient's point of view, the experience of undergoing CO(2) laser skin resurfacing. This article investigates the outcome of laser resurfacing for various cutaneous problems with respect to the patient's expectations and experiences and the surgeon's opinions. Patients were entered into the study prospectively and presented with a questionnaire, at 12 months after treatment, to evaluate the patient's skin resurfacing experience. All patients received standardized preoperative counseling and underwent a standardized surgical protocol, conducted by the same surgeon. Eighty-eight percent of patients considered the result of the laser resurfacing to be very good, and 97% indicated that they had experienced little pain or discomfort. Nevertheless, 77% of patients stated that they would be unwilling to undergo another resurfacing procedure. This discrepancy is most likely the result of the patients' experiences in relation to the degree of erythema afterward. Most patients stated a desire to have more information regarding the procedure, particularly with respect to their experiences concerning postoperative erythema and exudates in the treated area. From the study it can be concluded that patients require extensive preoperative counseling, including a full explanation of all possible sequelae of these procedures to improve the patient's experience.

A conserved Asn in transmembrane helix 7 is an on/off switch in the activation of the thyrotropin receptor

The thyrotropin (TSH) receptor is an interesting model to study G protein-coupled receptor activation as many point mutations can significantly increase its basal activity. Here, we identified a molecular interaction between Asp(633) in transmembrane helix 6 (TM6) and Asn(674) in TM7 of the TSHr that is crucial to maintain the inactive state through conformational constraint of the Asn. We show that these residues are perfectly conserved in the glycohormone receptor family, except in one case, where they are exchanged, suggesting a direct interaction. Molecular modeling of the TSHr, based on the high resolution structure of rhodopsin, strongly favors this hypothesis. Our approach combining site-directed mutagenesis with molecular modeling shows that mutations disrupting this interaction, like the D633A mutation in TM6, lead to high constitutive activation. The strongly activating N674D (TM7) mutation, which in our modeling breaks the TM6-TM7 link, is reverted to wild type-like behavior by an additional D633N mutation (TM6), which would restore this link. Moreover, we show that the Asn of TM7 (conserved in most G protein-coupled receptors) is mandatory for ligand-induced cAMP accumulation, suggesting an active role of this residue in activation. In the TSHr, the conformation of this Asn residue of TM7 would be constrained, in the inactive state, by its Asp partner in TM6.

The TXP motif in the second transmembrane helix of CCR5. A structural determinant of chemokine-induced activation

CCR5 is a G-protein-coupled receptor activated by the chemokines RANTES (regulated on activation normal T cell expressed and secreted), macrophage inflammatory protein 1alpha and 1beta, and monocyte chemotactic protein 2 and is the main co-receptor for the macrophage-tropic human immunodeficiency virus strains. We have identified a sequence motif (TXP) in the second transmembrane helix of chemokine receptors and investigated its role by theoretical and experimental approaches. Molecular dynamics simulations of model alpha-helices in a nonpolar environment were used to show that a TXP motif strongly bends these helices, due to the coordinated action of the proline, which kinks the helix, and of the threonine, which further accentuates this structural deformation. Site-directed mutagenesis of the corresponding Pro and Thr residues in CCR5 allowed us to probe the consequences of these structural findings in the context of the whole receptor. The P84A mutation leads to a decreased binding affinity for chemokines and nearly abolishes the functional response of the receptor. In contrast, mutation of Thr-82(2.56) into Val, Ala, Cys, or Ser does not affect chemokine binding. However, the functional response was found to depend strongly on the nature of the substituted side chain. The rank order of impairment of receptor activation is P84A > T82V > T82A > T82C > T82S. This ranking of impairment parallels the bending of the alpha-helix observed in the molecular simulation study.

[Prognostic factors in colorectal neoplasm. Multivariate analysis in 224 patients]

BACKGROUND

Staging of colorectal carcinoma has prognostic value and allows to take decisions about adjuvant therapy and follow up. Prognostic factors are not universally accepted and there are different staging classifications.

AIM

To assess the prognostic value of clinical and pathological variables in 224 patients subjected to a curative resection of a colorectal carcinoma.

PATIENTS AND METHODS

A retrospective analysis of 99 men and 125 women, aged 23 to 91 years old subjected to a curative resection of a colorectal carcinoma and followed up for a mean of 72 months.

RESULTS

Global survival at 60 months was 72%. Univariate analysis showed that tumor localization, vascular permeation, wall infiltration and number of involved lymph nodes had an influence on survival. A Cox regression model disclosed tumor localization (colon versus rectum), a carcino-embryonic antigen over 30 ng/ml, vascular permeation, presence of 1 to 4 involved lymph nodes, or 5 or more lymph nodes and the presence of an apical lymph node as variables with significant prognostic value.

CONCLUSIONS

Our series confirms the prognostic importance of lymph node involvement. This parameter is incorporated in Jass, GITSG (both modifications of Dukes classIfication) and TNM staging scores.

Synthesis and structure-activity relationships of a new model of arylpiperazines. Study of the 5-HT(1a)/alpha(1)-adrenergic receptor affinity by classical hansch analysis, artificial neural networks, and computational simulation of ligand recognition

A classical quantitative structure-activity relationship (Hansch) study and artificial neural networks (ANNs) have been applied to a training set of 32 substituted phenylpiperazines with affinity for 5-HT(1A) and alpha(1)-adrenergic receptors, to evaluate the structural requirements that are responsible for 5-HT(1A)/alpha(1) selectivity. The resulting models provide a significant correlation of electronic, steric, and hydrophobic parameters with the biological affinities. Although the derived linear Hansch correlations give good statistics and acceptable predictions, the introduction of nonlinear relationships in the analysis gives more solid models and more accurate predictions. In the ANN models on the basis of the obtained 3D plots, the 5-HT(1A) affinity has a nonlinear dependence on F, V(o), V(m), and pi(o), although the nonlinear relationship is not far from a planar one. The alpha(1)-adrenergic receptor affinity has a clear nonlinear dependence on F, V(o), V(m), pi(o), and pi(m). A comparison of both analyses gives an additional understanding for 5-HT(1A)/alpha(1) selectivity: (a) high F values increase the binding affinity for 5-HT(1A) receptors and decrease the affinity for alpha(1) sites; (b) the hydrophobicity at the meta-position has only influence for the alpha(1)-adrenergic receptor; (c) the meta-position seems to be implicated in the 5-HT(1A)/alpha(1) selectivity. While the 5-HT(1A) receptor is able to accommodate bulky substituents in the region of its active site, the steric requirements of the alpha(1)-adrenergic receptor at this position are more restricted. This information was used for the design of the new ligand EF-7412 (33) (5-HT(1A): K(i exptl) = 27 nM, alpha(1): K(i exptl) > 1000 nM; 5-HT(1A): K(i pred) (ANN) = 36 nM, alpha(1): K(i pred ANN) = 2745 nM) which was characterized as an antagonist in vivo in pre- and postsynaptic 5-HT(1A)R sites. Computational simulations of the complex between EF-7412 (33) and a 3D model of the transmembrane domain of the 5-HT(1A) receptor allowed us to define the molecular details of the ligand-receptor interaction that includes: (i) the ionic interaction between the protonated amine of the ligand and Asp 3.32; (ii) the hydrogen bonds between the m-NHSO(2)Et group of the ligand and Asn 7.39; and the hydrogen bonds between the hydantoin moiety of the ligand and (iii) Thr 3.37, (iv) Ser 5.42, and (v) Thr 5.43. These QSAR and ANN results in combination with computational simulations of ligand recognition will be useful for the design of potent selective 5-HT(1A) ligands.

Serine and threonine residues bend alpha-helices in the chi(1) = g(-) conformation

The relationship between the Ser, Thr, and Cys side-chain conformation (chi(1) = g(-), t, g(+)) and the main-chain conformation (phi and psi angles) has been studied in a selection of protein structures that contain alpha-helices. The statistical results show that the g(-) conformation of both Ser and Thr residues decreases their phi angles and increases their psi angles relative to Ala, used as a control. The additional hydrogen bond formed between the O(gamma) atom of Ser and Thr and the i-3 or i-4 peptide carbonyl oxygen induces or stabilizes a bending angle in the helix 3-4 degrees larger than for Ala. This is of particular significance for membrane proteins. Incorporation of this small bending angle in the transmembrane alpha-helix at one side of the cell membrane results in a significant displacement of the residues located at the other side of the membrane. We hypothesize that local alterations of the rotamer configurations of these Ser and Thr residues may result in significant conformational changes across transmembrane helices, and thus participate in the molecular mechanisms underlying transmembrane signaling. This finding has provided the structural basis to understand the experimentally observed influence of Ser residues on the conformational equilibrium between inactive and active states of the receptor, in the neurotransmitter subfamily of G protein-coupled receptors.

Molecular determinants of MAO selectivity in a series of indolylmethylamine derivatives: biological activities, 3D-QSAR/CoMFA analysis, and computational simulation of ligand recognition

A series of indolylmethylamine derivatives were assayed toward MAO-A and MAO-B inhibition. The K(i) values of these compounds are in the range from 0.8 to >10(6) nM for MAO-A or from 0.75 to 476000 nM for MAO-B. The most selective MAO-A or MAO-B inhibitors elicit a ratio of K(i) in the order of 1500 or 1000, respectively. Comparison of MAO-A and MAO-B CoMFA models showed that both the steric and electrostatic properties at the 5 position of the indole ring are determinant for MAO selectivity. Computational simulations of the complex between this part of the ligand and Phe-208 of MAO-A or Ile-199 of MAO-B, experimentally identified as responsible for substrate selectivity, allowed us to further characterize the nature of these enzyme-inhibitor interactions.

Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds

One of the common mechanisms of DNA bending by minor groove-binding proteins is the insertion of protein side chains between basepair steps, exemplified in TBP (TATA box-binding protein)/DNA complexes. At the central basepair step of the TATA box TBP produces a noticeable decrease in twist and an increase in roll, while engaging in hydrogen bonds with the bases and sugars. This suggests a mechanism for the stabilization of DNA kinks that was explored here with ab initio quantum mechanical calculations and molecular dynamics/potential of mean force calculations. The hydrogen bonds are found to contribute the energy necessary to drive the conformational transition at the central basepair step. The Asn, Thr, and Gly residues involved in hydrogen bonding to the DNA bases and sugar oxygens form a relatively rigid motif in TBP. The interaction of this motif with DNA is found to be responsible for inducing the untwisting and rolling of the central basepair step. Notably, direct readout is shown not to be capable of discriminating between AA and AT steps, as the strength of the hydrogen bonds between TBP and the DNA are the same for both sequences. Rather, the calculated free energy cost for an equivalent conformational transition is found to be sequence-dependent, and is calculated to be higher for AA steps than for AT steps.

The significance of orbital anatomy and periocular wrinkling when performing laser skin resurfacing

Knowledge of orbital anatomy and the interaction of muscle contractions, gravitational forces and photoagingis fundamental in understanding the limitations of carbon dioxide (CO2) laser skin resurfacing when rejuvenating the skin of the periocular area. Laser resurfacing does not change the mimetic behavior of the facial muscles nor does it influence gravitational forces. When resurfacing periocular tissue, the creation of scleral show and ectropion are a potential consequence when there is an over zealous attempt at improving the sagging malar fat pad and eyelid laxity by performing an excess amount of laser passes at the lateral portion of the lower eyelid. This results in an inadvertent widening of the palpebral fissure due to the lateral pull of the Orbicularis oculi. Retrospectively, 85 patients were studied, who had undergone periorbital resurfacing with a CO2 laser using anew treatment approach. The Sharplan 40C CO2 Feather Touchlaser was programmed with a circular scanning pattern and used just for the shoulders of the wrinkles. A final laser pass was performed with the same program over the entire lower eyelid skin surface, excluding the outer lateral portion (e.g. a truncated triangle-like area),corresponding to the lateral canthus. Only a single laser pass was delivered to the lateral canthal triangle to avoid widening the lateral opening of the eyelid, which might lead to the potential complications of scleral show and ectropion. When the area of the crows' feet is to be treated, three passes on the skin of this entire lateral orbital surface are completed by moving laterally and upward toward the hairline. Patients examined on days 1, 7, 15, 30, 60, and one year after laser resurfacing showed good results. At two months after treatment, the clinical improvement was rated by the patient and physician as being "very good" in 81 of the 85 patients reviewed. These patients underwent laser resurfacing without complications. The proposed technique of periocular resurfacing prevents complications of scleral show and laxity in the lateral eyelid opening and even ectropion, because treatment conforms to the osseo-muscular anatomical relationship of eyelid structures.