Research Resources

The CDDI aims to enable research progress by helping members access key capabilities.  For more details on the research resources available to CDDI members, please contact Michael Gilson (858-822-0622, mgilson@ucsd.edu) or Thomas Hermann (858-524-4467, tch@ucsd.edu).

Drug Discovery (early-stage research)

UCSD Center for Compound Resources (UCCR). The UCCR makes available to UCSD faculty novel, curated chemical compound libraries composed of natural products and their derivatives, synthetic chemicals, compounds that have reached clinical trials, and currently approved drugs. 

The Center for Discovery and Innovation in Parasitic Diseases (CDIPD), an interdisciplinary research center based at UC San Diego, is developing new treatments for diseases affecting hundreds of millions of people worldwide, but which are largely ignored by traditional drug and vaccine discovery companies.

Other Discovery Resources

Chemical Synthesis

Resource Description Contact
UCI Synthesis Facility This facility provides fee-based chemical synthesis services, including combinatorial and parallel synthesis. Dr. Richard Chamberlin
949-824-7089   
UCSF Small Molecule Discovery Center This facility provides some medicinal chemistry support. Dr. Adam Renslo
415-514-9698

Compound Libraries On-Campus

Resource Description Contact
Marine Natural Products Over 200 compounds derived from marine sources; available at 50-100ug ea in DMSO; 96-well plates Dr. William Gerwick, 858-534-0578
Amaro Library Screening library of ~2400 diverse small molecules >98% purity judged by LCMS.

Dr. Rommie Amaro

Computational Modeling

The cDDI and participating labs are making the Molecular Operating Environment (MOE) molecular modeling and visualization package from Chemical Computing Group available to UCSD labs. MOE includes tools for ligand design, conformational search, property calculations, and analysis.  For information on access, contact Dr. Michael Gilson.

Databases – Informatics

UC San Diego's Center for Drug Discovery Innovation (cDDI) and participating labs are making the Web-based CDD Vault available to cDDI members without charge. This database facilitates tracking and sharing of medium- to large-scale collections of assay and other data associated with small molecule drug discovery. For more information, training, and access, please contact Dr. Jair Lage Siqueira-Neto.

The BindingDB database provides browsing, search, and download access to over a million experimentally measured binding data for small, drug-like molecules with proteins that are or may become drug targets. For further information, contact Michael Gilson, mgilson@ucsd.edu.

High Throughput Screening Services

Resource and Contacts Description

UCLA Molecular Screening Shared Resource

Dr. Robert Damoiseaux
Director, 310-794-1974

UCLA's Molecular Screening Shared Resource (MSSR: http://www.mssr.ucla.edu/) is recommended for UCSD compound library and screening needs. It operates on a fee-for-service basis without intellectual property claims or negotiatiations. Key aspects:

Compound library
Curated, plated 200,000 compound library, filtered to exclude "junk" compounds; diversity, lead-like, FDA-approved, and target-class sublibraries. 

Capabilities and equipment
HTS capability to screen ~50,000 compounds/day, and off-line equipment for assay-development. Open 24/7.

Liquid handlers to replicate plates or cherry-pick compounds; plate readers for optical readouts, including fluorescence and luminescence

High-content confocal microscopy with servers to process images and extract data

Genome-wide assay tools include siRNA, cDNA and shRNA 

Business model and costs for UCSD users
UCSD labs are charged internal UCLA rates

Customer labs typically post a student or postdoc on-site for 3-4 weeks for training, assay-development, and execution of the screen

Assay development & initial screen of ~5,000 compounds: about $3K.   Going to 100,000 compounds raises cost to about $6K. Running all 200,000 compounds raises cost to about $10K. These prices do not include assay reagents, other consumables, or the costs of the on-site student or postdoc.

UCSF Small Molecule Discovery Center

Dr. Michelle Arkin
415-514-4313

Biochemical and cell-based assays utilizing liquid-handling robots and compound library of >150,000 compounds. Works with users to adapt assays to HTS fomats.

TSRI Molecular Screening Center

Dr. Lindsay Smith
858-784-2397

Robotic facility for 1536 well-based HTS runs; a 600,000-compound library. Capabilities to support assay development and hit validation.

Sanford Burnham Prebys
Medical Discovery Institute

Dr. Chris Hassid
858-646-3100 ext. 3465

HTS capabilities and compound library suitable for biochemical and cell-based high-content screens.

Molecular Structure Cores

Resource Description Contact
UCSD Biomolecule Crystallography Facility This facility provides fee-based chemical synthesis services, including combinatorial and parallel synthesis.

Nick Nguyen
858-534-2565

UCSD Crystallography Facility - Small Molecule Small molecule structural analysis by solid state crystallography for organic and inorganic compounds.

Dr. Arnold Rheingold
858-822-3870

SSPPS NMR Facility This facility houses two 600MHz NMR spectrometers for the structural analysis of biomolecules and small molecule compounds. One spectrometer has an automated sample changer available. Dr. Brendan Duggan
858-822-7826 

Protein Expression and Purification

Resource Description Contact

TSRI Protein Expression and Proteomics Core

The protein expression core facility is part of the larger Center for Aids Research Core found at TSRI and UCSD, yet stands alone to assist in protein expression needs. The Protein Expression core maintains vectors and cell lines necessary for expression cloning proteins and assist in their purification.

Dr. John Elder 

Drug Development (later-stage research)

The UCSD Drug Develoment Pipeline offers UCSD researchers and other clients a range of in vitro and in vivo DMPK studies, including pharmacokinetics, GLP PK/PD and toxicology.