Structural Studies to Enable Drug Discovery

Abstract

To better understand molecular interactions upon small-molecule binding, three different targets (MDH1, CD44, and Cas-3) for intervention in disease states were studied using biophysical and structural biology techniques. The detailed findings will hopefully guide future inhibitor design to provide better treatment options for individuals suffering from cancer and tauopathies. Malate dehydrogenase I (MDH1) is a cytosolic NAD-dependent oxidoreductase that has recently garnered attention for supplementing lactate dehydrogenase (LDH) in supplying adequate cytosolic NAD levels necessary during rapid cellular growth in cancer progression. The first ever human MDH1 crystal structure is described in detail and differences in the active site loop relative to MDH2, the mitochondrial isoform, could potentiate selective inhibitor design. CD44 is of the family of hyaladherins that is overexpressed in a variety of different cancers. Antagonism of CD44-HA interactions should block downstream signaling and therefore inhibit cancer development, progression, and metastasis. Three different approaches are discussed in the dissertation. The first uses structure-based drug design to link a small-molecule to a saccharide portion of HA. Second, SPR was used to quantify binding affinity of a series of modified-HA molecules. Finally, biophysical techniques were used to confirm binding of verbascoside to the HABD of CD44. The Caspases are of the family of endoproteases involved in apoptosis and pyroptosis pathways to maintain homeostasis. Caspase-3 was used as a surrogate for Caspase-2 (only Caspase to cleave tau at Asp314) to generate co-crystal complexes with a series of pentapeptides. Described structures show the binding modality of the pentapeptides and highlight conformational differences in the L4 loop.