Rapid rise of drug-resistant virile strains of bacteria has made it imperative that we search for new anti-bacterials, and more importantly, cost-efficient ways of producing them. Current pipeline of producing chemical drugs involves, at the very least, a decade of manpower and millions of dollars in investment. Nature has its own repertoire of potent therapeutic agents called Non – Ribosomal peptides (NRPs). These peptides show a wide range of pharmaceutical activity, for example as antibacterial and antitumor agents. Examples for the more famous ones include Penicillin, Gramicidin and Cyclosporin.
The diverse structures of the NRPs form promising scaffolds for the development of new and potent therapeutics. As the name suggests, these peptides are not synthesized by the ribosomal machinery, but by elegant molecular factories called Non-ribosomal peptide synthases or NRPSs. These mega-Dalton protein complexes have a modular architecture and work in an assembly line – like fashion. Each module incorporates a specific building block into the nascent chain and each module is composed of domains catalyzing a particular reaction in the pathway.
The core domains are the adenylation, condensation and thioesterase domains that catalyze the substrate uptake, peptide bond formation and product release. More importantly, a peptidyl carrier protein acts as a messenger, delivering the growing peptide chain to the various reaction centers and the downstream module via a covalently attached phosphopantetheinyl arm.
Figure 1. Schematic representation of the incremental steps involved in the assembly-line synthesis of non-ribosomal peptides by different modules of NRPSs. Figure by Dr Karanth
Structural information is available for some of the individual domains and a few of the interacting partners, which capture a few facets of the reaction pathway. These studies stress that conformational flexibility is fundamental to the catalytic activity. However, several crucial mechanistic features, such as the structural basis for the interaction between the NRPS modules, the details of peptide-bond forming condensation reaction and the ability of the messenger peptidyl carrier proteins to interact with several partners, are poorly understood.
We are currently using an integrative structural biology approach, wherein we combine cutting-edge techniques in solution state NMR with X-ray crystallography, a host of biophysical techniques such as mass spectrometry, solution angle scattering (SAXS, SANS and MALS) and computational modeling to answer these important questions. We hope that our research will make it possible to engineer NRPSs capable of yielding structurally and chemically optimized therapeutics.