Indraneel Ghosh
Professor, BIO5 Institute
Professor, Chemistry and Biochemistry-Sci
Primary Department
Department Affiliations
(520) 621-6331
Work Summary
The broad objective of our research program in Bioorganic Chemistry and Chemical Biology is to construct protein therapeutics, protein mimetics, biomaterials, and biosensors. Our research at the University of Arizona is highly multidisciplinary and utilizes techniques in organic synthesis, biochemistry, molecular biology, and a host of physical characterization methods. Our research motto is simple: Unraveling mysteries and Enabling discoveries.
Research Interest
Professor Neel Ghosh, is the Emily Davis and Homer Weed Distinguished Professor ’08 at the University of Arizona. His laboratory is broadly interested in Chemical Biology and Protein Design and Engineering with a focus on developing new tools and methods for advancing human health. The laboratory has a particular current interest in understanding protein kinases and protein-protein interactions and designing new ways to inhibit them in human diseases. Neel Ghosh is also a co-founder and Chief Scientific Officer for Luceome Biotechnologies. Neel received his doctoral degree in 1998 while working with Professor Jean Chmielewski at Purdue University. His doctoral research focused on designing inhibitors of protein-protein interactions and self-replicating peptides. In 1998 he joined Professor Andrew Hamilton and Professor Lynne Regan’s laboratories at Yale University as a joint postdoctoral fellow. At Yale, he discovered the first conditional split-Green Fluorescent Protein, which has been used as a means for measuring protein-protein interactions by many laboratories and the methodology is sometimes called fluorescent protein complementation. In 2001, Neel Ghosh joined the Department of Chemistry and Biochemistry at the University of Arizona as an Assistant Professor and was promoted to Associate Professor and then to the Davis & Weed Chair and Full Professor in 2011. Keywords: Chemistry, Biochemistry, Biomedical Engineering, Cancer

Publications

Jester, B. W., Gaj, A., Shomin, C. D., Cox, K. J., & Ghosh, I. (2011). Testing the Promiscuity of Commercial Kinase Inhibitors Against the AGC Kinase Group Using a Split-luciferase Screen. JOURNAL OF MEDICINAL CHEMISTRY, 55(4), 1526-1537.
Camacho-Soto, K., Castillo-Montoya, J., Tye, B., Ogunleye, L. O., & Ghosh, I. (2014). Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. Journal of the American Chemical Society, 136(49), 17078-86.

Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.

Ghosh, I., Shekhawat, S. S., Porter, J. R., Sriprasad, A., & Ghosh, I. -. (2009). An autoinhibited coiled-coil design strategy for split-protein protease sensors. Journal of the American Chemical Society, 131(42).

Proteases are widely studied as they are integral players in cell-cycle control and apoptosis. We report a new approach for the design of a family of genetically encoded turn-on protease biosensors. In our design, an autoinhibited coiled-coil switch is turned on upon proteolytic cleavage, which results in the complementation of split-protein reporters. Utilizing this new autoinhibition design paradigm, we present the rational construction and optimization of three generations of protease biosensors, with the final design providing a 1000-fold increase in bioluminescent signal upon addition of the TEV protease. We demonstrate the generality of the approach utilizing two different split-protein reporters, firefly luciferase and beta-lactamase, while also testing our design in the context of a therapeutically relevant protease, caspase-3. Finally, we present a dual protease sensor geometry that allows for the use of these turn-on sensors as potential AND logic gates. Thus, these studies potentially provide a new method for the design and implementation of genetically encoded turn-on protease sensors while also providing a general autoinhibited coiled-coil strategy for controlling the activity of fragmented proteins.

Porter, J. R., Stains, C. I., Segal, D. J., & Ghosh, I. (2007). Split β-lactamase sensor for the sequence-specific detection of DNA methylation. Analytical Chemistry, 79(17), 6702-6708.

PMID: 17685552;Abstract:

The methylation pattern of genes at CpG dinucleotide sites is an emerging area in epigenetics. Furthermore, the hypermethylation profiles of tumor suppressor genes are linked to specific tumor types. Thus, new molecular approaches for the rapid determination of the methylation status of these genes could provide a powerful method for early cancer diagnosis as well as insight into mechanisms of epigenetic regulation of genetic information. Toward this end, we have recently reported the first design of a split-protein sensor for the site-specific detection of DNA methylation. In this approach a split green fluorescent protein reporter provided a sequence-specific readout of CpG methylation. In the present work, we describe a sensitive second-generation methylation detection system that utilizes the split enzymatic reporter, TEM-1 β-lactamase, attached to specific DNA binding elements. This system, termed mCpG-SEER-β-Lac, shows a greater than 40-fold specificity for methylated versus nonmethylated CpG target sites. Importantly, the resulting signal enhancement afforded by the catalytic activity of split-β-lactamase allowed for the sensitive detection of 2.5 fmol of methylated target dsDNA in 5 min. Thus, this new sensor geometry represents a 250-fold enhancement in assay time and a 2000-fold enhancement in sensitivity over our first-generation system for the detection of specific sites of DNA methylation. © 2007 American Chemical Society.

Bishop, P., Ghosh, I., Jones, C., & Chmielewski, J. (1995). Basic-helix-loop-helix region of tal: Evaluation of structure and DNA affinity. Journal of the American Chemical Society, 117(31), 8283-8284.