The Institute of Theoretical and Computational Chemistry of the Universitat de Barcelona (IQTCUB) is integrated by more than 60 researchers, experts in several fields of the Theoretical and Computational Chemistry. The research activity carried out at the IQTCUB covers methods and computational tools development, application of several techniques of electronic structures and simulation to problems in materials science, the study of reactivity and reaction dynamics in chemical reactions as well as of biological systems and soft-matter. The main goal is to generate synergies between researchers encouraging the interdisciplinary activities that allow to tackle new challenges. Another important goal is to share expertise in handling the computational resources, which are the main tools in this type of research. See the IQTCUB director’s welcome. For a more detailed information see the 2017 IQTCUB Scientific Activity Report and the XRQTC disseminating video.
The Institute of Theoretical and Computational Chemistry of the Universitat de Barcelona (IQTCUB) was created by the university Government Board on 27th November 2007 involving professors and researchers of different departments of the Faculties of Chemistry and Physics of the Universitat de Barcelona. Nowadays, also some groups of the Faculty of Pharmacy belong to the Institute. The common theme of the research projects conducted at the Institute is the use of methods that are rooted in quantum chemistry, recently it is also open to experimental groups of our Departments with deep collaborations with those focusing on computational chemistry. This should help to increase the multidisciplinary character of our research. Although traditionally the research at IQTCUB is mainly focused on chemistry, it is different from one would expect of a traditional chemist. Indeed, the common tools employed by the researchers at IQTCUB do not belong to a typical laboratory, but to a virtual computational “laboratory”. This “laboratory” is usually a gateway to our computational resources or to the supercomputing centers with even larger computacional facilities. The main goal of theoretical and computational chemistry is to achieve a detailed understanding of chemical and physical processes in order to assist in the interpretation…
Direction team Prof. Eliseo Ruiz Sabin Director Prof. Jordi Poater Teixidor Secretary Prof. Iberio de P. Ribeiro Moreira Treasurer Prof. Francesc Illas i Riera Board Member
Here are of the annual IQTCUB activity reports that are available to download: IQTCUB report of 2018 ( CAT | ENG ) IQTCUB report of 2017 ( CAT | ENG ) IQTCUB report of 2016 ( CAT | ENG ) IQTCUB report of 2015 ( CAT | ENG ) IQTCUB report of 2014 ( CAT | ENG ) IQTCUB report of 2013 ( CAT | ENG ) IQTCUB report of 2012 ( CAT | ENG ) IQTCUB report of 2011 ( CAT ) IQTCUB report of 2010 ( CAT ) IQTCUB report of 2009 and 2008 ( CAT )
You are welcome to see this video elaborated by XRQTC.This is a project done with the support of Direccio General de Recerca de la Generalitat de Catalunya through AGAUR. Authors: Xavier Gimenez (UB), Lourdes Vega (Matgas), Jean Didier Marechal (UAB).
RESEARCH PRODUCT / RESEARCH GROUP Structure-based design and discovery of protein ligands have emerged as a new tool in medicinal chemistry. In particular, the knowledge of the three-dimensional structure of a protein can be used to derive new protein ligands with improved binding properties ( i.e. new drugs ). Within this approach, we need algorithms and methods to solve the following questions: What is the binding affinity of a novel ligand towards a receptor? What are the best conformations of a ligand to the binding site? What are the similarities of different ligands concerning their recognition capabilities? With which orientation will a ligand bind to the active site? We want to contribute to obtaining new answers for these questions and some problems concerning CANCER disease. http://www.ub.edu/cadrugdesign/index.html
POSITION DESCRIPTION
Research Project / Research Group Description
In recent years, one of the most important target family that has attracted attention to the pharmaceutical industry is the protein kinases family. In 2002 Manning et al. published a study in which they identified 518 genes corresponding to protein kinases in the human genome, which constitutes about 2% of the total genome [1]. Since then, its relevant role has been established in numerous diseases, including cancer [2]. However, kinases present a high degree of conservation of their global three-dimensional structure and have an important lack of structural diversity in the active site, making the design of selective therapeutic inhibitors a very difficult task. For these reasons, there is an increasing interest in the design of new compounds with an allosteric action mechanism. However, deciphering allosteric or cryptic binding sites has been proved as a difficult job. In the present project, we will address this problem using different methodologies recently developed in our research group. Therefore, Molecular Dynamics (MD) simulations in conjunction with a cosolvent approach and the ‘fragment dissolved Molecular Dynamics’ (fdMD), a method based on multiple solvated molecules around the target protein, will be used to determine possible allosteric binding sites for several members of the protein kinases family and other protein families to design novel drugs that overcome the resistance of current treatments. Furthermore, an Artificial Intelligence (AI) approach will be applied for the identification of potential new drugs using the generated data.
[1] Manning, G., et al., The protein kinase complement of the human genome. Science. (2002).
[2] Fleuren, EDG., Zhang, L., Wu, J., Roger J. Daly, RJ. The kinome ‘at large’ in cáncer. Nature Reviews Cancer. (2016)
Job position description
The Modelling of Biological Systems and Drug Design research group associated to the Materials Science and Physical Chemistry department at the University of Barcelona (UB) and to the Institute of Theoretical and Computational Chemistry (IQTCUB) (http://www.ub.edu/cadrugdesign/index.html) was created in 2002. The group has extensive experience in the field of Computational Chemistry and Molecular Modelling and in the use of structure-based drug design methodology for the design of new compounds with possible pharmacological activity. The main goal of the group is the design, using molecular modelling techniques, of compounds with pharmacological activity. Taking advantage of our previous experience we are also working in the development of new computational tools to make easier the drug design process and to increase its effectivity. Furthermore, we promote interdisciplinary research by means of collaborations with experimental groups that are basically working in protein targets related to the cancer disease. Because of this cooperation, we found promising compounds for many targets that show µMolar activity in in vitro assays and we are currently synthesizing new compounds to increase its biological activity.
The group is seeking a PhD student with a degree in Chemistry, Physics or Biochemistry and with a Master related to the use of computational methods in Molecular Modeling. We are interested in bringing people with different motivations to exploiting various cutting-edge Drug Design technologies for the design and development of new compounds targeting allosteric sites of protein kinase family. The PhD student will perform a temporary stay in the Evotec company (www.evotec.com ).
OTHER RELEVANT WEBSITES Prof Jaime Rubio collaborates in the project entitled “Identification of inhibitors of the Mpro protease of the virus COVID-19 by repositioning of drugs”, led by prof. Juan Jesus Perez Gonzalez from the Universitat Politècnica de Catalunya. The project has been granted by the Ministerio de Ciencia e Innovación and the Instituto de Salud Carlos III, in the COVID-19 extraordinary call (April 2020). https://www.iqtc.ub.edu/news/inhibidores-de-la-proteasa-mpro-del-virus-covid-19/
