The Comprehensive Chemo- and Clinical- Informatics Database (CCCID) is a free database of drug, protein, disease, and pathway information, along with tools to visualize connections between these data.
It includes tools to search based on chemical properties and structure, view drug-protein docking complexes, and visualize the network relationships between drugs, target-proteins, diseases, and pathways.
The most effective way to move from target identification to the clinic is to identify already approved drugs with the potential for activating or inhibiting unintended targets (repurposing or repositioning). This is usually achieved by high throughput chemical screening, transcriptome matching, or simple in silico ligand docking.
Our work with drug-repurposing has helped find experimentally-verified new indictions, including mebendazole acting to inhibit of VEGFR2 kinase activity and angiogenesis, and celecoxib binding cadherin-11 - an adhesion molecule important in rheumatoid arthritis and poor prognosis malignancies for which no targeted therapies exist.
Train, Match, Fit, Streamline (TMFS) is a protocol for increasing the accuraccy of in-silico screening. TMFS combines data on compound shape, topology, and chemical signatures, as well as the nature of it's contact with target protein ligands to predict drug-target binding with an accuraccy exceeding previous methods.
Application of this technique has been tested and confirmed, yielding several drug-repurposing discoveries including new indications for mebendazole and celecoxib (see above).
In collaboration with Dr. Hemayet Ullah at Howard Universty, we have have developed chemicals to aid in agricultural drought resistance. More specifically, we developed small molecule modulators of the scaffold protein RACK1A which induces environmental stress resistance in crops. Video of the experimental effect of these modulators is shown in the video above.
Toxiconomics looks at toxic effect of the industrial and medicinal chemicals upon exposure to human proteins. We are current pursuing the task of exploring toxicity of existing drugs/compounds, and EPA chemicals by in-silico protein profiling technology and correlate it with biological pathways and confirming it through experiments.
We are pursuing number of small molecule drug design projects ranging from CDH11 (adhesion protein) inhibitors (with Dr.Stephen Byers), AGBL2 (cytosolic carboxy peptidase) inhibitors, multi-kinase inhibitors, VEGFR2, Tie-2, and Uremic proteins.
We use QSA(P)R to predict binding affinity and toxicological properties for drugs and chemicals. We are pursuing several projects that seek the target structure data required to more accurately predict the relationship between chemical structure and bio-activity/biological-properties.