SIMoN
  Sanctuary Integrated Monitoring Network
Monitoring Project

Marine Biotechnology Development from Marine-Derived Actinomycetes

Principal Investigator(s)

  • Roger Linington
    University of California, Santa Cruz
Start Date: September 30, 2009

The Linington lab is focused upon contemporary applications of marine natural products chemistry to biological problems. We are interested in developing new methodologies in the areas of marine microbiology, chemical probe design and neglected infectious disease drug discovery. The research in this lab lies at the interface between chemistry and biology and aims to apply the traditional techniques of natural products drug discovery to novel target systems with the dual aims of identifying lead compounds for orphan diseases and furthering our understanding of basic biological processes in these organisms. Our growing library of unique natural products extracts provides a rich resource for the discovery of novel chemotypes with potent and selective biological profiles.

Summary to Date

Research divers have accompanied sanctuary staff on two separate occasions during research cruises along the Big Sur coastline. In October 2009 divers collected sediment samples from Grimes Creek, Lopez Point, Cape San Martin and near Anderson Landing. In September 2010 samples were also collected from Square Black Rock, Rat Creek, Pitkins Curve, and Graves Canyon.

Divers from the Linington Lab have also collected sample from other sites in CA, as well as Oregon and Washington.

Discussion

Marine natural products continue to be a source of inspiration and innovation in many areas of biomedical science. The research pursued in our laboratory focuses on two main areas of interest in this arena: drug discovery for neglected infectious diseases and the use of natural products as probes for biological systems. Within these two related areas we are interested in the discovery of novel therapeutics for diseases including malaria, TB and dengue fever; the identification of novel targets for drug intervention; the determination of specific protein function using small molecule probes and the concerted development of all of these ideas to push our initial drug leads from early-stage discovery to preclinical development.

Antimalarial drug discovery has been an area of research that has suffered from a lack of international attention over the last 30 years. The burden of this destructive disease on human health is immense with an estimated 515 million cases annually. The current resurgence of investigative effort in this area has led to a number of promising new developments including the falcipains and the 8-aminoquinolines however the progress of lead compounds from discovery to early- and late-stage development has been slow, and the identification of novel antimalarial therapies remains a serious challenge in global human health research. The availability of novel therapeutics with potent activity against resistant strains of the malaria parasite will provide healthcare professionals with vital new strategies for the treatment of both uncomplicated and complicated malarial infections. Our research group is engaged in the search for novel antimalarial lead compounds from marine microbes using a combination of orthogonal screening approaches, modern LC-MS based dereplication strategies, and chemical genetics-based methods for mode of action studies together to advance our lead compounds towards preclinical development.

Advances in our understanding of complex biological systems such as host-parasite interactions have highlighted a need for the development of methods for exploring individual protein function. The development of chemical biology and the use of small molecules as probes for biological systems is an emerging field in this arena. In an analogous fashion to the use of classical genetics techniques for determining protein function, chemical genetics can be used in either a forward or reverse sense to develop a more thorough understanding of the role of a protein of interest, or to identify proteins involved in the execution of an observed phenotypic response. In line with this idea, our research group is developing novel strategies for the use of natural products as probes for biological systems. Specifically we are interested in developing techniques for the systematic generation of libraries of tagged small molecules for use in sub-cellular localization studies, protein identification and the determination of protein-protein interactions for given target systems. This research aims to blend the biological relevance of natural product scaffolds with some of the modern developments in chemical probe design to produce bioactive compounds with utility as tools in a broad array of different areas of biochemistry, cell biology and molecular genetics.

Study Parameters

  • Diversity
  • Distribution
  • Genetics
  • bacterial diversity and isolation

Study Methods

The general workflow for this research is as follows:initial field collections of marine sediment (2 grams of sediment per sample) are collected by hand into sterile 15 mL Falcon tubes, using SCUBA. Samples are transported to UCSC on ice, in order to ensure sample integrity prior to plating. Samples are dried using sterile filter paper, and plated onto solid agar media using standard microbiology methods. These isolation plates are curated over a period of 6 months, and relevant microbial colonies selected for isolation and purification onto fresh marine media. Pure cultures are stored as glycerol frozen stocks under liquid nitrogen for long-term preservation.

Environmental samples therefore represent a source of bacteria from which all subsequent research is performed. In general, this research strategy requires samples from ares of high biodiversity that have a minimum degree of contamination due to surface runoff or other pollution sources. Typically we will collect up to 10 sediment samples from each sampling location, each consisting of 2 grams of material.


Figures and Images

Figure 1: This flow chart outlines the drug discovery pipeline for marine-derived microbial natural products.


Figure 2: Field collections in the Monterey Bay National Marine Sanctuary (photo credit S. Clabuesch). Divers collect small samples of sediment. These samples are full of different types of marine bacteria.


Figure 3: Marine microbiology facility at UC Santa Cruz. Bacterial samples are placed on agar plates and allowed to grow for several weeks. Promising colonies are isolated.


Figure 4: Liquid chromatography-mass spectrometry (LC-MS) analytical instrumentation in the Linington Lab at UC Santa Cruz. This allows detection and identification of targeted chemicals within a mixture of natural biochemical products.