Studying Molecular Systems With Digital High-throughput SPR

Ryan Denomme is the founder and CEO of Nicoya. The Kitchener, Ontario-based company was founded in 2012 after Denomme completed his Master’s in Engineering at the University of Waterloo. The idea for Nicoya came about during Denomme’s post-secondary education where he experienced the frustration faced by researchers unable to access the most advanced technologies due to their overly expensive and complex features. Denomme understood first-hand how this lack of access directly and negatively impacted progress, providing the motivation to innovate and find a way to break down barriers between scientists and the data they needed to make their next big drug discovery.

Speaking to Technology Networks, Denomme highlights the key challenges faced when using “traditional” surface plasmon resonance (SPR), how SPR is being used to aid drug discoveries, and explains the benefits of designing an SPR instrument that integrates digital microfluidics, artificial intelligence, and nanotechnology.

Laura Lansdowne (LL): How is SPR being harnessed to aid drug discovery efforts?

Ryan Denomme (RD): Surface plasmon resonance (SPR) is a key analytical technique that is used throughout the drug discovery process to provide scientists with essential insights into the molecular systems they are studying. SPR is a label-free binding assay capable of measuring real-time binding between two molecules. From this data, scientists can determine the on-rate, off-rate and affinity constant of the interaction. Many techniques can give scientists a measurement of the affinity, but very few can provide insight into the on and off rates. This is critical because the time-resolved binding profiles of an interaction have a significant impact on the selection of a drug candidate. If scientists only measure affinity, they are potentially missing crucial information. In addition to providing the most informative binding data, SPR is also molecule-agnostic and increasingly high-throughput, making it an irreplaceable tool for everything from target discovery to lead optimization.

LL: What would you consider to be the key challenges related to “traditional” SPR?

RD: There are a few key challenges that are holding SPR back from being a ubiquitous analytical technique. One is the lifetime cost of SPR – it’s a substantial capital purchase that requires significant maintenance to keep it running and a dedicated scientist to operate. One of the big drivers of the capital cost and maintenance is the flow injection fluidic systems used in SPR. SPR requires stringent fluid handling to get accurate data. There cannot be any mixing between the buffer and samples as this creates dispersion, flow rates must be high to eliminate mass transport effects, and there cannot be any cross-contamination. This pushes the limits of conventional fluidic handling technology (i.e. pumps, valves, and tubes), and gets exponentially worse as you scale up the instrument throughput to handle more and more samples simultaneously. Relying on these outdated technologies is what drives up the cost, complexity, and sample volume required for analysis, further reducing the scope of applications that can benefit from SPR.

In addition to these issues, the intricacy of assay design and data analysis also imposes a barrier to adoption. Without extensive experience in SPR, it can be challenging to find the right experimental conditions that result in accurate and high-quality binding curves that are needed for SPR. Analyzing large data sets with complex binding models or artefacts is an intimidating task without extensive experience. Even for experienced users, this can take a lot of time and effort, especially because the software is rarely designed to be intuitive and user-friendly.

LL: What is digital microfluidics (DMF) and how can this be coupled with SPR?

RD: DMF is a liquid-handling technology capable of accurately controlling and manipulating discrete nanodroplets with electricity. Fluidics are contained on a microwell plate and individual droplets can be split, mixed, merged, and dispensed to achieve a variety of sophisticated assay protocols.

DMF solves the major limitation of scaling up throughput and automation of SPR technology, which is in the fluidic handling. The complexity of the fluidic system increases exponentially as you scale the number of samples/channels and level of assay automation – affecting the accuracy of the data and the long-term reliability of the instrument. This leads to significant instrument downtime and service costs, and limits applications to only using purified samples.

DMF fluidic handling technology removes the need for any physical pumps, valves, or tubes and replaces them with a low-cost disposable cartridge that is compatible with the standard well-plate form factor. DMF-powered SPR directly addresses the challenges associated with traditional SPR, enabling scientists to steer away from the conventional paradigm of transporting fluids through channels.

At Nicoya, we’ve integrated our proprietary localized surface plasmon resonance (LSPR) sensors into DMF cartridges – creating 16 independently addressable channels on a single cartridge through the use of digital microfluidics. DMF’s superior liquid handling abilities paired with our flexible and customizable software enable researchers to have precise control over interaction time, automatic serial dilutions and data analysis. It also reduces the cost and complexity of the instrument, making it accessible to all scientists.

LL: What benefits result from designing an SPR instrument that integrates DMF, artificial intelligence, and nanotechnology?

RD: Ultimately, the integration of DMF and nanotechnology solves the leading issues inherent in traditional SPR technology. Paired with artificial intelligence, DMF-powered SPR provides a platform which increases hands-off time, decreases complexity, is affordable, and provides robust results in less time. More specifically, there are a number of key benefits that the integration of these technologies brings to SPR:

• Near instantaneous transition times between buffer and sample (<0.1s), virtually eliminating dispersion
• Decoupling of flow rate and sensor position from dispersion, increasing data quality
• 500X less sample volume required – you can get full kinetics from a 2µl sample volume
• Decoupling of interaction time from sample volume, increasing assay flexibility
• Automated serial dilutions on the cartridge - reducing human error and saving time
• Flexible high-throughput capabilities with many different assay formats available
• Ability to implement end-to-end assay automation
• No clogging, leaking, or contamination as there are no fluidic pathways in the instrumentation
• Flexible fluidic processes enabling on-line, real-time optimization through the use of AI driven experimental design
• Minimal moving parts so extremely low possibility of mechanical failures
• No instrument cleaning or service needed
  
  

Ryan Denomme was speaking to Laura Elizabeth Lansdowne,
Senior Science Writer for Technology Networks.