Research Unit on Biomedical Informatics GRIB

Barcelona, Spain

Research Unit on Biomedical Informatics GRIB

Barcelona, Spain
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Kaczor A.A.,University of Eastern Finland | Kaczor A.A.,Research Unit on Biomedical Informatics GRIB | Kaczor A.A.,University of Regensburg | Guixa-Gonzalez R.,Research Unit on Biomedical Informatics GRIB | And 5 more authors.
Molecular Informatics | Year: 2015

In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Pinto M.,Research Unit on Biomedical Informatics GRIB | Blasi D.,Drug Discovery Platform PDD | Nieto J.,Ramon Llull University | Arsequell G.,CSIC - Institute of Advanced Chemistry of Catalonia | And 4 more authors.
Amyloid | Year: 2011

A computational analysis was performed on a selected group of 13 TTR-ligand crystallographic complexes in order to deduce information useful for drug design and discovery. The results obtained can be summarized as follows: (1) the binding site of TTR is a large and very flexible cavity, which is composed of three regions with different chemical features; (2) ligands bind to TTR in forward or reverse modes depending on the conformation adopted by the serine and threonine residues located at the end of the cavity; (3) no relationship could be found between the binding mode of the ligands and their TTR fibrillogenesis inhibitory activity; (4) regardless of the structure, chemical properties or binding mode of the ligand to TTR, there is always a contribution of residues Lys15, Leu17, Ala108, Leu110, Ser117 and Thr119 to ligand binding and finally, (5) the most active compounds are characterised by the presence of at least one halogen atom in the HBP1/HBP1' or HBP3/HBP3' pockets.© 2011 Informa UK, Ltd.


PubMed | Research Unit on Biomedical Informatics GRIB, INCLIVA Biomedical Research Institute, IMIM Hospital del Mar Research Institute, IIS Fundacion Jimenez Diaz and Hospital Clinico Universitario
Type: Journal Article | Journal: British journal of cancer | Year: 2016

NF-B signalling appears deregulated in breast tumours. The purpose of this study was to determine whether the non-canonical NF-B pathway, is activated in oestrogen receptor positive (ER+) breast cancer, to identify any correlation between its activity and the clinico-pathological phenotype and to explore whether NF-B2 and RelB subunits and/or any of their target genes might be used as a predictive marker.Two independent cohorts of ER+ early breast cancer patients treated with adjuvant endocrine therapy were included in the study. Activation of RelB and NF-B2 subunits was determined in a training set of 121 patients by measuring DNA-binding activities in nuclear extracts from fresh frozen specimens by an ELISA-based assay. Samples of 15 ER- breast cancer patients were also included in the study. In a large validation cohort of 207 patients, nuclear immunostaining of RelB and NF-B2 on formalin-fixed paraffin-embedded specimens was performed. Statistical correlation within clinico-pathological factors, disease-free survival (DFS) and overall survival (OS) was evaluated. Publicly available gene expression and survival data have been interrogated aimed to identify target genes.Activation of NF-B2 and RelB was found in 53.7 and 49.2% of the 121 ER+ tumours analysed, with similar levels to ER- breast tumours analysed in parallel for comparisons. In the validation cohort, we obtained a similar proportion of cases with activation of NF-B2 and RelB (59.9 and 32.4%), with a 39.6% of co-activation. Multiplexing immunofluorescence in breast cancer tissue confirmed an inverse spatial distribution of ER with NF-B2 and RelB nuclear expression in tumour cells. Interestingly, NF-B2 and RelB mRNA expression was inversely correlated with ER gene (ESR1) levels (P<0.001, both) and its activation was significantly associated with worse DFS (P=0.005 and P=0.035, respectively) in ER+ breast cancer. Moreover, the co-activation of both subunits showed a stronger association with early relapse (P=0.002) and OS (P=0.001). Finally, higher expression of the non-canonical NF-B target gene myoglobin was associated with a poor outcome in ER+ breast cancer (DFS, P<0.05).The non-canonical NF-B pathway activation is inversely associated with oestrogen receptor expression in ER+ breast cancer and predicts poor survival in this subgroup. The myoglobin gene expression has been identified as a possible surrogate marker of the non-canonical NF-B pathway activation in these tumours.


PubMed | Research Unit on Biomedical Informatics GRIB, University of Eastern Finland and University of Regensburg
Type: Journal Article | Journal: Molecular informatics | Year: 2016

In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, opioid receptor dimer, 1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.


Kaczor A.A.,University of Eastern Finland | Kaczor A.A.,Medical University of Lublin | Selent J.,Research Unit on Biomedical Informatics GRIB | Poso A.,University of Eastern Finland
Methods in Cell Biology | Year: 2013

Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies. © 2013 Elsevier Inc.

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