Cheminfostream
News and views from the world of chemical information, modeling and informatics applied to drug discovery
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- Structure-based Drug Design
Structurally-informed approaches have increasingly demonstrated their value in drug design since the first biologically-relevant X-ray structures became available 30 years ago. The impact of these methods and technologies on early lead discovery and lead optimization is significant. Issues that are of current relevance include: - Are we maximizing the use of (the never-ending, increasing) current computer power in Structure-based Drug Design (SBDD)? - Virtual Screening (VS) is usually applied to enrich datasets with high-activity compounds. The "unusual" application of VS to weaker kinase binders is an interesting area of exploration. - Cross-docking applied to a structurally-rich CDK2 dataset can shed some light on the pros and cons of utilizing docking methods during lead optimization. - What is the function of modeling water molecules in SBDD? Instead of ignoring (or deleting) them, their influence on binding affinity should be considered. - What do we know, what do we we think we know or simply don’t know about SBDD? . On 17 October 2007 we will hold an eCheminfo Community of Practice conference session at Bryn Mawr College, Philadelphia to discuss latest advances in SBDD. The session will be chaired by Jose Duca (Schering-Plough) and includes a knowledgeable panel of speakers and discussion leaders: Daniel Cheney (Bristol-Myers Squibb), Natasja Brooijmans (Wyeth), Jose Duca (Schering-Plough), Terry Stouch (JCAMD) and Julian Tirado-Rives (Yale). A description of the session with presentation abstracts follows: Structure-based Drug Design http://echeminfo.com/COMTY_conferencesprog07sbdd - Fragment-based Drug Discovery
Fragment-based drug discovery (FBDD) is a rapidly emerging field to identifying novel, small molecule, preclinical development candidates. Because traditional high-throughput screening has had its challenges, due to the complexity and relatively large size of the compounds routinely being screened, FBDD had been gaining momentum as an alternative approach. It starts with very small, low molecular weight, drug fragments which have the potential to keep the overall complexity and molecular weight of each drug candidate low. Traditional bioassays are not able to detect small drug fragments because of their low potency binding to the protein target. Thus, FBDD integrates biophysical techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, isothermal calorimetry with fragment library design and a range of computational methodologies for an efficient hit-to-lead process. The ultimate success of any drug discovery program is measured by the quality and quantity of the drugs it produces. FBDD has been practical in the past decade only, thus too soon to put its stamp yet on marketed drugs. However, we have faith that it will indeed deliver on its promise. On 17 October 2007 we will hold an eCheminfo Community of Practice conference session at Bryn Mawr College, Philadelphia to discuss latest advances in fragment-based drug discovery. The session will be chaired by Maria Kontoyianni and includes a knowledgeable panel of speakers and discussion leaders: Chaohong Sun (Abbott), Renate Sekul (Graffinity), Woody Sherman (Schrodinger), Georgia McGaughey (Merck) and Stephen Burley (SGX Pharmaceuticals). A description of the session with presentation abstracts follows: Fragment-based Drug Discovery http://echeminfo.com/COMTY_conferencesprog07fragment - Structural Biology and Structure-based Drug Design
On 16 October 2007 we will hold an eCheminfo Community of Practice conference session at Bryn Mawr College, Philadelphia to discuss latest advances in structural biology related to drug discovery. The session will be chaired by Max Cummings (Tibotec Pharmaceuticals) and includes a knowledgeable panel of speakers and discussion leaders: Charles Lesburg (Schering-Plough), Heather Carlson (University of Michigan), Gerard Kleywegt (University of Uppsala), Paul Labute (CCG), Alan Cheng (Amgen), and Ajay Jain (UCSF). A description of the session with presentation abstracts follows: Structural Biology http://echeminfo.com/COMTY_conferencesprog07structbio Structural biology efforts bring the 3D structures of proteins to light, and thereby greatly enable many drug discovery efforts. In the affinity optimization phase of a medicinal chemistry effort the timely determination of the 3D structure of a relevant protein-ligand complex can have a huge positive impact. At the same time it is important to note that a wide range of structural information can be useful in guiding drug design efforts - from a single lowly 2D ligand structure to a set of high resolution 3D structures of protein-ligand complexes. Talks in this session cover different topics in the areas of structural biology and/or structure-based drug design. Ligand structures and their known activities can help to predict side effects, as well as possible new uses for known drugs. How reliable is a given 3D protein structure, and how can users evaluate this for themselves? Positioning of hydrogen atoms for biomolecular calculations is a longstanding issue, and a new approach to solving this problem is presented. Aspects of the recently popular concept of druggability are explored by two of the speakers. Protein flexibility is discussed in the context of protein-ligand structures related to the regulation of drug metabolism. Attendees will be exposed to various ways in which structural information is used in drug design, and should gain an appreciation for a few currently emerging challenges in the fields of structural biology and structure-based drug design. - eCheminfo Autumn Community of Practice meeting 2007
The eCheminfo Autumn Community of Practice meeting will take place the week of October 15 at Bryn Mawr College, Philadelphia to discuss latest research applications, methods and best practices in drug discovery informatics, design and modelling. The following conference sessions will be held: 16 October: Virtual Screening, chaired by Christopher Austin (NIH) and Ajay Jain (UCSF) 16 October: Structural Biology, chaired by Max Cummings (Tibotec Pharmaceuticals) 17 October: Structure-based Drug Design, chaired by Jose Duca (Schering-Plough) 17 October: Fragment-based Drug Discovery, chaired by Maria Kontoyianni (Crystax Pharmaceuticals) 18-19 October: Predictive ADME/Toxicology, chaired by Tony Hopfinger (University of New Mexico College of Pharmacy) - Brochure for Autumn 2007 eCheminfo Cheminformatics Conference Available
The brochure for the eCheminfo Cheminformatics Conference is not available. Latest Advances in Drug Discovery & Development 15-19 October 2007 Community of Practice Meeting, Autumn 2007 a joint InnovationWell and eCheminfo InterAction Meeting Bryn Mawr College, Philadelphia - Advancing Research and Best Practices in Predictive ADME and Toxicology
On the 17-19 October 2007 we will host a joint eCheminfo and InnovationWell Community of Practice Workshop and Forum at Bryn Mawr College, Philadelphia to discuss and advance best practices in predictive ADME and Toxicology, to develop best practices for comparison studies and validation, to review latest developments in method development and applications related to drug discovery and development, and to discuss the potential for collaborations between initiatives and international cooperation. This conference, forum and workshop activity will consist of the following parts: 1. Workshops to discuss developments, challenges and potential for collaborations. (afternoons of October 17-19). 2. Conference sessions on latest ADMET methods and application developments with presentations and panel discussions. (mornings of October 18 and 19) 3. Hands-on Workshop sessions with ADMET/Tox software (running during afternoons throughout week) 4. Evening Poster Sessions on latest modelling developments (evenings of October 17 and 18) Workshop Facilitators Anthony Klon (Pharmacopeia Drug Discovery), Joseph Tomaszewski (NCI), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer), Richard Beger (FDA), Anthony Klon (Pharmacopeia Drug Discovery), Tony Hopfinger (University of New Mexico College of Pharmacy), Joseph Contrera (FDA), Christoph Helma (University of Freiburg and in silico toxicology), Vladimir Poroikov (Russian Academy of Sciences), Judith Madden (Liverpool John Moores University), Ann Richard (EPA) - Advancing best practice in virtual screening and docking evaluation, comparison and scoring
On 15-16 October 2007 we will hold an eCheminfo Community of Practice Workshop and Forum at Bryn Mawr College, Philadelphia to discuss and advance best practice in virtual screening and docking, to develop co-created best practices for comparison studies, and to review latest developments in method development and applications related to drug discovery. - Drug Discovery Workshop, Oxford, September 10-14
I am pleased to announce that we will be holding the hands-on eCheminfo Drug Discovery Workshop week a second time this year in Oxford the week of 10-14 September. First option on places will go to the waiting list from the June workshop but there nevertheless still are additional places available. - International Cooperation in Predictive Toxicology
A variety of initiatives of relevance to the development of ADME/Toxicology resources of value to supporting improved productivity in drug discovery and development are in progress in different organisations and countries. There is potential for great benefits for collaboration and alignment between such initiatives so as to support the robust development of the emerging field of predictive toxicology and to advance goals related to heathcare safety and development as expressed in the FDA's Critical Path Initiative in the USA and the EU's Innovative Medicines Initiative in Europe. - Virtual Screening & Docking - Comparative Methodology & Best Practice
Considerable uncertainty currently exists in the performance and comparison of different virtual screening and docking methods on different targets and problems. There is a need for integrated high quality data to be made available for benchmarking. Furthermore numerous practice and methodological weaknesses exist in current screening and docking comparison studies which require collaborative development of new practices and methods of comparison for objective evaluation of different screening and docking methods.
