Identifying Potential Molecular Targets in Fungi Based on (Dis)Similarities in Binding Site Architecture with Proteins of the Human Pharmacolome

Abstract

Invasive fungal infections represent a public health problem that worsens over the years with the increasing resistance to current antimycotic agents. Therefore, there is a compelling medical need of widening the antifungal drug repertoire, following different methods such as drug repositioning, identification and validation of new molecular targets and developing new inhibitors against these targets. In this work we developed a structure-based strategy for drug repositioning and new drug design, which can be applied to infectious fungi and other pathogens. Instead of applying the commonly accepted off-target criterion to discard fungal proteins with close homologues in humans, the core of our approach consists in identifying fungal proteins with active sites that are structurally similar, but preferably not identical to binding sites of proteins from the so-called “human pharmacolome”. Using structural information from thousands of human protein target-inhibitor complexes, we identified dozens of proteins in fungal species of the genera Histoplasma, Candida, Cryptococcus, Aspergillus and Fusarium, which might be exploited for drug repositioning and, more importantly, also for the design of new fungus-specific inhibitors. As a case study, we present the in vitro experiments performed with a set of selected inhibitors of the human mitogen-activated protein kinases 1/2 (MEK1/2), several of which showed a marked cytotoxic activity in different fungal species.

Genomic Discovery and Structure–Activity Exploration of a Novel Family of Enzyme-Activated Covalent Cyclin-Dependent Kinase Inhibitors

“…Also isolated from the above purification was the title compound (1.5 g, 12%) as a white solid. 1 (16). Twelve batches of the following experiment were conducted then combined before purification.…”

“…15 These orthologs typically exhibit moderate overall sequence identity, but active site amino acid residues can be conserved almost identically. 16 However, it is exactly these functionally important and highly conserved regions that comprise important drug binding sites. While fungal GEMs can be assumed to have evolved to compete with organisms encountered in their native environments, such as other fungi, bacteria, or plants, there is considerable potential for cross-kingdom binding to homologous human proteins at conserved active sites.…”

“…Fungi and humans share many genes that can be considered evolutionarily conserved, and often perform the same or a related function in both organisms . These orthologs typically exhibit moderate overall sequence identity, but active site amino acid residues can be conserved almost identically . However, it is exactly these functionally important and highly conserved regions that comprise important drug binding sites.…”