Six years after it began working on its flagship SKi Pro technology, a small San Diego-based proteomics firm recently launched it and is now exploring the next phase of its business strategy: using the platform to develop diagnostic tools.
Silicon Kinetics, a 12-employee company, last month announced an agreement with SAIC-Frederick to evaluate the SKi Pro platform for possible adoption by the National Cancer Institute contractor. The platform debuted in June.
While protein-protein interactions can be studied on other technologies, “We’re the first and only company that has developed a three-dimensional biosensor surface,” company Founder, CEO, and President Hus Tigli told ProteoMonitor. The extra dimension, he said, gives SKi the highest sensitivity on the market while special surface chemistry gives it the lowest non-specific binding capability.
With the launch of the platform completed, the company is now exploring options for the next step in its business evolution. Though SKi was developed for proteomics research, “it’s possible to see applications down the road in diagnostics [that] can be protein-based or nucleic acid-based,” Tigli said. “I think it’s a technology potentially deployable to other areas.”
Interactions in 3D
Spun out of Trex Enterprises, a research and development incubator, in 2002, Silicon Kinetics has spent the past six years developing the nanoporous silicon surface that forms the basis of the SKi technology and developing detection optics and applications for the technology.
The nanoporous silicon technology was originally developed by researchers at the University of California, San Diego, then modified by Silicon Kinetics. Development of the nanopore silicon, Tigli said, turned out to be more complicated than anticipated.
The challenge was getting the “right pore structure and then … the right surface chemistry on the porous silicon to give you the specificity that was required,” he said.
According to an article published Nov. 4 in Proteome Science describing use of the SKi Pro platform, when a protein is covalently coupled to the porous surface or when protein binds to a receptor surface, the change of refractive index conferred by the immobilized protein leads to an interference pattern shift. This shift, called an interferogram, is a measure of protein mass bound to the surface.
Silicon Kinetics etches a porous region into a silicon wafer, with each pore between 80 nanometers to 100 nanometers in diameter “in most applications,” Tigli said. The porous structure surfaces are passivated with silane chemistry, which prepares the surfaces for additional hydrophilic surface chemistries. Silicon Kinetics currently offers three such hydrophilic chemistries — carboxyl, streptavidin, and benzaldehyde — with more in the works.
“We’re the first and only company that has developed a three-dimensional biosensor surface.”
White light is projected onto the porous silicon surface. Light reflected from the fluid/porous silicon interface and from the porous silicon/bulk silicon interfaces creates an interference pattern. Sensitive photo detectors then measure the shifts in this interference pattern in real time as the binding occurs in the pores. Shifts in the interference pattern resulting from protein binding are computed and translated into an optical path difference shift, which is proportional to the mass of surface-bound protein. Thus, real-time interferometry can sensitively measure binding or dissociation rates for biomolecular interactions.
According to Tigli, sensitivity achieved on the SKi Pro platform is “at least 10 times better” than with 2D flat or planar surface technology for biomolecular interaction analysis, and non-specific binding is 10 times lower. The platform, he added, offers two advantages to a scientist’s workflow — the ability to do a quick analysis on which protein pairs are binding, and then the ability to study the binding interactions in detail.
“What that means in terms of instrument design is we have a well-plate format that can determine yes [or] no on binding. And then the same instrument can analyze those important interactions using flow cells,” he said.
“Flow cells give you the kinetics of the binding, the binding rates and the association rates. So we’re the only instrument that can do a quick yes/no [analysis] and then deeper kinetic information on the same instrument,” he added.
One collaborator he declined to identify is using the SKi Pro to study the process of apoptosis. Cell death involves a chain of protein-protein interactions, but which proteins are involved in the process and how quickly the interactions occur are not well-known. SKi Pro would allow a researcher to determine both.
“The next stage is once you understand what happens, you want to be able to prevent it if it’s an undesirable interaction through the design of drugs to stop it,” Tigli said.
SAIC-Frederick is evaluating the SKi Pro as a participant in the Advanced Technology Partnerships Initiative, an NCI program directed at expediting the translation of research discoveries into new treatments for cancer and AIDS. The company will be testing the platform to see how it compares to surface plasmon resonance instruments from Biacore and Bio-Rad Laboratories that it already is using.
“We’re validating the instrument with regard to interactions that we’ve studied in high detail on our other biosensors,” said Andrew Stephen senior scientist in the protein chemistry laboratory at SAIC-Frederick. “For us right now, we want to [do quality control] and make sure the instrument behaves as expected.”
Specifically, his lab will be looking at two biomolecular interactions in its evaluation of SKi Pro: between a high-affinity antibody and a Herceptin receptor, and between DNA and an HIV nucleocapsid protein.
SAIC-Frederick has had the SKi Pro for about a month and done some work on it, though Stephen declined to comment on its performance. His company will continue its evaluation for another month or two, he said.
While SAIC-Frederick is keenly interested in new label-free technologies, it only occasionally has a chance to test new platforms, Stephen said. During the past two years, the company has evaluated three platforms for biomolecular interaction analysis to add to its Biacore instruments, eventually buying an SPR instrument from Bio-Rad.
If SKi Pro works as Silicon Kinetics says it does and SAIC-Frederick decides to purchase it, one specific application that SAIC-Frederick would be interested in using it for is drug-protein binding. “A lot of the small molecules that we look at often bind with quite rapid on-rates,” Stephen said. “We don’t have the resolution necessary right now with the Biacore” instrument to do such an analysis.
In addition to SAIC-Frederick, SKi Pro is being evaluated by pharma and academic researchers, Tigli said. Silicon Kinetics has sold a number of the platform, though Tigli declined to elaborate.
He also declined to quote the price of the platform, saying only that it is “significantly less expensive than similar platforms.” The company also has a fee-for-service business though Tigli said that business is intended to be only a small part of the company’s total revenue source.
The company is now eyeing the next phase of its business strategy, to apply the technology for diagnostics development, particularly for biomarker-based tests. The advantage that SKi Pro would bring to that research field would be specificity, Tigli said, adding that among other things, biomarker research has been plagued by too many false-negatives and false-positives that have rendered the biomarkers useless.
The platform would need to be modified in order to enable higher throughput in order for it to have any real utility for biomarker work. “We would need to design new sensors with the same technology,” Tigli said. “It’s just a matter of having a lot more spots on the silicon.”
Silicon Kinetics is in discussions with “several” firms about possible partnerships, he said. In particular, the company would need access to a “wide range” of antibodies in order to fully forge ahead with its diagnostics-development goals.
“We really need to decide who we will work with first, and then we will work on that instrument,” Tigli said.