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Satisfying REACH Requirements in Predictive Toxicology

The OpenTox workshop on "Satisfying REACH Requirements in Predictive Toxicology" to be held at the ISS in Rome 10-11 September 2009. 

Participants at the workshop will involve cross-industry users and regulatory experts in addition to solution developers and providers who will discuss the requirements and use cases of users in chemical toxicology evaluation and risk assessment, and including satisfaction of current and future requirements of the REACH legislation using alternative testing methods. The workshop format involves short presentations to provide user, regulatory and solution needs perspectives, followed by knowledge cafe discussions discussing use cases, challenges, issues, solutions, collaboration opportunities and ways forward in small groups.

PROGRAM

Thursday 10 September

08.30 Welcome Coffee

09.00 Introduction & Workshop Overview, Barry Hardy (OpenTox and Douglas Connect, Switzerland)

09.15 The Use of Computational Methods for the in silico  Prediction of Chemical Properties in REACH, Andrew P Worth (Systems Toxicology Unit, Institute for Health and Consumer Protection, European Commission -Joint Research Centre, Italy)

09.40 Automated Workflows for Hazard Assessment, Elena Fioravanzo (S-IN Soluzioni Informatiche, Italy)

10.05 OpenTox Predictive Toxicology Use Cases, Barry Hardy (OpenTox and Douglas Connect, Switzerland)

10.30 Coffee Break

11.00 Knowledge Café Discussions

12.30 Group Discussion

13.00 Lunch

14.00 Opportunities for using  Systems Biology Data for in silico  Modeling of Personalized Medicine, Richard D. Beger  (Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, USA)

14.25 A Framework for Using Structural, Reactivity, Metabolic and Physicochemical Similarity to Evaluate the Suitability of Analogs for SAR-based Toxicological Assessments, Joanna Jaworska (Procter & Gamble, Modeling & Simulation, Biological Systems, Brussels Innovation Center, Belgium)

 14.50 Integration of Integrated Assessment Tools for Environmental Risk Assessment, Willie Peijnenburg (National Institute for Public Health and the Environment, The Netherlands)

15.15 Prediction of Animal Toxicity Endpoints for ToxCAST Phase I Compounds using a Combination of Chemical and Biological in vitro Descriptors, Alex Tropsha (Carolina Center for Computational Toxicology and Carolina Environmental Bioinformatics Research Center, University of North Carolina at Chapel Hill, USA)

15.40 Coffee Break

16.00 Knowledge Café Discussions

17.30 Group Discussion

18.00 Close

 

Friday 11 September

08.30 Welcome Coffee

09.00 Predictive Toxicology for Cosmetics - An Industry Perspective, Stephanie Ringeissen (Safety Research Department, L’Oréal R&D, France)

09.25 OECD (Q)SAR Application Toolbox: Progress and Ongoing Developments, (OECD, Paris, France)

09.50 Italian Specialty Chemical Industry Perspective on Predictive Toxicology, Maurizio Colombo (Health & Safety Evaluation, Industrial Regulation Management, Lamberti S.p.A., Italy)

10.15 Coffee Break

10.45 Knowledge Café Discussions

12.00 Group Discussion

12.30 Lunch

13.30 The Italian Chemical Industry and the REACH impact on SMEs, Antonio Conto (Chemsafe Srl, Italy)

13.55 Classification- and Regression-Based QSAR of Chemical Toxicity on the Basis of Structural and Physicochemical Similarity, Oleg Raevsky (Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds of Russian Academy of Sciences, Moscow, Russia)

14.20 Analysis of Toxcast Data and in vitro / in vivo Endpoint Relationships, Romualdo Benigni (Istituto Superiore di Sanità, Italy)

14.45 Coffee Break

15.15 Knowledge Café Discussions

16.30 Group Discussion

17.00 Close

More Information including Abstracts:

http://www.opentox.org/data/blogentries/public/opentoxworkshoprome09

Overcoming the challenges to reducing animal experimentation through an Open Source community-based development of in silico methods

In a recent study by the European Chemical Bureau, it has been estimated that the new EU chemical legislation REACH will require 3.9 million additional test animals, if no alternative methods are accepted. The same study shows that it is possible to reduce the number of test animals significantly by utilizing existing experimental data in conjunction with (Quantitative) Structure Activity Relationship ((Q)SAR) models. Chronic and reproductive toxicity, in vivo mutagenicity and carcinogenicity are the endpoints that will require the largest number of test animals within REACH, because no alternative in vitro assays are currently available.

Recent (Q)SAR developments allow a much more accurate prediction of complex toxicological endpoints than a few years ago. This progress has been caused by (i) the development of improved (Q)SAR algorithms and (ii) by the availability of larger and  better curated public databases.

The routine application of these new generation models is however still rare, because

l  Toxicity data has been collected in a variety of different databases.

l  These databases use different formats, that are frequently not compatible with (Q)SAR programs

l  Many databases lack important information for (Q)SAR modeling (e.g. chemical structures)

l  It is hard to integrate confidential in-house data with public data for model building and validation

l  (Q)SAR models have been published in a variety of different formats (ranging from simple regression based equations to full-fledged computer programs)

l  There is no straightforward integration of predictions from various programs

l  There is no commonly accepted framework for the validation of (Q)SAR predictions and many (Q)SAR tools provide limited support for reliable validation procedures

l  The application, interpretation, and development of (Q)SAR models is still difficult for most toxicological experts. It requires a considerable amount of statistical, chemoinformatics and computer science expertise and the procedures are labor intensive and prone to human errors.

The overall objective of the FP7-funded OpenTox is to develop a framework, that provides a unified access to toxicity data, (Q)SAR models, procedures supporting validation and additional information that helps with the interpretation of (Q)SAR predictions. OpenTox will be accessible at three levels:

l  A simple and intuitive interface for toxicological experts, that provides unified access to (Q)SAR predictions, toxicological data, (Q)SAR models and supporting information

l  An expert interface for the streamlined development and validation of new (Q)SAR models

l  An application programming interface (API) for the development, integration and validation of new (Q)SAR algorithms

The OpenTox framework is being developed as an Open Source project to optimize the dissemination and impact, to allow the inspection and review of algorithms and to attract external contributors. Our approach is to closely collaborate with related projects (e.g. OECD QSAR toolbox, CADASTER, Leadscope’s ToxML development), industry users, developers and regulatory authorities to agree on common standards and to avoid duplicated and redundant work.

Do consider joining the OpenTox community effort through signing up on the website!

eCheminfo Virtual Community Activities in Cheminformatics

When I started the eCheminfo community of practice in late 2003 we focused initially on using the approach of virtual conferencing and communications to get the community started.  More recently I have given more attention to developing face-to-face conference and workshop activity and initiating collaborative research. While on this journey it has been personally rewarding to have met and made contact with hundreds of scientists in the international community and to additionally be involved in supporting their networking, career development and research in drug design, discovery and modelling. It has also been rewarding to have just met so many great people and to have had the chance to interact with them, be it on a computer, in a workshop exercise, or on a punt trying to get down the river as we usually do when we are in Oxford.  So far we seem to be better on computer-based physics than boat physics!

And so I have come full circle and can see the need to prioritise the virtual community aspects of eCheminfo further again, to support the continuation of all these worthwhile interactions in the community.  So LinkedIn is one place to start.  I have been on there for some years and we have had a group area, but have not really done much with it.  It has primarily been useful for some introductions between people.  However recent feature additions for discussion, posting of news, job announcements etc. have been added, so it seems worthwhile to try using it more for supporting continuing interactions in the community.  So I am initiating today invitations to the eCheminfo community to join us there for discussion, news and networking on what is happening in the world of drug discovery informatics, cheminformatics, bioinformatics, etc.  Use of the group is intended for scientific and professional exchange purposes only.  As included in our mission we encourage cross-disciplinary cross-sector participation so from medicinal chemists in the pharmaceutical industry through toxicologists in government institutes through PhD students working on their modelling research problems are welcome!

To request joining the eCheminfo LinkedIn group please follow the following link and introduce yourself with a group joining request:

https://www.linkedin.com/e/gis/1173/77EB680070FF/

I also really welcome suggestions from the community there on what you would like to see as further developments in coming years!

Barry

OpenTox Predictive Toxicology Framework

The OpenTox Predictive Toxicology project has now been launched. We welcome collaboration with both developers and users on this project.  A project description follows in the continuation below. Please contact me to discuss collaboration opportunities or your needs in this area.

Barry Hardy

OpenTox Predictive Toxicology eCheminfo InnovationWell cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening ADME ADMET QSAR toxicology Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Critical Path Life Sciences Drug Discovery Research and Development Drug Development Healthcare Innovation Knowledge Management

Schedule for InnovationWell and eCheminfo Autumn 2008 Community of Practice Meeting

I provide below a schedule for the upcoming InnovationWell and eCheminfo Community of Practice meetings at Bryn Mawr.

I also include a location map here which may be useful upon arrival:

Download bryn_mawr_campus_map_douglas_connect_meeting.pdf

[Please follow continuation here to view schedule.]

Chemogenomics eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Oxford Critical Path toxicology Bursary Life Sciences Pharma Drug Discovery Research and Development Drug Development Healthcare Innovation Knowledge Management events

Predictive ADME: guiding the lead development and optimization process

The prediction of absorption, distribution, metabolism, and excretion (ADME) properties has become increasingly important as failures late in the drug discovery process become more costly. Increasingly, stringent in vitro and in vivo requirements have been placed on the hit-to-lead and lead optimization stages of the drug discovery process. Although it is tempting to dismiss ADME modeling and simply conduct an in vitro or in vivo experiment to get “the correct answer”, this approach is not practical. A skilled, competent medicinal chemist working on a lead optimization program can easily conceive of far more compounds than can reasonably be synthesized during the time of a lead optimization effort. In vivo studies are expensive and time-consuming and may become the rate-limiting step for some projects, particularly for small pharmaceutical companies. Rather than providing “the correct answer”, modeling provides a means of “stacking the deck” in favor of the medicinal chemistry effort, increasing the likelihood that a given compound will show the desired effect in vitro or in vivo.

At our Predictive ADME session chaired by Anthony Klon running October 16 at Bryn Mawr recent developments in the predictive modeling of ADME properties will be presented and discussed. Speakers will present their research into modeling microsomal stability, drug-drug interactions, and membrane transport processes such as blood-brain barrier penetration, intestinal absorption, and skin penetration. One topic of the accompanying discussions will be the appropriateness of relevant biological endpoints for ADME/PK modeling.

The session will be followed in the evening by a Knowledge Café to discuss Collaboration Opportunities in Predictive ADME & Predictive Toxicology.

A description of the session with presentation abstracts follows.  Please add your comments, discussion or questions at the end of the post.

Predictive ADME

http://echeminfo.com/COMTY_confprog08adme

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Computational Biology: Data Mining in Biomedical Research

Biomedical research, be it in the biopharmaceutical industry, academia or governmental laboratories, is becoming an information driven science. An enormous amount of data is either present in published literature and patents or being generated using high-throughput technologies (such as DNA sequencing, microarrays, genome-wide association, proteomics etc.). The resulting computational biology challenges currently involve the development of intelligent data mining methodologies for these high-dimensional data and the development of databases that facilitate the hosting and integration of these diverse data-sets. The computational advances being made in these areas are significantly impacting biomedical research ranging from fundamental biological findings that relate genes and environment to disease all the way to molecular biomarkers for drug efficacy or toxicity.

In our InnovationWell session chaired by Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.) taking place 14 October 2008 at Bryn Mawr, we have gathered a set of top researchers who have significant experience in the areas of data mining and integration. Presentation and discussion topics will include: molecular network reconstruction from genetically segregating populations (Paul McDonagh), the use of molecular networks for environmental risk assessment (Stephen Edwards), semantic web technologies for modeling biological pathways (Christopher Bouton), application of integrated genomics and genetics in pharmaceutical discovery (Debraj GuhaThakurta), and comparative genomics in drug discovery (James Brown).

A description of the session with presentation abstracts follows.  Please add your comments, discussion or questions at the end of the post.

Computational Biology

http://innovationwell.net/comty_confprogr08compbio

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Advances in Drug Discovery Informatics

The eCheminfo Autumn Community of Practice Meeting will take place 14-17 October 2008 at Bryn Mawr College, Bryn Mawr, Philadelphia, USA to discuss the latest advances in drug discovery informatics including the following topics:

Cheminformatics, Bioinformatics, Medicinal Chemistry, Drug Discovery Innovation, Structure-based Drug Design, Screening, Docking, Structural Biology, Predictive Toxicology, Predictive ADME, Chemogenomics

Program Summary
Docking & Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline)
Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College)
Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group)
In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT)
PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health)
Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery)
Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia)

Pre-Conference Workshop, 13 October 2008
Best Practices Virtual Screening Workshop chaired by Barry Hardy (Douglas Connect)

Speakers
John Irwin (UCSF), Georgia McGaughey (Merck), Johannes H. Voigt (Schering Plough), Lance Westerhoff (Quantum Bio), Zsolt Zsoldos (SimBioSys), Alexey Ornufriev  (Virginia Tech), David Case (Rutgers University), Rommie Amaro (USCD), Peter Coveney (Univ. College London), Anna Kohlmann (Ariad Pharmaceuticals), Scott Brown (Abbott), Emil Alexov (Clemson University), Jens Erik Nielsen (University College Dublin, Ireland), Darren Flower (Jenner Institute, UK), Maja Mihajlovic (City College of New York), Michael Keiser (UCSF), Brian Marsden (University of Oxford, UK), Alex Tropsha (UNC), John Westbrook (Rutgers), Howard J Feldman (CCG), Igor V. Filippov (NCI), Raul Cachau (ATP, SAIC-Frederick), Vincent T. Moy (University of Miami), Paul Hawkins (OpenEye), Yulia Borodina (NCBI), Gerhard Wolber (Inte:Ligand, Austria), Marc Nicklaus (NCI), James P. Snyder (Emory), Anne Chaka (NIST), Esther Kellenberger (Univ. Strasbourg, France), Renxiao Wang (SIOC, Shanghai, PR China), Jim Dunbar (University of Michigan), Janna Wehrle (NIGMS), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Barry Hardy (Douglas Connect), Weida Tong (FDA)

CFP
We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome.

Abstracts (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008.

Bursary
Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants can be working in any area of research related to drug discovery at the postdoctoral, graduate student and senior undergraduate levels.

To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to drug discovery (300-500 words) to echeminfo -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008.

Poster Session
All InterAction Meeting registrants are eligible to present a Conference Poster. The Poster Sessions will take place in the evenings in Thomas Great Hall on campus, where refreshments and dinner are also served. Poster Abstracts (300-500 words) with Title, Institution, Authors and Contact Information should be submitted to barry.hardy -[at]-
douglasconnect.com  Abstracts will be considered based on date of submission and quality, and will be reviewed and accepted as they are received. To be considered for the formal program, they should be submitted at the very latest by 31 August 2008.

Download Program Brochure (pdf):

Download eChemProgramBrynMawr08-Final-v3.pdf

Contact:
Program: Dr. Barry Hardy, eCheminfo Community of Practice, Douglas Connect. Tel: +41 61 851 0170. barry.hardy -[at]- douglasconnect.com

Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo -[at]- douglasconnect.com or go to:

http://echeminfoBM810.eventsbot.com

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Docking pKas Virtual Screening PDB Ligands PDB Chemogenomics ADME ADMET Free Energy Predictive Toxicology Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting conference workshop Bryn Mawr Critical Path toxicology Bursary Life Sciences Pharma Innovative Medicines Drug Discovery Research and Development Drug Development Healthcare Innovation Knowledge Management events

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)

Additional workshop activity on virtual screening best practices, knowledge management in R&D and advances in predictive ADME and toxicology will also be held.

Conference speakers include:
Stephen Burley (SGX Pharmaceuticals), Georgia McGaughey (Merck), Charles Lesburg (Schering-Plough), Rick Beger (FDA), Marc Nicklaus (NIH), Woody Sherman (Schrodinger), Daniel Cheney (Bristol Myers Squibb), Paul Labute (Chemical Computing Group), Ajay Jain (UCSF), Alan Cheng (Amgen), Tony Hopfinger (University of New Mexico), Anthony Klon (Pharmacopeia Drug Discovery), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer), Chaohong Sun (Abbott), Xavier Barril (University of Barcelona), Jose Duca (Schering-Plough), Terry Stouch (JCAMD), Natasja Brooijmans (Wyeth), Gerard Kleywegt (University of Uppsala), Vladimir Poroikov (Russian Academy of Sciences), Christoph Helma (in silico toxicology), Ann Richard (EPA), Judy Madden (Liverpool John Moores University), Julian Tirado-Rives (Yale), Heather Carlson (University of Michigan), Joseph Tomaszewski (NCI), Joseph Contrera (FDA), Christopher Austin (NIH), Jerome Hert (UCSF), Renate Sekul (Graffinity), Gunther Stahl (Tripos), John W Liebeschuetz (CCDC), Wilfried Langenaeker (Silicos), Zsolt Zsoldos (SimBioSys), Paul Hawkins (OpenEye Scientific Software), François Delfaud (MEDIT), Anatoly Ruvinsky (University of Kansas), Robin Taylor (CCDC), Eric Jamois (Strand Life Sciences), David Gilmour (Tacit), Alex Heiphetz (Delta L Training), Frank Guerino (TraverseIT), Salvatore Alesci (Wyeth), Darius Dziuda (CCSU), Laszlo Boros (Sidmap) Fred Cohen (Fast Track Systems), Alex Tropsha (UNC), Dimitris Agrafiotis, (Johnson & Johnson), Carl Elkin (Schering-Plough)

Poster Session
We will be running poster sessions in the evenings at the meeting with themes: knowledge management (Tuesday), drug design (Wednesday) and drug development and ADMET (Thursday). This option is available to all meeting attendees. Please send your abstract and biography of ca. 300-500 words each to eCheminfo -(at)- douglasconnect.com for approval.

Program Brochure:

Download eChemProgramBrynMawr07-web2.PDF

More information at http://echeminfo.com/COMTY_conferences

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Oxford Critical Path toxicology Bursary Life Sciences Pharma Drug DiscoveryResearch and Development Drug Development Healthcare Innovation Knowledge Management events

eCheminfo Membership & Workshop Activity for 2007

During November I will be planning the 2007 programs for the eCheminfo Advanced Training Week in Oxford and the InterAction Meeting in Bryn Mawr.  Please contact me with your interests and proposals!

Latest Advances in Drug Discovery Design & Planning Methods
a Hands-on 5 Day eCheminfo Advanced Training Workshop Week
June 25-29, Chemical Research Laboratory, Oxford University, Oxford, UK

Latest Advances in Drug Discovery & Development
eCheminfo Community of Practice InterAction Meeting
15-18 October 2007, Bryn Mawr College, Philadelphia, PA, USA
Themes: Screening, Medicinal Chemistry, Drug Design, Toxicology, Structural Biology, Bioinformatics, Cheminformatics

eCheminfo Gold membership
This entitles members to access eCheminfo meeting proceedings including audio, access to our Executive Insights reports from meeting and community of practice activities, and additional member discounts on meeting and training registration fees. 

Download eCheminfo2007MembershipForm.pdf

Barry Hardy

eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Docking Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop conference management Bryn Mawr Philadelphia Critical Path toxicology personalised medicine Life Sciences Pharma Drug DiscoveryResearch and Development Drug Development Healthcare Innovation Knowledge Management events