ID’ing Molecules from the Briny Deep

In a pioneering research project, scientists at IBM and the University of Aberdeen have collaborated to “see” the structure of a marine compound from the deepest place on the Earth using an atomic force microscope (AFM). Their results open up new possibilities in biological research, which could lead to the faster development of new medicines.

Their findings were reported in the online Aug. 1 issue of the journal Nature Chemistry.

Last year, scientists from the university’s Marine Biodiscovery Centre began work on a species of bacterium from a mud sample taken from the Mariana Trench — the deepest place on Earth, located 10,916 m (35,814 ft) beneath the Pacific Ocean surface. The samples came from professor Koki Horikoshi at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) in Japan, who used a deep-sea remotely operated submersible vehicle dubbed Kaiko. The pressure-tolerant bacterium — Dermacoccus abyssi — produced a chemical compound that could not be recognized.

Kaiko, or “Ocean Trench,” is a remotely operated underwater vehicle built by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). As of 2010, Kaiko became the second of only three vessels ever to reach the bottom of the Challenger Deep, an 11-km-deep trough at the tip of the Mariana Trench, near Guam. From 1995 to 2003, the 10.6-ton Kaiko conducted more than 250 dives, collecting 350 species (including 180 bacteria). It provided samples that scientists at IBM and the University of Aberdeen studied. (Image: JAMSTEC)

Using a technique called noncontact AFM, scientists from IBM Research imaged individual molecules with atomic resolution within a week. These images, together with density functional theory calculations, confirmed the identification as cephalandole A, which is actually known and originally isolated from a Taiwanese orchid.

The AFM uses a sharp tip attached to a small spring to measure the tiny forces between the tip and the sample, such as a molecule, to create an image. To image the chemical structure of a molecule with an AFM, it is necessary to operate in very close proximity to the molecule; the range, where chemical interactions give significant contributions to the forces, is less than a nanometer. To achieve this, IBM scientists increased the sensitivity of the tip by deliberately picking up a carbon monoxide (CO) molecule. When close enough to the sample, the CO-terminated tip senses tiny repulsive forces, resolving individual atoms within the investigated molecule and revealing its atomic-scale chemical structure.

“Sourcing unique chemical compounds from some of the Earth’s most extreme regions and identifying the structure of these compounds can be an extremely time-consuming process,” said Leo Gross, a scientist with IBM Research in Zurich. “This technique demonstrates that scanning probe microscopes can add powerful functionality and speed in identifying the structure of molecules which are challenging to resolve with conventional techniques.”

The experiment was the first successful use of an AFM in the determination of what was, at the time, an unknown molecular structure.

In a pioneering research project, scientists from IBM and the University of Aberdeen have collaborated to “see” the structure of a marine compound from the deepest place on Earth using an atomic force microscope (AFM). The results of the project could lead to faster development of new medicines. The experiment was the first successful use of an AFM in the determination of what was, at the time, an unknown molecular structure. In this image, a low-pass filtered three-dimensional representation of the unknown compound is shown. (Image: PRNewsFoto/IBM and Nature Chemistry)

“The Earth’s natural environment is rich with a diverse range of unique organisms from which a vast array of chemical compounds can be sourced, many of which are entirely unknown to science,” said professor Marcel Jaspars, director of the Marine Biodiscovery Centre. “These compounds have the potential to be used in the development of pharmaceuticals and other novel biomedical products. But in order to harness this potential, we must first understand these compounds in terms of their molecular structure in order to determine whether they are viable for use in medicine.”

For hundreds of years, scientists have understood that a wide range of unique resources — in the form of chemical compounds — exists in the natural environment, such as in oceans and deserts, and that these compounds have the potential to be used in the development of new medicines.

Nature offers a huge variety of small molecules and compounds with potential pharmaceutical applications. Such natural products are the cornerstone of drug discovery because they exhibit novel chemical structures and potent biological properties. Studies of the US National Cancer Institute have shown that the marine environment — and in particular also remote and largely untouched areas — is a significant source for novel, unstudied biologically active compounds.

Structure determination of organic molecules is normally achieved using techniques such as mass spectrometry, which defines the molecular formula, and nuclear magnetic resonance (NMR) spectroscopy, the molecular cousin of magnetic resonance imaging. Each carbon and hydrogen atom in a molecule has a defined frequency in the NMR spectrum. Using sophisticated variants of this technique, researchers can determine how hydrogen and carbon atoms are connected together, thus mapping out the molecular structure. However, when there are few hydrogen atoms in the molecule, as occurred in this case, these techniques fail to come up with a unique solution, meaning that other methods are needed to solve the problem.

The remotely operated Kaiko is shown ready to acquire biological samples that may become useful sources of pharmaceuticals. (Image: JAMSTEC)

Motivated by the prospect of new viable biocompounds, scientists at the Marine Biodiscovery Centre are focusing on harnessing the potential of marine organisms as a source for the discovery of chemical compounds that could be used to develop new treatments for cancer, inflammation, infection and parasitic diseases.

Using high-resolution mass spectrometry, the scientists quickly identified the chemical composition of the compound, but determining its exact molecular structure was more challenging. Even the use of state-of-the-art NMR techniques would not allow them to determine the exact structure because of the small number of protons and the positioning of certain atoms in the compound.

The scientists were left with four potential structures, none of which could be ruled out by the NMR data alone. The only remaining possibility to find the correct structure would be to take a chemical synthesis of the proposed structures, which is a very complex task that can take several months.

“Determining the structure of an unknown compound is a time-consuming process which could take months. Therefore, the ability to immediately ‘see’ the structure of a chemical compound simply by looking through a microscope is a tremendous feat,” Jaspars said. “This new approach could lead to much faster identification of unknown compounds and ultimately speed up the process of the development of new medicines.”

For more information, visit: www.abdn.ac.uk/chemistry/research/biodiscovery