1. Protein interactions as drug targets: One of the main goals in the field of drug design is developing molecules that can inhibit, modify, or regulate protein–protein interactions (PPI). Currently, the vast majority of therapeutic compounds are small molecules that act by binding to small cavities/grooves within target proteins such as enzymes and receptors and are not effective in PPI inhibition since such binding pockets usually do not exist on the PPI interfaces. Synthetic peptides have tremendous potential as PPI inhibitors because they can readily mimic natural interaction motifs and cover a larger interaction area compared to a small molecule. Our lab focuses on developing peptide inhibitors for PPI and then improving their activity, stability and bioavailability using synthetic methods we develop in our lab, such as peptide cyclization. See below examples of proteins we are studying and relevant references.

2. Intrinsically disordered proteins: About one third of the genome encodes for intrinsically disordered proteins (IDPs) or disordered regions in proteins (IDRs). These lack stable tertiary structures and are composed of a large ensemble of extended and flexible conformations interchanging dynamically. Our research focuses on the molecular mechanisms of action of the IDRs and how they mediate and regulate the interactions and activity of the protein. IDRs can either directly mediate the interactions of the protein or regulate the interactions and activity of the structured domains. IDPs are involved in many human diseases, making them attractive targets for drug design. However, more than 90% of current drug targets are enzymes or receptors and IDPs still cannot be targeted due to the lack of specific binding pockets for small molecules. Our ultimate goals in IDP research are: (i) understanding the cross-talk between structured and disordered domains in the same protein, and (ii) setting IDPs and IDRs as drug targets.

See examples of proteins and biological systems we are studying and relevant references.

3. Using protein interactions for developing selective biosensors (in collaboration with Prof. Shlomo Yitzchaik): Peptides derived from PPI interfaces are being used as a basis for developing electrochemical biosensors for kinases. Kinases are important cancer biomarkers and are conventionally detected based on their catalytic activity. Kinases regulate cellular activities by phosphorylation of motif-specific multiple substrate proteins, resulting in a lack of selectivity of activity-based kinase biosensors. We developed an alternative approach of sensing kinases based on the interactions of their active sites or allosteric docking sites with a specific partner protein, and not on their catalytic activity. This results in highly selective, cheap and label-free sensors (Amit E et al., Chem. Sci., 2015; Solomon O. et al., Chem. Eur. J., 2022; Joshi P. N. et al., Biosens. Bioelectron., 2022).

(Solomon et al., 2022)

4. Development of new synthetic methods for peptide modifications: Our lab is specializing at developing new methods for peptide synthesis and especially peptide modifications. For example, we developed a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions using simultaneous in situ deprotection, cyclization and TFA cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N-terminus (Chandra K. et al., Angew. Chem., 2014). We also developed a new general N-acetylation method for solid phase synthesis. Malonic acid is used as precursor and the reaction proceeds by in situ formation of a reactive ketene intermediate (Chandra K. et al., Org. Biomol. Chem., 2014). Another example is the development of a new method for covalent inhibition of proteins by succinimide-labeled peptides (Chandra K. et al., ChemMedChem, 2016).

(Chandra et al., 2016)

5.  A new methodology for preparing multi-phosphorylated peptides (in collaboration with Dr. Mattan Hurevich): A special focus is given to the development of methods for the efficient synthesis of peptides with multiple post-translational modifications, and especially multi phosphorylation. Multi-phosphorylation of proteins is one of the most important ways of regulating their biological function and for selecting between different signalling pathways. Multi phosphorylated peptides are the essential tools for studying the specific biological role of each phosphorylation pattern, however their synthesis is extremely difficult and, in many cases, impossible. We developed several efficient new strategies for synthesizing libraries of multi-phosphorylated peptides with up to seven phosphorylated Serine (pSer) and Threonine (pThr) residues that are very close in sequence. This opens the way for the synthesis of multi-phosphorylated peptides for a variety of applications, which was impossible until now, and enables studies of the mechanism of action of multi-phosphorylated proteins and how the phosphorylation barcode is responsible for selecting the pathway in which the protein acts (Mamidi S. et. al., Org. Biomol. Chem., 2019; Mayer D. et al., Nat. Comm., 2019; Mamidi S. et. al., Org. Biomol. Chem., 2020; Grunhaus D. et al., Eur. J. Org. Chem., 2021).

(Grunhaus et al., 2021)