#232 - Co-sponsored Sessions

ACS National Meeting
Fall, 2006
San Francisco, CA

SUNDAY MORNING

COMP - Careers for Computational Chemists in Pharma, Biotech, Patent Law, Software Vendors, National Labs, and the National Institutes of Health
Moscone Convention Center
Wendy D. Cornell, Organizer
9:00   Introductory Remarks
9:05 10 Peer review at the National Institutes of Health
George Chacko, chackoge@csr.nih.gov, Center for Scientific Review, National Institutes of Health, 6701 Rockledge Dr, Rm 4186, Bethesda, MD 20817

Peer review has produced an effective partnership between the National Institutes of Health (NIH) and research institutions. The mission of the Center for Scientific Review (CSR) is to ensure that grant applications to NIH receive fair, independent, expert, and timely review -- free from inappropriate influences -- so that the most promising research can be funded. At CSR, approximately 250 Scientific Review Administrators (SRAs) manage the review of over 50,000 grant applications each year. SRAs work with the academic community and Program Officers at NIH to sustain the high quality of the extramural funding process. An overview of the peer review process and the responsibilities of the SRA will be provided.

9:30 11 Guiding health science – and having fun!
Janna P. Wehrle, WEHRLEJ@nigms.nih.gov, Cell Biology and Biophysics, National Institute of General Medical Sciences, 45 Center Drive, Rm 2AS.19K, Bethesda, MD 20892

What do get when you cross the Godfather with an NIH program director? Someone who gives you advice you can't refuse. As the face (or at least the telephone voice) of the NIH, a program director assists investigators to make sense of the vast jungle of NIH goals and intentions, policies and procedures. The job can be a real pleasure for anyone who loves to mentor, is interested in a wide range of science, and can find ways to make things work. If you have a high tolerance for change and you like to read the front pages of “Science,” here's a job you should consider.

9:55 12 Intramural research at the National Center for Biotechnology Information
Evan Bolton, bolton@ncbi.nlm.nih.gov, National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894

As a national resource for molecular biology information established in 1988, NCBI's mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. More specifically, the NCBI has been charged with creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally; and performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules. To carry out its diverse responsibilities, NCBI, among other things, develops, distributes, supports, and coordinates access to a variety of databases and software for the scientific and medical communities, including PubChem, an information resource linking chemistry and biology. As a Staff Scientist at NCBI involved in the PubChem project, I help coordinate development efforts and write chemically-aware software for automated standardization, validation, and analysis of chemical information. I continually draw on my past experiences and knowledge gained over the past fifteen years as an independent scientific consultant, as a computational chemistry researcher, for both small and large pharmaceutical companies, and as a graduate student.

10:20   Intermission
10:35 13 Academia or industry?
Ramy Farid, Schrödinger, Inc, 120 W. 45th Street, 29th Floor, New York, NY 10036

I'm currently Senior Vice President at Schrödinger, Inc. However, when I started graduate school at Caltech 20 years ago, I had no idea I would end up in industry in such a position. In fact, after completing my graduate work and postdoctoral fellowship at the University of Pennsylvania, I accepted a position as an Assistant Professor in the Chemistry Department at Rutgers-Newark. After 7 years of teaching Chemistry classes to undergraduate and graduate students and doing research in an academic environment, I decided to accept a position at Schrödinger. My talk will focus on my experiences in both academia and industry, and what decisions I would have made differently with the benefit of 20/20 hindsight.

11:00 14 Long and winding road as a computational chemist in biotech
Erin K. Bradley, ebradley@sunesis.com, Computational Sciences, Sunesis Pharmaceuticals Inc, 341 Oyster Point Blvd., South San Francisco, CA 94080

There are many roads that lead to a career in computational chemistry, and there are many paths one can tread as a computational chemist. I will share my path as a an example of different roles and work environments one might encounter as a computational chemist in the start-up/biotech arena. Along the way, I hope to demonstrate both pros and cons of this career choice, as well as point out key communication skills necessary to be successful.

11:25 15 Putting science skills to work in the legal profession
Michael Shuster, MShuster@fenwick.com, Intellectual Property Group, Fenwick & West LLP, Embarcadero Center West, 275 Battery Street, San Francisco, CA 94111

Michael Shuster is a Partner at the Fenwick & West law firm where he Co-Chairs the Life Sciences Practice. He received training in neuroscience at the department of Physiology and Molecular Biophysics of Columbia University, and completed a post-doctoral fellowship in structural biology in the department of Biochemistry and Biophysics of UCSF. Following up on a serendipitous lead from a friend, he found himself working at a law firm helping vet scientific arguments and theories as applied to complex patent litigation. He'll talk about navigating the transition from scientist to lawyer and about lessons learned in the process.

11:50 16 Computer assisted drug discovery in pharma: Catch that trade wind in your sails
Veerabahu Shanmugasundaram, Veerabahu.Shanmugasundaram@pfizer.com, Computer-Assisted Drug Discovery, Pfizer Global Research & Development, 2800 Plymouth Road, Ann Arbor, MI 48105

Increasing pressures on the pharmaceutical industry necessitate an ever increasing improvement in the discovery and development processes, to reduce attrition in later stages of drug discovery, lower the cost of discovering and developing medicines and produce results in the market. This is especially true in early drug discovery stages where the identification of a novel therapeutic target, search for the initial lead compound and subsequent lead optimization begins. The efforts involved here, just by the nature of the drug discovery process, can have important consequences for therapeutic area project teams which will either set a project team on the right course or completely derail them and send them on a wild goose chase. This presents very interesting, challenging, cross-disciplinary career opportunities for scientists who have a broad background, have versatile skill sets, are innovative problem solvers and are very good team players who can lead project teams to swift decision points. A discussion on the utilization of computational approaches and a career in CADD in a pharmaceutical drug discovery setting will be presented.

12:15   Panel Discussion

MONDAY MORNING

CHED - Chemical Information and Chemical Information Education in the Electronic Age
Marriott Salon 11
F. Bartow Culp, Organizer & Presiding
8:30   Introductory Remarks
8:35 143 Beyond Google®: Goals for chemical information instruction in the electronic age
Adrienne W. Kozlowski, Department of Chemistry, Central Connecticut State University, 194 Blake Road, New Britain, CT 06053 and F. Bartow Culp, Mellon Library of Chemistry, Purdue University, 504 West State Street, West Lafayette, IN 47907-2058

Many students believe they can meet all their information needs surfing the Web, and that printed resources are no longer relevant. It is important to teach students at all levels how to find reliable data with a reasonable expenditure of time and money. Electronic resources make the process speedy, but to make it efficient and precise, good search skills ane necessary. Students need to know data bases, their content and policies, and to practice developing good search strategies. Each course should include an information component so students may develop expertise in information retrieval and evaluation.

9:00 144 Exploring chemistry through the chemical literature co
Allan K. Hovland, Department of Chemistry, St. Mary's College of Maryland, 18952 E Fisher Road, St. Mary's City, MD 20686

Using the primary literature, demonstrating the ability to learn independently, and writing clearly are all abilities we want to cultivate in our students. I have been using an assignment in my advanced inorganic chemistry course that incorporates all of these. The students write a letter nominating a chemist for the ACS Award in Inorganic Chemistry. In selecting a candidate, students need to explore the primary literature to identify an appropriate nominee. After their selection is approved, they read several papers by their candidate to gain modest mastery of the candidate's chemistry. Students often contact their candidates and are thrilled by the resulting correspondence. The writing of the letter involves multiple drafts. Oral presentations are the culminating activity. The assignment has generated excitement for learning new chemistry. Over the years I've used the assignment, several of the student selected nominees have subsequently won ACS awards, including the inorganic award.

9:25 145 Teaching students how to use patent databases
Lawton Shaw, Centre for Science, Athabasca University, 1 University Drive, Athabasca, AB T9S 3A3, Canada and Margy MacMillan, Library, Mount Royal College, 4825 Mount Royal Gate S.W, Calgary, AB T3E 6K6, Canada.

Chemical patents are a primary source of chemical information. As such, it is easy to make the case that chemistry students should be taught how to find information in the patent literature and how to read patents. In a second year Industrial Organic Chemistry course for engineering students, students were tasked with a group research project that required the use of chemical patents as a source of information. The class was provided with formal instruction into patents and other information sources, which was facilitated by a librarian. Students gained skill in searching the U.S. Patent and Trademark Office database, including time-saving search tactics, cross-referencing, and where to find the most useful information.

9:50   Intermission
10:00 146 From standards to practice: Incorporating chemical information literacy standards into the classroom
Carrie L. Newsom, Marston Science Library, University of Florida, PO Box 117011, Gainesville, FL 32611

Information literacy standards are all the rage. However, for instructors these standards are often philosophical rather than practical documents. This presentation will explore the importance of standards, review current chemical information literacy standards, map current standards to classroom activities and provide examples of courses implementing these standards.

10:25 147 Teaching chemical principles using the Cambridge Structural Database
Gary M Battle and Ian Bruno. Cambridge Crystallographic Data Centre, 12 Union Rd, Cambridge, CB21EZ, United Kingdom

As the definitive library of experimentally determined structures the Cambridge Structural Database (CSD) contains a wealth of information on molecular geometry and intermolecular interactions. In this talk we will show how the CSD can be used in lecture demonstrations to illustrate important concepts in chemistry, including: aromaticity, stereochemistry, metal-coordination geometry, hydrogen bonding and crystal packing. Use of the CSD for laboratory and homework assignments will also be discussed.

11:05 148 Chemical information instruction in the age of Google®
Charles F. Huber, Davidson Library, University of California, Santa Barbara, Santa Barbara, CA 93106-9010

Making chemistry students literate in the ways of chemical information has always been a challenge. However, the nature of the challenge has changed over the years. With many of the most important resources for chemical information now available electronically, the present-day might be regarded as the Golden Age of Information (in more ways than one.) But to most of our students this is the Google® Age of Information. What are the new challenges for the chemical information instructor posed by the age of the ubiquitous web search engine? Examples from the author's classes will be given.

WEDNESDAY MORNING

ORGN - Chemical Information and Organic Chemistry: The Road Ahead
Moscone Convention Center 131
Guenter Grethe, Martin G. Hicks, Organizers; Martin G. Hicks Presiding
8:25   Introductory Remarks
8:30 625 ACE, a computational tool predicting the stereochemical outcome of asymmetric reactions
Nicolas Moitessier, Department of Chemistry, McGill University, 801, Sherbrooke St. W, Montreal, QC H3A 2K6, Canada

ACE (Asymmetric Catalyst Evaluation), a computational tool for virtual screening of asymmetric catalysts will be presented. The proposed method is based on locating transition states using molecular mechanics. Application of this method to well established asymmetric reactions validated ACE. First the method closely reproduced DFT-computed TS structures and energies. Second, virtual screening of catalysts led to the discrimination between more or less efficient catalysts

9:00 626 ROBIA: Computational analysis of synthetic processes
Jonathan M Goodman and Ingrid M Socorro. Unilever Centre for Molecular Science Informatics, Cambridge University, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom

The ROBIA (Reaction Outcome By Informatics Analysis) program analyses organic transformations using conformation analysis and molecular modeling to generate and to evaluate competing reaction pathways. This can be used both to assess the likely stability of candidate structures and also to examine synthetic pathways towards these molecules. The strategy is based on trusting molecular modeling more than the synthetic literature, so that the results can be used as a test for reported reactions.

9:30 627 Will computer-assisted synthesis design have an impact on organic chemistry?
Johann Gasteiger, Computer-Chemie-Centrum, University of Erlangen-Nuremberg, Erlangen, 91052, Germany

The first efforts on developing computer systems for assisting chemists in the design of organic syntheses started nearly 40 years ago. However, it must be realized that no synthesis design system has yet found wide-spread use. The reasons for this are manifold and will be discussed. On the other hand, it also has to be stressed that many important developments in chemoinformatics – from the Beilstein database to reaction databases – can be traced back to research groups active in the development of synthesis design systems. Furthermore, methods have recently been developed that can greatly assist the organic chemist in planning their syntheses more efficiently and thus will have an impact on the way syntheses are being planned and performed.

10:00 628 SynSPROUT: Virtual synthesis in protein cavities
A. Peter Johnson, Krisztina Boda, Shane Weaver, and Vilmos Valko. School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom

De Novo design is an important computational tool in protein structure based drug design in which structures are built up by linking together small 3D fragments within the binding cavity of the protein target. Although de novo design systems, like SPROUT, can generate many structurally diverse ligands which are predicted to bind tightly to a target protein, these hypothetical ligands have no practical significance unless they are also synthetically accessible. SYNSPROUT, a variant of SPROUT, incorporates synthetic constraints directly into the actual structure generation process, by using a library of readily available starting materials as well as fragment joining operations which mirror known chemical reactions. A variant, SPROUT LeadOpt, employs both retrosynthetic analysis and knowledge of available starting materials to suggest analogues of leads with improved predicted binding affinity. Experimental results relating to the application of these systems to the design and synthesis of specific enzyme inhibitors will be presented.

10:30 629 CAVEAT as a tool for molecular design
Dale G. Drueckhammer, Yongliang Yang, Haidong Huang, Chen Lin, Qi Chen, Wei Yang, Yimin Zhu, and Dmitri Nesterenko. Department of Chemistry, State University of New York, Stony Brook, NY 11794-3400

CAVEAT is a unique computer program that searches a 3-dimensional molecular database for vector relationships among bonds. We have been developing a general method for molecular design based on the use of CAVEAT to identify molecular frameworks that can serve as templates to position functional groups in a specific relative orientation. Applications demonstrated in this lab include the positioning of boronic acid groups for binding and sensing of glucose, ligand groups for metal ion binding, aryl groups for aromatic group binding by pi-stacking, and catalytic groups for enolate formation. New databases have also been developed specifically for the application of CAVEAT in molecular design.

11:00 630 Relating proteins through the ligands they recognize
Brian Shoichet, Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, QB3 Building, Room 508D, San Francisco, CA 94143

Many drugs are recognized by seemingly unrelated targets, at least as measured by bioinformatic metrics. Chemically, however, the drugs themselves are typically related. It should thus be possible to relate protein targets based on the similarities among the ligands that bind to them. To investigate this, we used sets of ligands annotated for several hundred targets, comparing the topological similarity of every ligand across every set. A statistically significant similarity score for each pair of ligand sets can be calculated once a model of random similarity is developed. A minimum spanning tree can be found that maps all the sets together using their most significant links. Although no biological information is used in calculating these maps, biologically sensible clusters nevertheless appear as an emergent property. Relating ligand sets, and the mapping it enables, may reveal pharmacological effects and mechanisms for new chemical entities.

11:30 631 Cross-sectional analysis of small-molecule performance in diverse biological assays
Paul A. Clemons, Initiative for Chemical Genetics, Chemical Biology Program, Broad Institute of Harvard & MIT, 7 Cambridge Center, Room 3018, Cambridge, MA 02142

Advances in high-throughput and high-content screening (HTS/HCS) and data analysis increasingly make possible global and cross-sectional analysis of small-molecule performance in biological systems. The Chemical Biology Program at the Broad Institute of Harvard and MIT, which functions in an open data-sharing environment, combines synthetic chemistry and compound acquisition to equip its screening facility with small molecules of many structural classes and from many points of origin. The screening facility, in turn, provides access to these molecules for a large community of both internal and visiting screeners, resulting in the annotation of these small molecules with a wide array of biological measurements using multiple screening technologies and approaches. We have developed a biology- and technology-agnostic scoring system for small-molecule annotation in "biological measurement space". Using this scoring system, we have analyzed multiple parallel experiments performed to annotate a common compound collection including natural products, commercially available drug-like molecules, and compounds resulting from diversity-oriented organic synthesis (DOS). We frame the overall collection of such measurements as a metric space in which similarities and differences in mutlidimensional small-molecule performance can be calculated. We further connect such unbiased analyses with term-based biological annotation both from the literature and by using controlled vocabularies to describe experiments carried out in the Broad Institute screening facility. We have implemented this overall strategy using ChemBank, a publicly available data repository and data-analysis environment, funded by the National Cancer Institute, that provides an evolving set of data, analysis tools, and visualizations to the global research community.

 

 

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