Pipeline for Discovery and Diversification of Novel, Bioactive Marine Natural Products (DRENCHED from the Oceans - Discovering Renewable ENzymes and CHemistries, and Enabling their Diversification, from microbes from the Oceans)

Supervisors: Rebecca Goss, Stephen Gillespie

Project Description:

The quest for new antibiotics, especially those with activity against Gram negative and recalcitrant bacteria, is urgent. Over 13 million lives world-wide are currently claimed each year due to infectious diseases. Over the last decade this figure has doubled due to the emergence of multi drug resistant strains. Conversely very few new antibiotics have been introduced to the market in the last 40 years. [1] The Global cost of antimicrobial resistance (AMR) to GDP is calculated as between $2.1 trillion-$124.5 trillion dollars. (RAND report)

We propose a marine microbial pipeline for the discovery of novel antibiotics with which to address AMR. Compounds isolated from microorganisms and plants provide an unparalleled starting point for drug discovery. Over the past 3 decades over 70% of antibiotics entering clinical trials have been based on such compounds. Genome scanning reveals that only a small fraction of the molecules that microbes are capable of producing have so far been isolated. The marine environment represents a particularly rich and largely untapped source of natural products, with marine organisms representing approximately half of the earth’s biodiversity. Despite the success and enormous demand of natural products as drugs, many pharmaceutical companies abandoned their natural product drug discovery programmes due to high rates of re-discovery of known compounds and the difficulty of accessing synthetic analogues.4 The traditional way of discovering bacterial-based natural products employs microbial fermentation, followed by screening of extracts for any promising bioactive compounds. As the same highly potent compound may be produced by many microbes, with this approach there is always the risk of rediscovery.

However, in the last decade there has been a revolution in sequencing technologies enabling microbial genomes to be to be sequenced in a quick and cost effective manner. Excitingly, genomic analysis demonstrates that so far only a small fraction of the microbial compounds available for discovery have been found. Many of these clusters have so far remained silent or cryptic, and their encoded natural products remain to be revealed. Series of approaches are being developed to enable the unlocking of these pathways and revealing the natural products that they encode. [2]

Figure 1: DRENCHED from the Oceans.
Refining the antibiotic discovery pipeline from drop to deluge

State-of-the-Art

In our marine antimicrobial discovery pipeline for novel antibiotics we will increase the likelihood of success by exploring marine microbes and uniquely combining the three strands of genomic, metabolomic, and bioassay guided compound identification.

Specifically we will :

  1. use combined genomic, metabolic and bioactivity analysis to identify biosynthetic gene clusters (BGCs) that encode enzymes with the potential to biosynthesize structurally novel natural products with medicinally useful activities
  2. use appropriate combinations of heterologous expression and promoter refactoring (specifically tailored to each system) to unlock the production of  unusual enzymes and novel natural products
  3. natural products will be isolated, purified and structurally characterized using cutting edge approaches that combine detailed mass spectrometric analysis, genome analysis and 2DNMR experiments
  4. first steps will be taken to enable analogue generation to initiate target identification and structure activity relationship analysis of the bioactive molecules identified. [3]
     

References:

[1]        G. D. Wright, ACS Infect. Dis. 2015, 1, 80

[2]        J.S. Zarins-Tutt,  R.J.M.Goss et al. Nat. Prod.Rep. 2016, 33, 54.

[3]        J.S. Zarins-Tutt,  R.J.M.Goss Emily Abraham and Rebecca J. M. Goss*, Prog. Mol. Biol.,Blue Biotechnology, 2017, 55, 159-186.

Other: