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University of Nebraska Medical Center

Nebraska Pediatric Drug Discovery Group

Nebraska Pediatric Drug Discovery Group members standing outside on UNMC campus

The major goal of the Nebraska Pediatric Drug Discovery Group (NPDDG) is to develop small molecules that bind to, inactivate, or degrade fusion oncoproteins that drive pediatric cancer by functioning as regulators of transcription.

We have assembled a team that will focus on the discovery and development of small molecule modulators that perturb fusion oncoproteins that drive pediatric cancers. The team brings expertise in viz., CHemoINformatics (CHIN), Medicinal Chemistry & Chemical Biology (MCCB), Hit-to-Lead Characterization Core (H2LCC) and Cancer Cell & Molecular Biology (CCMB) to NPDDG. The multidisciplinary team, will enable the development of a therapeutic pipeline to accelerate drug discovery focused on developing NCEs that target fusion oncoproteins.

The assembled investigators are experts in protein folding, virtual screening, neural network methods to integrate heterogenous data (CHIN), hit-to-lead optimization, structure-activity-relationship studies, lead optimization, photocrosslinkable and clickable probes (MCCB), structural biology, biophysics, pharmacokinetics, toxicity, chemical proteomics (H2LCC), mechanism-based assay design and development, animal models of fusion oncoprotein driven pediatric cancer models, and pediatric oncology (CCMB). This group of investigators have published together and are PIs on a total of 16 R01/R00 grants (CA197999, CA226436, CA244900, CA250383, CA260749, CA263504, CA276846, GM136859, GM138920, GM141232, GM145647, HD106590, NS106879, NS116037, NS119266, and NS127439), thus demonstrating the cohesive nature and the high scientific caliber. Please note: Drs. Hopkins, Natarajan, & Trippier (MCCB) are listed as inventors on a combined 41 patents, thus demonstrating their ability to develop intellectual property (IP).

ChemoINformatics (CHIN)

Babu Guda, PhD

CHIN Principal Investigator
Professor, Vice Chair for Bioinformatics Research & Training, UNMC Department of Genetics, Cell Biology, and Anatomy

Babu Guda

Hari Arthanari, PhD

Associate Professor, Biological Chemistry and Molecular Pharmacology, Harvard Medical School

Kabhilan Mohan, PhD

Instructor, UNMC Eppley Institute for Research in Cancer and Allied Diseases

Medicinal Chemistry and Chemical Biology (MCCB)

Amar Natarajan, PhD

MCCB Principal Investigator
Ruth Branham Professor, UNMC Eppley Institute for Research in Cancer and Allied Diseases

Amar Natarajan

Corey Hopkins, PhD

Professor, UNMC Department of Pharmaceutical Sciences

Corey Hopkins

Paul Trippier, PhD

Professor, UNMC Department of Pharmaceutical Sciences

Paul Trippier

Hit-to-Lead Characterization Core (H2LCC)

Gloria Borgstahl, PhD

H2LCC Principal Investigator
Professor, UNMC Eppley Institute for Research in Cancer and Allied Diseases

DJ Murry, PharmD

Professor, UNMC Department of Pharmacy Practice and Science

DJ Murry

Nick Wood, PhD

Assistant Professor, UNMC Eppley Institute for Research in Cancer and Allied Diseases

Cancer Cell and Molecular Biology (CCMB)

Gargi Ghosal, PhD

CCMB Principal Investigator
Gargi Ghosal, PhD Associate Professor, Department of Genetics, Cell Biology, and Anatomy

Gargi Ghosal

Sandipan Bramha, PhD

Assistant Professor, Department of Genetics, Cell Biology, and Anatomy

Sandipan Bramha

Don Coulter, MD

Professor, UNMC Division of Hematology and Oncology, Department of Pediatrics

Don Coulter

Kate Hyde, PhD

Kate Hyde, PhD Associate Professor, UNMC Department of Biochemistry and Molecular Biology

Kate Hyde

Research Project Information

The specific goals of the NPDDG are the following:

  • Design, synthesize and evaluate small molecule modulators of EWS::FLI1 for Ewing sarcoma therapy
  • Design, synthesize and evaluate small molecule modulators of Cbfb::MYH11 for pediatric AML therapy
  • Design, synthesize and evaluate small molecule modulators of SS18::SSX for sinovial sarcoma therapy
Our research plan is to engage investigators with relevant expertise to establish a drug discovery program focused on developing small molecular modulators of fusion oncoproteins that drive pediatric cancers. The fusion oncoproteins to be targeted are all regulators of transcription and are intrinsically disordered proteins (IDPs), thus making it highly innovative and yet high-risk high reward ventures

The entire team is currently focused on developing small molecule modulators that target EWS::FLI1. CHIN will use the in silico methods to develop an EWS::FLI1 protein-protein interaction complex and explore virtual high throughput screen (vHTS) with billion compound libraries to identify hits. The tight binders will be subjected to pan-assay interference (PAINS) filter, and those that pass the PAINS filter will be subjected to Schrödinger QikProp predictive in silico DMPK and ACD percepta ADME/Tox module to eliminate compounds that are likely to have adverse effects in animals. MCCB will analyze the data using visualization software such as data explorer and prioritize compounds that should be considered for synthesis. Structure activity relationship (SAR) by catalog and hit-to-lead optimization will be supported by H2LCC and CCMB.