Commemoration of the International Year of Crystallography
In commemoration of the International Year of Crystallography (IYCr2014) many organizations, journals and institutions have prepared special activities. Among them, the National Research Council of Spain (CSIC) has sponsored the publication of a special issue of its official publication entitled Arbor. This number has recently appeared on line and among the contributions the first article is a review of the advances in macromolecular crystallography in the second half of the 20th century from a personal perspective, related to the development of Dr. Cele Abad-Zapatero as a professional scientist, from his boyhood years in Spain, soon after the end of the Spanish Civil war. The article is accessible from the following link: http://arbor.revistas.csic.es/index.php/arbor/issue/current<br>This article could be of interest to any budding scientist/crystallographer. Any interested reader should be able to download this or any other article from this special issue of Arbor from the above website. Otherwise, copies can be requested from the author, from his e-mail address (see contact tab).
Image of the ‘Chronophage Clock’ in King’s Parade in Cambridge
Among other things, this amazing clock is an homage to the 18th English clockmaker John Harrison who invented the ‘grasshoper escapement’ that allowed him to develop the chronometers that permited the accurate determination of the longitude at sea. A problem that had defied the most brilliant minds of his time. The clearly visible text in the lower ledge of the window is part of the full inscribed sentence on the window: Mundus transit et concupiscentia eius. This inscription is also present in the sun dial in one of the courtyards of Corpus Christi college. An reflection on the passing of time and our desires and wishes.
A manuscript entitled ‘Celebrating Macromolecular Crystallography: A Personal Perspective’ is currently in press in a special edition of the Journal ARBOR, Ciencia, Pensamiento y Cultura . This special issue is intended to commemorate the International Year of Crystallography (IYCr2014). This article is a review of the origins and advances of structural biology in the second half of the 20th Century from the personal perspective of the author, as he matured as a professional scientist. The journal ARBOR is a publication of the Natural Research Council of Spain (CSIC, Consejo Superior de Investigaciones Cientificas). It will be published as an open-access and so if any reader is interested it can probably be found in the internet. Contact me if you are interested and have difficulties in obtaining a copy. The publication is imminent.
Return to UIC early in April
Working with UIC colleagues on SBDD projects.
Currently in Cambridge, UK. I am spending two months (Feb 1-April 1) in the neighborhood of Cambridge, UK continuing the research on the update and applications of the AtlastCBS to drug discovery, and also on the use of Ligand Efficiency Indices (LEIs) as part of a Multiple Parameter Optimization (MPO) strategy to expedite drug discovery and to make it more rigorous. The hosting institutions are Optibrium, Ltd and the European Bioinformatics Institute (EBI) at the Wellcome campus in Hixton (ChEMBL: Chemical Biology group).
Participated in a Structure-Based Drug Design workshop/course at the Institute Pasteur de Montevideo (Montevideo, Uruguay, Nov. 3-8)This was an intensive drug discovery workshop in collaboration with Profs. P. Michels (University of Edinburg) and W. Hol (University of Washington, Seattle). The course was focused on novel methods and techniques for drug discovery with emphasis on Neglected Diseases. You can find more about the course and the Institute Pasteur de Montevideo here. There were lectures during an entire week , posters, and also practical sessions reviewing several computational techniques, among them ‘docking techniques’. There was also a full practical session devoted to the use of the AtlasCBS webserver. (Images courtesy of Prof. W. Hol, University of Washington, Seattle).
Presented two talks at 23rd International Congress of Crystallography in Montreal, Canada (IUCr2014), Aug. 5-12
The first one was related to the presentation of Crystallography in a dramatic context. I reviewed the work that I have been doing on my own (Play: Picasso Meets Crystallography) and later in collaboration with Jill Campbell and Greg Gerhard (play: Bernal’s Picasso) to present the concepts and history of Crystallography in a dramatic content. Further details can be found in the ‘Bernal’s Picasso’ tab of this website. More details can also be found on the blog: www.crystaledges.org.
The second was related to the presence of symmetry in Art forms and particularly in Rosewindows in Gothic Cathedrals. This presentation focused on the paper recently published in Acta Cryst vol. D70, published this past March. This is a theme that was mentioned before in this ‘news and views’ . The abstract of this presentation can also be presented in the www.crystaledges.org
There will be an upcoming paper in Future of Medicinal Chemistry (FMC)
There will be an upcoming paper in Future of Medicinal Chemistry (FMC) relating to the incorporation of the AtlasCBS and Ligand Efficiency framework into the StarDrop™ software (www.Optibrium.com). There have been quite a few publications in the field, particularly relating to the value of ‘Ligand Efficiency Metrics’ to guide drug discovery. Some of the papers are reviewed in the upcoming paper in FMC and perspectives for the future are presented. Abad-Zapatero C, Champness EJ & Segall M. Alternative variables in drug discovery: promises and challenges. Future Med. Chem. 6(5), 577-593.
I’ll be in Cambridge, UK, Jan. 25-Feb. 4 working with my colleagues at Optibrium on the implementation of the AtlasCBS software in their StarDrop(TM) software package. I should be back in Chicago, Feb. 8 and at the UIC campus soon thereafter.
I will be in Paris, Jan. 20-24 for the events related to the commemoration of the International Year of Crystallography (IYCr2014), sponsored by the IUCr and UNESCO. This is to celebrate the 100th year anniversary of the unveiling of the very first crystallographic structure (NaCl) using X-rays by the Bragg’s (W.H. and W.L Bragg) in Cambridge, UK in 1913. Consult the blog ‘crystaledges.org‘ for more details.
Leaving the UIC campus for a month stay in Europe. Landing in Paris, Jan. 11, I’ll be in Saarbrucken, Germany, giving a Workshop on Protein Crystallography and Structure-Based Drug Design in the laboratory of Prof. Rolf Hartmann, University of Saarlandes, Department of Drug Optimization.
Happy New Year and best wishes to you and your family, friends and colleagues for 2014 and beyond. See the last posting on the blog for a reflective poem entitled ‘Season’s Lament’ about Christmas trees.
Returned to UIC after first successful workshop about the concepts and usage of the AtlasCBS concepts and tool at the Helmholtz Institute of Pharmaceutical Research in Saarbruecken, Germany (Sept. 30-Oct. 1).
The workshop was run in collaboration with the colleagues of Optibrium, Ltd (UK) that now offers the AtlasCBS application as an add-on to their software Stardrop(TM). Link
After the workshop, attended meeting in Getxo, Bilbao (Spain) in honor of Jorge Navaza (Grenoble, France), recognizing his contributions to the implementation of the Fast Rotation Function and other mathematical and computational tools in crystallography and electron microscopy. (See Crystal Edges Blog.)
Currently at UIC. Blog ‘Crystal Edges’ inaugurated to commemorate the International Year of Crystallography in 2014 (IYCr2014). Please visit new leftmost tab ‘Crystal Edges’.
Visiting professor at the University of Alcala de Henares (Madrid) in the Department of Pharmacology, sponsored by the Foundation Giner de los Rios to update, develop the AtlasCBS server and train students and medicinal chemistry professionals. Laboratory of Prof. F. Gago. Feb.-June.2013.
Recently published book: Ligand Efficiency Indices for Drug Discovery Towards an Atlas–Guided Paradigm. See Books
Contribution of indazolinone tautomers to kinase activity. Vasudevan A, Verzal MK, Villamil CI, Stewart KD, Abad-Zapatero C, Oie T, Djuric SW. Bioorg Med Chem Lett. 2012 Jul 15;22(14):4502-5.
Exploration of diverse hinge-binding scaffolds for selective Aurora kinase inhibitors. Ji Z, Dai Y, Abad-Zapatero C, Albert DH, Bouska JJ, Glaser KB, Marcotte PA, Soni NB, Magoc TJ, Stewart KD, Wei RQ, Davidsen SK, Michaelides MR. Bioorg Med Chem Lett. 2012 Jul 15;22(14):4528-31. Epub 2012 Jun 7.
AtlasCBS server beta-version available (see AtlasCBS).
Control can compensate for the damage induced in protein crystals by alien solutions. C. Abad-Zapatero, R. Oliete, S. Rodriguez-Puente, J. Pous, L. Martinelli, M. E. Johnson and A. Guasch. Acta Crysta. (2011) F67, 1300-1308.
Zapatero, Daniel H. Albert, Jennifer J. Bouska, Keith B. Glaser, Terry J. Magoc, Patrick A. Marcotte, Donald J. Osterling, Kent D. Stewart, Steven K. Davidsen, Michael R. Michaelides. Bioorganic & Medicinal Chemistry Letters 21 (2011) 5620–5624.
S Gutka, H., S.G. Franzblau, F. Movahedzadeh and Cele Abad-Zapatero. (2011). Acta Cryst. Section F, F67, 710-173.
Ligand Efficiency Indices (LEIs): More than a Simple Efficiency Yardstick. (2011). Cele Abad-Zapatero & D. Blassi. Review in Molecular Informatics. 30(2-3), 122-132.
Time-Trajectories in Efficiency Maps as Effective Guides for Drug Discovery Efforts. (2011). Serge Christmann-Franck, Daniel Cravo and Cele Abad-Zapatero.Molecular Informatics. 30 (2-3), 137-144.
Retrospective Mapping of SAR Data for TTR Protein in Chemico-Biological Space Using Ligand Efficiency Indices as a Guide to Drug Discovery Strategies. (2011). Daniel Blasi, Gemma Arsequell, Gregori Valencia, Joan Nieto, Antoni Planas, Marta Pinto, Nuria B. Centeno, Cele Abad-Zapatero, Jordi Quintana. Molecular Informatics. 30 (2-3), 161-167.
Recent article about 4th generation synchrotons appeared in the electronic version of the Spanish Newspaper ‘El País’ Feb. 15, 2011.
Destellos brillantes y ultracortos iluminarán la nueva biología estructural. More…
A novel non-ATP site in Protein Kinases of the MAP group (an interesting paper of SBDD).
Discovery and Characterization of non-ATP site Inhibitors of the Mitogen Activated Protein (MAP) Kinases. Chemical Biology. (2010). K. M. Comess, C. Sun, C. Abad-Zapatero, D. Borhani, E. Goedken, M. Argiriardi, D. R. Groebe, R. J. Gum, Y. Jia, J. E. Clampit, D. L. Haasch, H. T. Smith, S. Wang, D. Song, M. L. Coen, T. E. Cloutier, H. Tang, X. Cheng, C. Quinn, B. Liu, Z. Xin, G. Liu, E. H. Fry, V. Stoll, T. I. Ng, D. Banach, D. Marcotte, D. J. Burns, P. J. Hajduk. American Chemical Society. Chemical Biology. in press. (available online).
This number has recently appeared on line and among the contributions the first article is a review of the advances in macromolecular crystallography in the second half of the 20th century from a personal perspective, related to the development of Dr. Cele Abad-Zapatero as a professional scientist, from his boyhood years in Spain, soon after the end of the Spanish Civil war. The article is accessible from the following link: http://arbor.revistas.csic.es/index.php/arbor/issue/current<br>This article could be of interest to any budding scientist/crystallographer. Any interested reader should be able to download this or any other article from this special issue of Arbor from the above website. Otherwise, copies can be requested from the author, from his e-mail address (see contact tab).
