eCombiChem Leads

Open Seminar & Knowledge Cafe on ELNs and Knowledge Management in R&D

InnovationWell will hold an Open Seminar & Knowledge Cafe on Electronic Laboratory Notebooks (ELNs) at Bryn Mawr on Tuesday 17 October 2006 to discuss the emerging roles of Knowledge Management and Electronic Laboratory Notebook solutions in managing multidisciplinary research activities, innovation and collaboration.  The Open Event will take place alongside the InnovationWell and eCheminfo Autumn InterAction Meetings.  Attendance at the Open Event & Knowledge Café involves no registration fee. However seated places are limited and will be restricted to a confirmed guest list of 100. Please send an RSVP with your name and organisation via email to innovationwell [at] douglasconnect.com

More information is available at: http://barryhardy.blogs.com/theferryman/2006/09/electronic_lab_.html

The Electronic Laboratory Notebook – Systems for Managing Research Knowledge, Supporting Collaboration and Driving Innovation

We are holding the following Open Event at Oxford University on discussing the role of Electronic Lab Notebooks in supporting R&D on July 6.  For those of you able to make this free event, please simply send an RSVP via email to innovationwell [at] douglasconnect.com.

InnovationWell Open Seminar & Reception

The Electronic Laboratory Notebook – Systems for Managing Research Knowledge, Supporting Collaboration and Driving Innovation

Wolfson Seminar Room
Chemistry Research Laboratory
Mansfield Road, Oxford University

Thursday July 6, 4.30pm-8pm

Join us to discuss the emerging roles of Electronic Laboratory Notebooks in managing multidisciplinary research activities, innovation and collaboration

This is an Open Seminar and involves no registration fee. However seated places are limited and will be restricted to a confirmed guest list. Please send an RSVP with your name and organisation via email to innovationwell [at] douglasconnect.com

Agenda

4.30pm Welcome coffee

5.00pm Electronic Laboratory Notebooks and the Management of Modern Scientific Research and Development – an Industry Perspective
John Trigg, Managing Director, phaseFour Informatics, UK

John Trigg has over 20 years’ experience of working in the field of R&D data, information and knowledge management including 10 years experience of the world’s first enterprise level implementation of an Electronic Lab Notebook at Kodak. He will provide an overview of the critical emerging role of ELNs in modern industry research.

5.30pm Electronic Laboratory Notebooks as Engines of Knowledge for Research and Development – a Knowledge Management Perspective
Dr. Barry Hardy, Founder of the InnovationWell Community of Practice and Director, Knowledge Management Institute, Switzerland

Barry Hardy will provide an overview of the critical knowledge management strategies and methodologies for enabling productivity and successful outcomes in collaborative-based R&D. He will discuss knowledge assessment approaches aimed at the continuous improvement of the innovation and performance of the R&D organisation and its support ELN systems.

6.00pm ELN Framework Requirements to Support Collaborative Multidisciplinary R&D – A Solutions Perspective
Dr. Jeff Spitzner, President & Chief Science Officer, Rescentris; Ohio, USA

Jeff Spitzner is a leading expert in bioinformatics, knowledge management, and electronic laboratory notebook systems. In 1997 he co-authored the BSML data standard for bioinformatics, the pioneering XML technology in the life sciences; today he provides the vision and guides the development of Rescentris products. He will discuss the design and implementation of collaboration frameworks for the management of scientific research, and the role of semantic web technologies in record-keeping solutions that support the integrated R&D organization.

6.30pm Panel Discussion with Audience

The speakers and audience will discuss Electronic Laboratory Notebooks and their role in managing and supporting R&D in today’s complex multidisciplinary scientific environment.

7.00pm Reception

Drinks, Snacks, Software Demos … and more discussions!


This event takes place alongside the following workshop activities running in Oxford that week:

Innovation & Knowledge Management in Research & Product Development
a 3 day Interactive Management Workshop, 5-7 July 2006
Chemistry Research Laboratory, Oxford University, Oxford, UK

led by leading industry experts and practitioners including Victor Newman, Paul Lefrere, David Gurteen, David Snowden, Jeff Spitzner, John Trigg, Iain Bitran and Barry Hardy

Program Brochure:
http://barryhardy.blogs.com/theferryman/files/innovationwellrd_oxford_web1.PDF

These workshops are aimed to bring leading best practice and issue discussion to industry researchers and managers striving to use the latest innovation and knowledge management techniques and tools to maximise productivity and return in investment from R&D activities. Workshop groups will work through and discuss complex issues highlighted by detailed case studies presented by instructors. The following topics will be discussed:

Strategic Knowledge Management in R&D
Intellectual Property, Licensing & Valuation
Effective Deployment Strategies for Electronic Laboratory Notebooks
Knowledge Assessment & Auditing
Ontologies & Knowledge Discovery
Integrating Innovation Management & Research Activities
Communication & Collaboration between Research Teams & Partners
Organisational Development & Culture in R&D
Decision Support for Research Project & Portfolio Management
Integration of Tools & Data in R&D
Complex Systems Approaches to Product Development

More Information at:
http://innovationwell.net/COMTY_rpdtraining/


Latest Advances in Drug Discovery Design & Planning Methods
a Hands-on 5 Day eCheminfo Advanced Training Workshop Week
3-7 July 2006, Oxford University, Oxford, UK

These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. Participants should return to their labs with new ideas, best practices and software experiences to maximise productivity in their own drug discovery research activities.

You can download a copy of the program brochure from:
http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford06-v7web.pdf

Further information is available at:
http://echeminfo.colayer.net/COMTY_training


Barry Hardy, PhD
Douglas Connect, Switzerland
+41 61 851 0170 (office)
www.douglasconnect.com

In silico Library Enumeration of Synthetically Feasible Libraries

Virtual synthesis programs are not yet widely used by synthetic chemists and many may doubt that such approaches can match the skills of the experienced chemist.  Nevertheless ChemAxon have created a Java-based Reactor system to process reactions according to rules captured in the syntax of the Chemical Terms language for reactivity, selectivity, and side reaction exclusion.  Using such a system, discovery enumeration is significantly extended beyond a desired product library to create instead a reaction library, which has taken into account availability of starting compounds, experimental conditions, and prior available chemistry reaction knowledge on reaction types and their chemo-, regio-, and stereoselectivity issues.  A combinatorial synthesis library of a million such reactions can currently be built using several hours of CPU.

Oxford-based Inhibox, founded by Graham Richards, chairman of Chemistry at the University of Oxford, and headed by CEO Paul Finn, who pioneered the implementation of virtual screening methodologies for Pfizer at Sandwich, have been developing novel computational discovery methods and created Scopius, a very large database of chemical structures for drug discovery. Inhibox are using ChemAxon’s Reactor software to establish optimum conditions to give 'synthetically accessible' libraries with favourable properties for their research, and to create a reaction service, with workflows to create de novo libraries for client projects. “The core functionality to enumerate focused de novo type libraries in Oracle for a number of organic transformations is already available”, according to lead developer Dan Butler at Inhibox who continued “In a nutshell what we are attempting to do with Reactor is create a service which will primarily allow creation of focused de novo approach libraries and secondarily, exhaustive sets, for organic transformations that have (a) a reasonable set of suitable reactants in our commercial database and thus a tangible starting point and (b) are well defined reactions in the literature. In addition the Chemical Terms functionality of Reactor may help us create more accurate product sets. Overall this is quite a large undertaking in many respects, not least of which are the amount of organic transformations available to implement!”

Dan Butler will be joined in Oxford by ChemAxon’s CTO and virtual synthesis expert György Pirok to reveal the results of this work for the first time at the eCheminfo Drug Discovery Training Week at Oxford University (3-7 July 2006). Attendees to their workshop will be able to use provided software to create virtual reaction libraries and to work with the workshop leaders to establish optimum conditions to give 'synthetically accessible' libraries with favourable properties for their research. Dr. Pirok commented that “Currently we are developing a GUI so that synthetic chemists, who are not familiar with programming or command line tools, will be able to generate these reaction libraries. This GUI also contains an editor for modifying existing reactions or creating new ones. Workshop participants in Oxford will be one of the first set of users trying the new desktop Reactor application and GUI, and will get to try the newest features not previously released.  We will try to create new selective reactions and libraries together during the workshop, that will be of relevance to participants’ interests.”

Barry Hardy
eCheminfo Community of Practice

Training eCheminfo meeting workshop conference management chemistry Life Sciences Pharma Drug Discovery Drug Design Synthetic Chemistry Organic Chemistry Virtual Synthesis Innovation Informatics cheminformatics chemoinformatics IT Molecular Modeling Molecular Modelling events

Autumn InterAction Meeting Program on Drug Discovery & Development

I summarise below the list of sessions with over 100 top speakers and discussion leaders for the program listing for the upcoming Autumn InterAction Meetings taking place in Philadelphia and Basel. Please add a traceback or link for other like-minded folk to find!

I also provide an electronic brochure for download here for the InnovationWell Autumn Program on Knowledge-based Innovation in Life Science Product Development:
http://barryhardy.blogs.com/theferryman/files/InnovationWell-ProgramAutumn05.PDF

And the equivalent eCheminfo brochure on Drug Discovery:
http://barryhardy.blogs.com/theferryman/files/eCheminfo-ProgramAutumn05.pdf

Note: The poster sessions will be run as electronic poster sessions using tabletop spaces, a wireless network and Internet facilities at the meetings, in addition to virtual access through the website, i.e., the posters will be electronic but the access can be face-to-face or virtual. You can participate in person and virtually in the poster sessions.  We can supply nourishment and refreshments locally; remote participants may have to order out! [We also expect, subject to on-site testing, to have live conference call capabilities for remote participating members to join local discussions.]  Anyone interested in presenting such an "electronic poster" should directly contact us via email at innovationwell at douglasconnect.com

Look forward to seeing you in Philadelphia or Basel!

Barry Hardy
Community of Practice Manager
Douglas Connect
http://douglasconnect.com/
+41 61 851 0170 (office)

InnovationWell & eCheminfo InterAction Meetings
Philadelphia, US, 11-12 October 2005 and Basel, Switzerland, 9-10 November
List of Sessions with Speakers & Schedule (InterAction Autumn Meetings)
http://innovationwell.net/ and http://echeminfo.com/

Registration to attend the meetings or to access virtually is available through the websites or through contacting Nicki Douglas [nicki.douglas at douglasconnect.com]

InnovationWell eCheminfo meeting workshop conference management executive drug safety KM Life Sciences Pharma Drug Discovery Drug Development Healthcare Innovation Informatics cheminformatics Knowledge Management events

…PROGRAM LISTING CONTINUING IN FULL POSTING…..

Virtual Screening, Docking & Scoring

Specific binding interactions are central to many biological processes and pathways. Similarly, most drugs act by binding specifically to a site on a target protein, thereby modulating protein activity. The quest for new drugs relies on many approaches, including computer-based docking. This computational approach has the potential to have a profound positive impact on drug discovery, justifying the keen interest in this field by pharmaceutical researchers. Over the past fifteen years, subsequent to the initial description of the DOCK program and in parallel with the exponential increase in the number of available high-resolution protein structures, many docking programs of use as virtual screening tools in the drug discovery process have emerged. Understanding the similarities and differences of different methods as well as their capabilities and limitations is both important and increasingly challenging.

Our eCheminfo InterAction Autumn meeting sessions on Virtual Screening, Docking & Scoring will be chaired by Max Cummings (Johnson & Johnson) and Miklos Vargyas (ChemAxon).  The main objective of the program is to foster discussion amongst researchers working on both development of screening and docking methods and the application of such methods to drug discovery. This interaction should lead to a better understanding of the current state-of-the-art, improved screening and docking tools in the future, and enhanced awareness of how to apply the current set of tools.

eCheminfo InterAction Meeting Session, Bryn Mawr College, Philadelphia, 11 October 2005
Virtual Screening, Docking & Scoring
chaired by Max Cummings (Johnson & Johnson)
eCheminfo 2005 InterAction Meeting, 11-12 October 2005, Philadelphia, USA

Presenters & Discussion Leaders:
Emanuele Perola (Vertex)
Mark McGann (Openeye)
John Irwin (UCSF)
Renee DesJarlais (Johnson & Johnson)
Willem Nissink (Cambridge Crystallographic Data Centre)

eCheminfo InterAction Meeting Session, Swissôtel, Basel, Switzerland, 9 November 2005
Virtual Screening, Docking & Scoring
chaired by Miklos Vargyas (ChemAxon)
eCheminfo 2005 InterAction Meeting, 9-10 November 2005, Basel, Switzerland

Presenters & Discussion Leaders:
Graham Richards (University of Oxford)
Xavier Barril (Vernalis)
Amedeo Caflisch (ETH-Zurich)
David Morley (Enspiral Discovery Ltd)
Didier Rognan (University of Strasbourg)

Further information will be made available through the Program area of the eCheminfo website.

Existing invited seminars on screening and docking currently available on eCheminfo:

An Automatic Virtual Screening System, John Irwin (UCSF)

Enrichment and cross-validation studies of the eHiTS high throughput screening software package, Darryl Reid (Simbiosys)

Screening a Virtual Compound Space, Miklos Vargyas (Chemaxon)

Successful Virtual Screening for Human AICAR Transformylase Inhibitors against NCI Diversity set Using AutoDock, Chenglong Li (Scripps)

Virtual screening using binary kernel discrimination, Peter Willet (University of Sheffield)

Virtual Screening Using Atom Environments and Surface Point Environments (MOLPRINT) – Evaluation of Complementary 2D and 3D Methods, Andreas Bender (University of Cambridge)

Application of Novel Structural Fingerprints and Bayesian Learning to HTS Data Mining and Screening Prioritization, Robert Brown (Scitegic)

Physics-Based Computational Methods for Drug Design, Matthew P. Jacobson (UCSF)

Leveraging HTS Data using Drug Profiling, Andrew Lemon (ID Business Solutions Ltd)

Peptide to Non-Peptide: a Revolution in Virtual Screening, Mark Mackey (Cresset BioMolecular Discovery Ltd)

Systematic analysis of large screening sets for drug discovery, Paul E. Blower, Jr. (Leadscope)

eHiTS: electronic High Throughput Screening, Zsolt Zsoldos (SimBioSys, Inc)

Optimized Virtual Screening, Miklos Vargyas (Chemaxon)

Extended pharmacophores in virtual screening for drug discovery, David Lloyd (De Novo Pharmaceuticals)

MyMol: web-based molecular database, Matteo Floris (University of Padova)

If you miss any of these meetings or seminars, please consider joining our rapidly growing global community of practice in cheminformatics and chemical modelling to access the seminars at any time from any place, and to network and discuss issues with your peers.

eCheminfo is committed to the core value of outreach with diverse groups in the commercial, government and academic sectors for the sharing of best practices and the development of strategies, resources and methodologies that address specific issues in improved drug discovery and productivity. Communications activities deploy virtual approaches and a collaboration environment, in addition to regional discussion- and networking-designed face-to-face InterAction meetings.

Barry Hardy
eCheminfo Community of Practice Manager
Douglas Connect, Switzerland

Solid-Phase Synthesis on Dual Linkers with a Reference Cleavage Site

Professor Viktor Krchnák, University of Notre Dame, presents the following seminar at the eCombiChem “Cutting Edge Technologies in Combinatorial Chemistry” Web Conference running at http://ecombichem.com/:

Solid-Phase Synthesis on Dual Linkers with a Reference Cleavage Site

Optimization of reaction conditions is a key factor for successful solid-phase synthesis. The assessment of a chemical transformation on solid phase includes cleavage of the resin-bound reaction components followed by analysis of the cleaved sample. To obtain meaningful information regarding the composition of components on solid phase, all components need to be cleaved from the support. Information that cannot be obtained from this simple experiment is the rate of cleavage from the solid support. An independent quantification analysis is required in order to assess the cleavage yield.

We report a general, yet very simple, concept that secures cleavage of all polymer-supported components and, at the same time, estimates the cleavage rate. The synthesis is carried out on a polymer-supported dual linker with a reference cleavage site consisting of two sequential linkers separated by a spacer. The spacer is designed to allow its cleavage from the Linker 1 under standard conditions. Linkers 1 and 2 have to be cleavable with the same reagent. In a cleaved sample, the presence of the desired compound still attached to Linker 2 reveals incomplete cleavage; its absence indicates complete cleavage of compound from Linker 2.

The dual linker contributes in development of solid-phase transformations in several aspects: (i) It ensures cleavage of all resin-bound components. (ii) It allows simple estimation of the cleavage rate of polymer-supported compounds. (iii) It is suitable for straightforward optimization of cleavage protocol, including evaluation of new cleavage cocktails. (iv) It assists in selection of the most suitable linker for given compound classes. (v) It can be used for design of new linkers with altered sensitivity towards cleavage conditions.

Barry Hardy
Douglas Connect
www.douglasconnect.com
Cutting Edge Technologies in Combinatorial Chemistry: ecombichem.com
eCombiChemLeads Blog: http://barryhardy.blogs.com/ecombichemleads/

Making real molecules in virtual space

Gyorgy Pirok, Chief Technology Officer at ChemAxon, will present the following seminar at the eCombiChem “Cutting Edge Technologies in Combinatorial Chemistry” Web Conference running at http://ecombichem.com/, and opening 20th September 2004:

Making real molecules in virtual space

Good quality virtual enumeration of combinatorial libraries requires the manual intervention of an experienced chemist (selecting appropriate reactants, assignment of the corresponding reaction sites, removing unlikely products) slowing down the entire enumeration process. Encoding the valuable knowledge of preparative organic chemists into the reaction schemes decreases the human factor in the library generation phase and opens new possibilities for researchers.

ChemAxon builds a reusable "smart" reaction library consisting of the most important synthetic reactions. These reaction definitions contain a generic transformation scheme and additional chemo-, regio- and stereoselectivity rules. The virtual synthesis application based on this technology is not only able to enumerate entire combichem libraries in a single pass, but also to build a diverse molecular space of synthetically feasible virtual compounds from available chemicals.

Barry Hardy
Douglas Connect
www.douglasconnect.com
Cutting Edge Technologies in Combinatorial Chemistry: http://ecombichem.com/
eCombiChemLeads Blog: http://barryhardy.blogs.com/ecombichemleads/

Discovery and Development of a Library of Novel (Pyrrolidino)diketopiperazines

Kevin Short, Johnson & Johnson will present the following seminar at the eCombiChem “Cutting Edge Technologies in Combinatorial Chemistry” Web Conference running at http://ecombichem.com/, and opening 20th September 2004:

Discovery and Development of a Library of Novel (Pyrrolidino)diketopiperazines

Over the last 10 years, there has been great interest in the development of solid-phase synthetic approaches to small molecules, particularly those that embrace polyfunctional heterocyclic targets. As part of Ontogen's Combinatorial Chemistry program, we had an interest in developing synthetic strategies and chemistries applicable to combinatorial libraries of multisubstituted heterocycles. Following our early successes in the area of multisubstituted imidazoles, we applied the highly powerful Ugi reaction to the synthesis of hydantoin imides, tetrazoles and lactams. In addition, we reported on an Ugi-based library of diketopiperazines.

This seminar will describe the discovery of a novel bicyclic chemotype, prepared via a facile 2-step procedure, thus:

• an azomethine ylide-olefin [3+2] cycloaddition, followed by;
• a lactam forming reaction.

The procedure was adapted for use in an on-resin format, and a cyclative cleavage procedure utilizing the 2nd step furnished products in high purity. This presentation will detail the extensive optimization of the individual steps, both in solution and on-resin, followed by a ‘screening' of reagent inputs. Solid phase ‘rehearsal' of the library was carried out in ‘Test Plates', using the OntoBLOCK (TM) system. Extensive use of LC-MS and 1 H NMR analyses ensured a high information content for the rehearsal Test Plates, and ultimately a high confidence level for the ultimate production library's overall quality. The goal was to prepare a moderately large library of compounds.

Barry Hardy
Douglas Connect
www.douglasconnect.com
Cutting Edge Technologies in Combinatorial Chemistry: http://ecombichem.com/
eCombiChemLeads Blog: http://barryhardy.blogs.com/ecombichemleads/

Combinatorial Screening of Polymeric Coating Formulations

Jaime Grunlan, Senior Research Engineer, Avery Research Centre, will present the following seminar at the eCombiChem “Cutting Edge Technologies in Combinatorial Chemistry” Web Conference running at http://ecombichem.com/, and opening 20th September 2004:

Combinatorial Screening of Polymeric Coating Formulations

A combinatorial factory for the preparation and screening of polymeric coatings is outlined here. The coating formulations are prepared and coated using a novel combinatorial coating technique to obtain combinatorial libraries of varying composition and thickness. The thickness of each film in a combinatorial array is rapidly determined via visible-light absorbance of optical dyes in conjunction with the Beer-Lambert relationship. These combinatorial libraries are then tested and screened using a variety of custom-made high-throughput methods. Combinatorial screening of oxygen and moisture transmission rate, along with pressure-sensitive adhesive properties, is presented. OTR and MVTR are determined using spectrometric techniques. For adhesion, a spherical probe adhesive tester is able to generate parameters linked to tack, peel, and shear in one measurement. In addition to describing the testing methodology, benefits and shortcomings of these techniques will be highlighted.

Barry Hardy
Douglas Connect
www.douglasconnect.com
Cutting Edge Technologies in Combinatorial Chemistry: http://ecombichem.com/
ECombiChemLeads Blog: http://barryhardy.blogs.com/ecombichemleads/

Utilizing SynPhase Scavenger Lantern Technology for the Synthesis of Small Molecule Combinatorial Libraries via solution-phase methodologies

Nicholas Ede, Head of the Discovery Products business unit of Mimotopes, will present the following seminar at the eCombiChem “Cutting Edge Technologies in Combinatorial Chemistry” Web Conference running at http://ecombichem.com/, and opening 20th September 2004:

Utilizing SynPhase (TM) Scavenger Lantern Technology for the Synthesis of Small Molecule Combinatorial Libraries via solution-phase methodologies

Scavenging of unwanted reagents/reactants from solution phase reaction mixtures has emerged as an important alternative to contemporary purification of reaction mixtures in combinatorial chemistry. This allows for the parallel synthesis of large number of compounds in solution phase rapidly.

Mimotopes have designed and prepared several high loading Lanterns for use in scavenging applications. Combining the handling advantages with excellent scavenging capabilities, these new scavenger Lanterns are ideally suited for solution phase synthesis, particularly in a high throughput array format. This presentation will highlight a number of examples where scavenger Lanterns are used to make interesting drug-like compounds from, for example, Maybridge Reactive Intermediates such as 3,5-dimethylisoxazole-4-sulfonyl chloride. In addition, a simple and convenient solid phase synthesis of disubstituted guanidines which utilises the TMI-isocyanate SynPhase scavenger lantern 1 as a starting point will be presented (see Scheme below).

Barry Hardy
Douglas Connect
www.douglasconnect.com
Cutting Edge Technologies in Combinatorial Chemistry: http://ecombichem.com/
eCombiChemLeads Blog: http://barryhardy.blogs.com/ecombichemleads/