Discovery of Natural Products and Natural Product-Like Inhibitors

National Institute Of Diabetes And Digestive And Kidney Diseases

Investigators

Linked publications & trials

Abstract

Natural products, also referred to as specialized metabolites, are small molecules and peptides that are biosynthesized by microorganisms, fungi and invertebrates. They possess enormous structural diversity and exhibit a broad range of biological activities. Natural products and their synthetic derivatives account for most of the prescribed therapeutics currently used in the clinic, especially among the antibiotic and antitumor drug classes. With the growing incidence of drug-resistant bacterial infections, there is a critical need for basic and clinical research aimed at the discovery and development of new classes of antibiotics and new antimicrobial targets. With an emphasis on marine invertebrates and understudied environmental bacteria as natural product source organisms, we carry out interdisciplinary research that includes antibiotic discovery, determination of mechanisms of action, and complete structural determination. We are also using genome mining techniques to identify, characterize and produce new classes of ribosomally-encoded natural products known as RiPPs (Ribosomal Post-translationally modified Peptides). A few representative projects and findings include the following. In recent work we have used X-ray crystallography, circular dichroism techniques and computational ECD experiments to determine the absolute configuration of the bis-indane natural products haliclonadiamine and papuamine and demonstrate unexpected chiroptical properties where a macrocyclic diene accounts for the sign of the optical rotation and Cotton effect in a small molecule rather than the chiral centers. Through ecology-biased microbial collections and genome mining we discovered, characterized and produced a new class of ribosomally-encoded multicycle peptide natural product class names the chryseoviridins. The chryseoviridin precursor peptide CdnA3 comprises a leader and core sequence and is unusual in that the post-leader sequence contains multiple core motifs. Macrocyclization is catalyzed by the ATP-dependent ligases CdnC and CdnB. Using X-ray crystallography and Mass Spectrometry (MS) we determined the structural basis for peptide macrocyclization of CdnA3 and demonstrated that the ligase undergoes a major conformational change upon substrate binding and release to accommodate successive rounds of cyclization on a single polypeptide precursor and demonstrated that multi-core cyclization takes place in an N-terminal to C-terminal direction. This work has important implications in the engineering of the graspetide family of RiPP natural products and has the potential to obtain diverse classes of protease inhibitors. Our work also aims to identify new antibiotics and antivirals. Recently we have identified new structural classes of secondary metabolites that inhibit growth of wild type and drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. In vitro enzyme assays, in vivo antibacterial assays, and genome sequencing of resistant variants has revealed diverse mechanisms and targets. Those include disruption of cell division through inhibition of the cytoskeletal protein FtsZ, inhibitors of cell wall biosynthesis coupled with cell division, and discovery of a novel import mechanism via the exporter NorA for some natural products containing a nucleoside core. Ongoing work includes characterization of a novel polyketide tetramic acid (patent pending).