Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools

Proteinprotein docking methodology is frequently used to model complexes of transmembrane proteins, in particular oligomers of G protein-coupled receptors (GPCRs), even if its applicability for these systems has never been fully validated. The aim of this work is to perform a systematic study on the suitability of some widely-used proteinprotein docking software for modeling complexes of transmembrane proteins. In this study we tested the programs ZDOCK, ClusPro, HEX, GRAMM-X, PatchDock, SymmDock, and HADDOCK, using a set of membrane protein oligomers for which the 3D structure has been obtained experimentally, including opsin dimer, the recently published chemokine CXCR4 and kappa opioid receptor dimers. The results show that the docking success depends on the applied docking algorithm and scoring functions, but also on inherent structural features of the transmembrane proteins. Thus, proteins with large interface surfaces, rich in surface cavities, high-order symmetry, and small conformational change upon complex formation are well predicted more often than proteins without these features. The results of this systematic analysis provide guidelines that can be used for obtaining reliable models of transmembrane proteins, including GPCRs. Therefore they can be useful for the application of structure-based methods in drug discovery projects involving these targets.

The state-of-the-art of approved and under-development cholera vaccines

Cholera remains a huge public health problem. Although in 1894, the first cholera vaccination was reported, an ideal vaccine that meets all the requirements of the WHO has not yet been produced. Among the different approaches used for cholera vaccination, attenuated vaccines represent a major category; these vaccines are beneficial in being able to induce a strong protective response after a single administration. However, they have possible negative effects on immunocompromised patient populations. Both the licensed CVD103-HgR and other vaccine approaches under development are detailed in this article, such as the Vibrio cholerae 638 vaccine candidate, Peru-15 or CholeraGarde(®) and the VA1.3, VA1.4, IEM 108 VCUSM2 and CVD 112 vaccine candidates. In another strategy, killed V. cholerae vaccines have been developed, including Dukoral(®), mORCAX(®) and Sanchol™. The killed vaccines are already sold, and they have successfully demonstrated their potential to protect populations in endemic areas or after natural disasters. However, these vaccines do not fulfill all the requirements of the WHO because they fail to confer long-term protection, are not suitable for children under two years, require more than a single dose and require a distribution chain with cold storage. Lastly, other vaccine strategies under development are summarized in this review. Among these strategies, vaccine candidates based on alternative drug delivery systems that have been reported lately in the literature are discussed, such as microparticles, proteoliposomes, LPS subunits, DNA vaccines and rice seeds containing toxin subunits. Preliminary results reported by many groups working on alternative delivery systems for cholera vaccines demonstrate the importance of new technologies in addressing old problems such as cholera. Although a fully ideal vaccine has not yet been designed, promising steps have been reported in the literature resulting in hope for the fight against cholera.

2D- and 3D-QSAR studies of a series of benzopyranes and benzopyrano[3,4b][1,4]-oxazines as inhibitors of the multidrug transporter P-glycoprotein

The ATP-binding cassette efflux transporter P-glycoprotein (P-gp) is notorious for contributing to multidrug resistance in antitumor therapy. Due to its expression in many blood-organ barriers, it also influences the pharmacokinetics of drugs and drug candidates and is involved in drug/drug- and drug/nutrient interactions. However, due to lack of structural information the molecular basis of ligand/transporter interaction still needs to be elucidated. Towards this goal, a series of Benzopyranes and Benzopyrano[3,4b][1,4]oxazines have been synthesized and pharmacologically tested for their ability to inhibit P-gp mediated daunomycin efflux. Both quantitative structure–activity relationship (QSAR) models using simple physicochemical and novel GRID-independent molecular descriptors (GRIND) were established to shed light on the structural requirements for high P-gp inhibitory activity. The results from 2D-QSAR showed a linear correlation of vdW surface area (Ų) of hydrophobic atoms with the pharmacological activity. GRIND (3D-QSAR) studies allowed to identify important mutual distances between pharmacophoric features, which include one H-bond donor, two H-bond acceptors and two hydrophobic groups as well as their distances from different steric hot spots of the molecules. Activity of the compounds particularly increases with increase of the distance of an H-bond donor or a hydrophobic feature from a particular steric hot spot of the benzopyrane analogs.

Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs

Functioning of G protein-coupled receptors (GPCRs) is tightly linked to the membrane environment, but a molecular level understanding of the modulation of GPCR by membrane lipids is not available. However, specific receptor-lipid interactions as well as unspecific effects mediated by the bulk properties of the membrane (thickness, curvature, etc.) have been proposed to be key regulators of GPCR modulation. In this review, we examine computational efforts made towards modeling and simulation of (i) the complex behavior of membrane lipids, (ii) membrane lipid-GPCR interactions as well as membrane lipid-mediated effects on GPCRs and (iii) GPCR oligomerization in a native-like membrane environment. We propose that, from the perspective of computational modeling, all three of these components need to be addressed in order to achieve a deeper understanding of GPCR functioning. Presently, we are able to simulate numerous lipid properties applying advanced computational techniques, although some barriers, such as the time-length of these simulations, need to be overcome. Implementing three-dimensional structures of GPCRs in such validated membrane systems can give novel insights in membrane-dependent receptor modulation and formation of higher order receptor complexes. Finally, more realistic GPCR-membrane models would provide a very useful tool in studying receptor behavior and its modulation by small drug-like ligands, a relevant issue for drug discovery.

Rational design of the survivin/CDK4 complex by combining protein-protein docking and molecular dynamics simulations

Survivin, the smallest inhibitor of apoptosis protein (IAP), is a valid target for cancer research. It mediates both the apoptosis pathway and the cell cycle and has been proposed to form a complex with the cyclin-dependent kinase protein CDK4. The resulting complex transports CDK4 from the cytosol to the nucleus, where CDK4 participates in cell division. Survivin has been recognized as a node protein that interacts with several partners; disruption of the formed complexes can lead to new anticancer compounds. We propose a rational model of the survivin/CDK4 complex that fulfills the experimental evidence and that can be used for structure-based design of inhibitors modifying its interface recognition. In particular, the suggested complex involves the alpha helical domain of survivin and resembles the mode of binding of survivin in the survivin/borealin X-ray structure. The proposed model has been obtained by combining protein-protein docking, fractal-based shape complementarity, electrostatics studies and extensive molecular dynamics simulations.

Near-roadway pollution and childhood asthma: implications for developing "win-win" compact urban development and clean vehicle strategies

BACKGROUND

The emerging consensus that exposure to near-roadway traffic-related pollution causes asthma has implications for compact urban development policies designed to reduce driving and greenhouse gases.

OBJECTIVES

We estimated the current burden of childhood asthma-related disease attributable to near-roadway and regional air pollution in Los Angeles County (LAC) and the potential health impact of regional pollution reduction associated with changes in population along major traffic corridors.

METHODS

The burden of asthma attributable to the dual effects of near-roadway and regional air pollution was estimated, using nitrogen dioxide and ozone as markers of urban combustion-related and secondary oxidant pollution, respectively. We also estimated the impact of alternative scenarios that assumed a 20% reduction in regional pollution in combination with a 3.6% reduction or 3.6% increase in the proportion of the total population living near major roads, a proxy for near-roadway exposure.

RESULTS

We estimated that 27,100 cases of childhood asthma (8% of total) in LAC were at least partly attributable to pollution associated with residential location within 75 m of a major road. As a result, a substantial proportion of asthma-related morbidity is a consequence of near-roadway pollution, even if symptoms are triggered by other factors. Benefits resulting from a 20% regional pollution reduction varied markedly depending on the associated change in near-roadway proximity.

CONCLUSIONS

Our findings suggest that there are large and previously unappreciated public health consequences of air pollution in LAC and probably in other metropolitan areas with dense traffic corridors. To maximize health benefits, compact urban development strategies should be coupled with policies to reduce near-roadway pollution exposure.

Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function

Protein surface roughness is a structural property associated with ligand-protein and protein-protein binding interfaces. In this work we apply for the first time the concept of surface roughness, expressed as the fractal dimension, to address structure and function of G protein-coupled receptors (GPCRs) which are an important group of drug targets. We calculate the exposure ratio and the fractal dimension for helix-forming residues of the β₂ adrenergic receptor (β₂AR), a model system in GPCR studies, in different conformational states: in complex with agonist, antagonist and partial inverse agonists. We show that both exposure ratio and roughness exhibit periodicity which results from the helical structure of GPCRs. The pattern of roughness and exposure ratio of a protein patch depends on its environment: the residues most exposed to membrane are in general most rough whereas parts of receptors mediating interhelical contacts in a monomer or protein complex are much smoother. We also find that intracellular ends (TM3, TM5, TM6 and TM7) which are relevant for G protein binding and thus receptor signaling, are exposed but smooth. Mapping the values of residual fractal dimension onto receptor 3D structures makes it possible to conclude that the binding sites of orthosteric ligands as well as of cholesterol are characterized with significantly higher roughness than the average for the whole protein. In summary, our study suggests that identification of specific patterns of roughness could be a novel approach to spot possible binding sites which could serve as original drug targets for GPCRs modulation.

Figure

Tungstate activates BK channels in a β subunit- and Mg2+-dependent manner: relevance for arterial vasodilatation

AIMS

Tungstate reduces blood pressure in experimental animal models of both hypertension and metabolic syndrome, although the underlying mechanisms are not fully understood. Given that the large-conductance voltage- and Ca(2+)-dependent K(+) (BK) channel is a key element in the control of arterial tone, our aim was to evaluate whether BK channel modulation by tungstate can contribute to its antihypertensive effect.

METHODS AND RESULTS

Patch-clamp studies of heterologously expressed human BK channels (α + β(1-4) subunits) revealed that cytosolic tungstate (1 mM) induced a significant left shift (∼20 mV) in the voltage-dependent activation curve only in BK channels containing αβ(1) or αβ(4) subunits, but reduced the amplitude of K(+) currents through all BK channels tested. The β(1)-dependent activation of BK channels by tungstate was enhanced at cytosolic Ca(2+) levels reached during myocyte contraction, and prevented either by removal of cytosolic Mg(2+) or by mutations rendering the channel insensitive to Mg(2+). A lower concentration of tungstate (0.1 mM) induced voltage-dependent activation of the vascular BKαβ(1) channel without reducing current amplitude, and consistently exerted a vasodilatory action on wild-type but not on β(1)-knockout mouse arteries pre-contracted with endothelin-1.

CONCLUSION

Tungstate activates BK channels in a β subunit- and Mg(2+)-dependent manner and induces vasodilatation only in mouse arteries that express the BK β(1) subunit.

Strengthening community capacity to participate in making decisions to reduce disproportionate environmental exposures

Environmental exposures impose a disproportionate health burden on low-income populations and communities of color. One contributing factor may be the obstacles such communities face to full participation in making policy decisions about environmental health. This study described and analyzed the characteristics that contributed to communities' capacity to participate in making environmental decisions and suggested steps public agencies could take to achieve more meaningful participation. By strengthening community capacity, advancing authentic participation, and building democratic power, it might be possible to alter current patterns of health inequities. Strengthening participation by working with communities to develop the capacities needed to be effective in such processes is a key role for local, state, and national environmental agencies.

Progress in the structural prediction of G protein-coupled receptors: D3 receptor in complex with eticlopride

Predicting the three-dimensional structure of ligand-receptor complexes involving G protein-coupled receptors (GPCRs) is still a challenging task in rational drug design. To evaluate the reliability of the GPCR structural prediction, only a couple of community-wide assessments have been carried out. Our participation in the last edition, DOCK2010, involved the blind prediction of the dopaminergic D(3) receptor in complex with the D(2)/D(3) selective antagonist eticlopride for which the crystal structure has been recently released. Here, we describe a methodology that succeeded to produce a correctly predicted eticlopride-D(3) receptor complex out of three submitted models. Ranking the obtained models in the correct order is the main challenge due to subtle structural differences in the complex that are not sufficiently captured by conventional scoring functions. Importantly, our work reveals that a correct ranking is obtained by including a more sophisticated description of conformational ligand energy on binding. All in all, this case study highlights the current progress in modeling GPCR complexes and underlines that in silico modeling can be a valuable complement in GPCR drug discovery.

A gain-of-function SNP in TRPC4 cation channel protects against myocardial infarction

AIMS

The TRPC4 non-selective cation channel is widely expressed in the endothelium, where it generates Ca(2+) signals that participate in the endothelium-mediated vasodilatory response. This study sought to identify single-nucleotide polymorphisms (SNPs) in the TRPC4 gene that are associated with myocardial infarction (MI).

METHODS AND RESULTS

Our candidate-gene association studies identified a missense SNP (TRPC4-I957V) associated with a reduced risk of MI in diabetic patients [odds ratio (OR) = 0.61; confidence interval (CI), 0.40-0.95, P= 0.02]. TRPC4 was also associated with MI in the Wellcome Trust Case-Control Consortium's genome-wide data: an intronic SNP (rs7319926) within the same linkage disequilibrium block as TRPC4-I957V showed an OR of 0.86 (CI, 0.81-0.94; P =10(-4)). Functional studies of the missense SNP were carried out in HEK293 and CHO cells expressing wild-type or mutant channels. Patch-clamp studies and measurement of intracellular [Ca(2+)] in response to muscarinic agonists and direct G-protein activation showed increased channel activity in TRPC4-I957V-transfected cells compared with TRPC4-WT. Site-directed mutagenesis and molecular modelling of TRPC4-I957V suggested that the gain of function was due to the presence of a less bulky Val-957. This permits a firmer interaction between the TRPC4 and the catalytic site of the tyrosine kinase that phosphorylates TRPC4 at Tyr-959 and facilitates channel insertion into the plasma membrane.

CONCLUSION

We provide evidence for the association of a TRPC4 SNP with MI in population-based genetic studies. The higher Ca(2+) signals generated by TRPC4-I957V may ultimately facilitate the generation of endothelium- and nitric oxide-dependent vasorelaxation, thereby explaining its protective effect at the vasculature.

Synthesis, 3D-QSAR, and structural modeling of benzolactam derivatives with binding affinity for the D(2) and D(3) receptors

A series of 37 benzolactam derivatives were synthesized, and their respective affinities for the dopamine D(2) and D(3) receptors evaluated. The relationships between structures and binding affinities were investigated using both ligand-based (3D-QSAR) and receptor-based methods. The results revealed the importance of diverse structural features in explaining the differences in the observed affinities, such as the location of the benzolactam carbonyl oxygen, or the overall length of the compounds. The optimal values for such ligand properties are slightly different for the D(2) and D(3) receptors, even though the binding sites present a very high degree of homology. We explain these differences by the presence of a hydrogen bond network in the D(2) receptor which is absent in the D(3) receptor and limits the dimensions of the binding pocket, causing residues in helix 7 to become less accessible. The implications of these results for the design of more potent and selective benzolactam derivatives are presented and discussed.

Induced effects of sodium ions on dopaminergic G-protein coupled receptors

G-protein coupled receptors, the largest family of proteins in the human genome, are involved in many complex signal transduction pathways, typically activated by orthosteric ligand binding and subject to allosteric modulation. Dopaminergic receptors, belonging to the class A family of G-protein coupled receptors, are known to be modulated by sodium ions from an allosteric binding site, although the details of sodium effects on the receptor have not yet been described. In an effort to understand these effects, we performed microsecond scale all-atom molecular dynamics simulations on the dopaminergic D₂ receptor, finding that sodium ions enter the receptor from the extracellular side and bind at a deep allosteric site (Asp2.50). Remarkably, the presence of a sodium ion at this allosteric site induces a conformational change of the rotamer toggle switch Trp6.48 which locks in a conformation identical to the one found in the partially inactive state of the crystallized human β₂ adrenergic receptor. This study provides detailed quantitative information about binding of sodium ions in the D₂ receptor and reports a possibly important sodium-induced conformational change for modulation of D₂ receptor function.

G-protein coupled receptors represent more than 50% of the current drug targets, hence playing a crucial role in drug discovery today. A deeper understanding of G-protein coupled receptor functioning and modulation will help in the development of new drugs that are able to interact with such systems in a more subtle way than simple agonists or antagonists. In the present work, we studied the energetics of sodium ions, which have been described to act as an allosteric regulator within the D₂ receptor using long-time molecular dynamics simulations, in order to gain insight into the molecular mechanism by which they exert this effect. In our simulations, we observed how sodium ions are able to induce a conformational change of the Trp6.48, a molecular rotamer switch which is implicated in the activation mechanism of G-protein coupled receptors. This observation, never reported before, has interesting implications for the design of drugs able to interact in a proper way with D₂ receptor in particular and GPCR in general.

A Morphological Study of 608 Cases of Canine Malignant Lymphoma in France With a Focus on Comparative Similarities Between Canine and Human Lymphoma Morphology

This study reports cytomorphological, histomorphological, and immunological characterization of 608 biopsy cases of canine malignant lymphoma, with epidemiological and clinical data, collected from 7 French veterinary pathology laboratories. It compares morphological characteristics of malignant lymphoma in canines, per the updated Kiel classification system, with those reported in humans, per the World Health Organization (WHO) classification system. Of tumors described, 24.5% and 75.5% were classified as low- and high-grade malignant lymphomas, respectively. Presenting clinical signs included generalized or localized lymphadenopathy (82.4%) and extranodal diseases (17.6%) involving the skin (12.34%) and other sites (5.26%). Immunohistochemistry confirmed 63.8% B-cell (CD3–, CD79a+), 35.4% T-cell (CD3+, CD79a–), and 0.8% null-cell (CD3–, CD79a–) lymphomas. Most B-cell cases (38.49%) were of high-grade centroblastic polymorphic subtype; most T-cell cases (8.55%), high-grade pleomorphic mixed and large T-cell lymphoma subtypes. Some B-cell tumors showed morphologic characteristics consistent with follicular lymphomas and marginal zone lymphomas per the Revised European American Classification of Lymphoid Neoplasms and WHO canine classification systems and the WHO human classification system. Unusual high-grade B-cell subtypes included an atypical high-grade small B-cell lymphoma (0.66%), Burkitt-type B-cell lymphoma (1.64%), plasmacytoid lymphoma (0.99%), and mediastinal anaplastic large B-cell lymphoma (0.16%). Unusual T-cell subtypes included a previously undescribed high-grade canine immunoblastic T-cell type (1.15%), a rare low-grade prolymphocytic T-cell lymphoma (0.16%), and a recently described high-grade canine T-cell entity—aggressive granulocytic large-cell lymphoma (0.16%). Marginal zone lymphomas were common (10.86%); follicular lymphomas were rare (0.49%). Canine primary cutaneous malignant lymphoma subtypes were present (11.84%). There was no significant difference between B- and T-cell malignant lymphoma in regard to canine age and sex. A significant overrepresentation of Boxers (24.19%) was found for T-cell lymphomas.

Impact on Survival of Primary Tumor Resection in Women with Metastatic Breast Cancer at Initial Diagnosis. The Alamo Project

Background: Recent medical and scientific reports suggest that surgery of the primary tumor (PT) could be taken into account, although far from the current standard of care, in metastatic breast cancer (MBC) patients. The mechanistic basis for these findings stem from crosstalk between the PT and metastatic foci, immunosuppressive effects, and/or the avoidance of metastatic re-seeding from the primary source. We have focused on implementing surgical excision of the PT in certain settings and tumor types in order to ascertain whether this aggressive treatment modality can be justified in a classic palliative setting. Methods: The ALAMO Project (A) is a retrospective analysis of patients (pts) diagnosed with BC between 1990 and 1997 across 43 GEICAM hospitals. Patterns of BC presentation (tumor and host characteristics), treatment and survival were recorded in 2 cohorts, AI (1990-93, 4532 pts, closed by 2000) and AII (1994-97, 10849 pts, closed by 2003). Only MBC pts at first diagnosis were included, excluding those with secondary tumors, without a minimum of 2 months follow-up at the same institution, and without complete information regarding their PT surgery. Descriptive, Kaplan-Meier and Cox regression analyses were carried out. Results: 6.12% of the ALAMO database pts were initially diagnosed with MBC (605 fulfilled the present analysis criteria), with a medium age of 61.6 years (yrs). 54.2% had single-organ metastasis, anatomically distributed in skin/soft tissue (18.8%), bone (35.9%), lung (9.8%), and other viscera (35.5%). 26.3% of pts had surgery of the PT (83.7% of them radical procedures, 73.3% of them axillary dissected and 5.6% received radiotherapy). Chemotherapy (30.7%), endocrine therapy (23.1%) or both (41.7%) were the systemic approaches, and 4.5% received supportive care. Women in the surgery (S) group (159 pts) were younger, with skin/soft tissue or bone metastasis and oligometastatic disease. 5-yr overall survival (OS) was 18.84%, 2.94 yrs median OS in the S-group versus 1.83 yrs in the nS-group (p<0.001). A stratified analysis by organ showed relevant effects of surgery for pts with skin/soft tissue metastasis, 4.52 yrs versus 1.77 yrs median OS in the S and nS arms respectively. The multi-adjusted HR for surgery in this subgroup was 0.30 (p<0.001), which was not significantly modified considering a propensity score (PS) factor (HR 0.29, p<0.001). Surgery (p<0.001), systemic treatment (p<0.001), and the interaction between surgery and metastatic location (p<0.004) were included in the multivariate predictive model of survival for the whole series. Discussion: Local surgery of the PT is associated with an increase in OS for pts with skin/soft tissue metastasis and is maintained in multi-adjusted models. These analyses suggest that loco-regional control of the PT should be considered for the treatment of advanced disease in selected patients, but must be further investigated in randomized controlled trials in MBC at first diagnosis.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3104.

A novel multilevel statistical method for the study of the relationships between multireceptorial binding affinity profiles and in vivo endpoints

The present work introduces a novel method for drug research based on the sequential building of linked multivariate statistical models, each one introducing a different level of drug description. The use of multivariate methods allows us to overcome the traditional one-target assumption and to link in vivo endpoints with drug binding profiles, involving multiple receptors. The method starts with a set of drugs, for which in vivo or clinical observations and binding affinities for potentially relevant receptors are known, and allows obtaining predictions of the in vivo endpoints highlighting the most influential receptors. Moreover, provided that the structure of the receptor binding sites is known (experimentally or by homology modeling), the proposed method also highlights receptor regions and ligand-receptor interactions that are more likely to be linked to the in vivo endpoints, which is information of high interest for the design of novel compounds. The method is illustrated by a practical application dealing with the study of the metabolic side effects of antipsychotic drugs. Herein, the method detects related receptors confirmed by experimental results. Moreover, the use of structural models of the receptor binding sites allows identifying regions and ligand-receptor interactions that are involved in the discrimination between antipsychotic drugs that show metabolic side effects and those that do not. The structural results suggest that the topology of a hydrophobic sandwich involving residues in transmembrane helices (TM) 3, 5, and 6, as well as the assembling of polar residues in TM5, are important discriminators between target/antitarget receptors. Ultimately, this will provide useful information for the design of safer compounds inducing fewer side effects.