Date Completed: 3/27/09
Faculty Name: Debasish Chattopadhyay
UAB Department: Medicine
UAB School: Medicine
Campus Address: CBSE 250
Campus Zip: 4400
Email Address: firstname.lastname@example.org
Office Fax: 934-0480
Research Program Area: Drug Discovery and Development
Project Title: A Fragment-Based Approach to Discovering Novel Antifolates
Project Status: Already up-and-running
Proposed Start Date: April 15
Proposed End Date: August 14
Number of Weeks of Internship: 15
Number of Interns: 1
Other faculty, staff, or graduate students who may help supervise intern: Kiera Walker
Expected Number of Work Hours Per Week: Negotiable
Number of Hours of Personal Supervision from Preceptor: 2
Expected Work Schedule for Intern: Flexible, intern can largely set his or her own schedule
Category of Research: Laboratory Research
Cancer Research: Breast
Project Description: Methotrexate (MTX), a classical antifolate inhibitor of human dihydrofolate reductase (hDHFR), is widely used in chemotherapy of breast cancer. However, drug resistance and toxicity of MTX poses major challenges in the continued use of MTX and related drugs.
The use of hDHFR inhibitors with novel scaffolds, different from the typical 2,4-diaminopyrimidine or 2,4-diaminopteridine scaffolds of currently used antifolates, will circumvent the problem of MTX drug resistance. Applying a fragment-based drug discovery strategy will allow identification of novel scaffolds and development of potent antifolates.
Fragment libraries contain collections of small (<250Da), low complexity organic molecules amenable to chemical modifications. The first step is to identify fragments that bind to the target usually using biological or biophysical screening. Then the binding mode of individual fragments (to the target) is determined by X-ray crystallography or NMR. Finally, binding of an inhibitor is optimized by chemically linking selected fragments that bind to neighboring pockets or by chemical modification of a single fragment using medicinal chemistry tools (chemical synthesis).
The main strength of FBDD over conventional drug discovery approaches arises from the high ligand efficiency of small fragments. A small The main strength of FBDD over conventional drug discovery approaches arises from the high ligand efficiency of small fragments. A small compound can scan the chemical space of a target binding pocket much more efficiently than a large size molecule. Although binding affinities of such fragments are generally low, it allows identification of novel scaffolds that can specifically occupy small and unique binding pockets inaccessible to larger (and more complex) molecules and therefore, these pockets remain largely undiscovered. The success of FBDD depends on the quality of the library used in screening and the ability to determine the binding mode. Recent applications of FBDD and its success in developing highly potent molecules starting from low affinity fragments have been reviewed in refs. [1-4].
GOALS AND RESEARCH DESIGN
The major goal of this project is to identify fragments that inhibit hDHFR. We have prepared highly purified functional recombinant enzyme and optimized an in vitro enzyme assay for rapid screening of inhibitors. We have obtained a portion of a high quality fragment library which will be used for screening. Active fragments will be tested for cytotoxicity against normal and cancer cell lines (collaboration).
Once one/more active inhibitor fragments are identified we will identify the binding site and binding mode of these fragments by resolving the crystal structure of enzyme-inhibitor complex. The human DHFR has already been crystallized by several laboratories. These structures will provide an insight about the binding site and protein-inhibitor interactions. This knowledge will guide further optimization.
Active fragments will be optimized to develop therapeutically useful agents.
Intern's Anticipated Duties:
Duty 1: Conducting experiments: enzyme activity/inhibition assay, preparation of protein sample, if necessary, site directed mutagenesis of necessary
Preceptor will provide intern with access to the following: office or desk space; computer and printer; laboratory work bench space; equipment needed to complete project; supplies needed to complete project
Likelihood of authoring publications: Possible
Background, education, experience, or expertise preferred: Commitment to learn and apply yourself
This faculty member has been a CaRES Preceptor for one summer.
Intern 1: Tara Mitchell Intern 2: Adam Scott