Proof of concept : recognition as a disruptive technology

 

Abstract 

The transformation of a beautiful idea born via simulation into a commercial opportunity is recognised as a disruptive technology. At the heart of this ongoing story is advanced simulation using massively parallel computation, rare-event methods and genetic engineering. 


Proof of concept : recognition as a disruptive technology

Author: Donal Makernan, University College Dublin, Ireland
 

Last week I received an email asking if I would be willing to accept the ‘2021 NovaUCD Licence of the Year Award’ for the licence of the disruptive molecular switch platform technology to a US based company with an initial application as a point-of-care medical diagnostic for COVID-19 and influenza.  Of course I said yes, and since then received a beautiful statue of a metal helix mounted on a black marble plinth via courier (displayed on the right). It is nice that our work gets this sort of recognition given all of the effort it has taken to get to this point. In my last blog post I wrote of the first steps towards commercialization of our technology.  Since then, everything has intensified. The  company funding this research collaboration with University College Dublin has now over 20 people in the USA dedicated to its commercialization – including old hands hired from well known immuno-diagnostic and pharmaceutical companies, medical doctors, engineers and sales-persons.  On our side, our team has grown and now includes two software-engineers/simulators trained in part through E-CAM while they were studying theoretical physics,  and four molecular biologists.  In addition, contract research and manufacturing organizations are also now being engaged so as to be ready for  clinical testing and scale-up when we have fully optimized our diagnostic sensors for COVID 19.  Hard to believe it is only one year since we met the key commercial people.   We continue to simulate various forms of the sensor so as to optimize its performance and commercialization, and for that HPC resources from PRACE partners from Ireland (ICHEC), Switzerland (CSCS) and Italy (Cineca) have been of huge help. We also are dedicating a lot of effort  in software development so as to speed up our ability to estimate free energy properties such as binding affinities, which turn out to be much tricker than one might expect when proteins are very large, such as between antibodies and target antigens such as the COVID 19 spike protein. That methodology and software arose from an E-CAM pilot project – and would appear to have a potential utility way beyond our first expectations.  The E-CAM Centre of Excellence grant from the EU will be finished soon (31st March). Hopefully it will emerge soon again.

 

Previous blog posts related to this work

Share

Protein based biosensors: application in detecting influenza

Donal MacKernan, University College Dublin & E-CAM

An E-CAM transverse action is the development of a protein based sensor (pending patent filled in by UCD[1,2]) with applications in medical diagnostics, scientific visualisation and therapeutics. At the heart of the sensor is a novel protein based molecular switch which allows extremely sensitive real time measurement of molecular targets to be made, and to turn on or off  protein functions and other processes accordingly (see Figure 1). For a description of the sensor, see this piece

One of the applications of the protein based sensor can be to detect influenza, by modifying the sensor to measure ‘up regulated Epidermal growth factor receptor’ (EGFR) in living cells. The interest of using it for the flu, is that it is cheap, easy to use in the field by non-specialists, and accurate – that is with very low false negatives and positives compared to existing field tests. UCD’s patent pending sensors have these attributes built into their ‘all-n-one’ design, through a novel type of molecular switch, that thrived in the laboratory proof of concept phase. A funded research project to continue this development at UCD is almost certain, and likely to start within weeks.

And the answer to the current frequently asked question “can we modify this sensor to quickly detect the COVID 19 ?” is yes, provided we know amino acid sequences of antibody -epitope pairs specific to this coronavirus.

Figure 1. Schematic illustration of a widely used sensor on the left of Komatsu et al[3] and the “all-n-one” UCD sensor on the right in the “OFF” and “ON” states corresponding to the absence and presence of the target biomarker respectively. The “all-n-one” substitutes the Komatsu flexible linker with a hinge protein with charged residues q1,q2,..which are symmetrically placed on either side of the centre so as to ensure that in the absence of the target, the Coulomb repulsion forces the hinge to be open. Their location and number can be adjusted to suit each application. The spheres B and B’ denote the sensing modules which tend to bind to each other when a target biomarker or analyte is present. The spheres A and A’ denote the reporting modules which emit a recognisable (typically optical) signal when they are close or in contact with each other i.e. in the presence of a target biomarker or analyte.

[1] EP3265812A2, 2018-01-10, UNIV. COLLEGE DUBLIN NAT. UNIV. IRELAND. Inventors: Donal MacKernan and Shorujya Sanyal. Earliest priority: 2015-03-04, Earliest publication: 2016-09-09. https://worldwide.espacenet.com/patent/search?q=pn%3DEP3265812A2  

[2] WO2018047110A1, 2018-03-15, UNIV. COLLEGE DUBLIN NAT. UNIV. IRELAND. Inventor: Donal MacKernan. Earliest priority: 2016-09-08, Earliest publication: 2018-03-15. https://worldwide.espacenet.com/patent/search?q=pn%3DWO2018047110A1

[3] Komatsu N., Aoki K., Yamada M., Yukinaga H., Fujita Y., Kamioka Y., Matsuda M., Development of an optimized backbone of FRET biosensors for kinases and GTPases. Mol. Biol. Cell. 2011 Dec; 22(23): 4647-56.

Share

New publication is out: “Unimolecular FRET Sensors: Simple Linker Designs and Properties”

 

A new publication by researchers at University College Dublin and Boston University including E-CAM funded corresponding author Dr. Donal MacKernan was published in Nano Communication Networks. The measurement of biomarkers and ligands are increasingly used to study transport, signaling, and communication in cells, and as diagnostics/prognostics of disease, or the presence of pathogens, allergens and pollutants in foods, and the environment. Accurate measurement in assays or cellular environments is important, and protein-based biosensors can be used in this context. Using simple Coarse-Grained models of unimolecular fusion protein based FRET sensors of target ligands, the authors address four main questions. Can simple CG models reproduce qualitatively experimental results? Is there an advantage in replacing flexible protein linkers with hinge-like peptides? To enhance the precision of measurement, is it  better to increase or decrease the Föster radius of fluorescent proteins? Is precision enhanced or reduced if the binding energy of the ligand and sensor domains is attractive or repulsive in the absence of the target ligand? The answers are disclosed in the paper.

The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher’s version can be found at https://doi.org/10.1016/j.nancom.2018.10.003.

This work is a particular part of  E-CAM Pilot Project on Food and Pharmaceutical Proteins focused on the development of protein-based sensors and therapeutics. The software used in the publication will soon be published in the E-CAM software library. Industry partners of the Pilot Project include Kerry GroupAPC and others.

Article

Title: Unimolecular FRET Sensors: Simple Linker Designs and Properties

Authors: Shourjya Sanyal, David F. Coker, Donal MacKernan

Abstract: Protein activation and deactivation is central to a variety of biological mechanisms, including cellular signaling and transport. Unimolecular fluorescent resonance energy transfer (FRET) probes are a class of fusion protein sensors that allow biologists to visualize using an optical microscope whether specific proteins are activated due to the presence nearby of small drug-like signaling molecules, ligands or analytes. Often such probes comprise a donor fluorescent protein attached to a ligand binding domain, a sensor or reporter domain attached to the acceptor fluorescent protein, with these ligand binding and sensor domains connected by a protein linker. Various choices of linker type are possible ranging from highly flexible proteins to hinge-like proteins. It is also possible to select donor and acceptor pairs according to their corresponding Föster radius, or even to mutate binding and sensor domains so as to change their binding energy in the activated or inactivated states. The focus of the present work is the exploration through simulation of the impact of such choices on sensor performance.

Share

From Rational Design of Molecular Biosensors to Patent and potential Start-up

 

Dr. Donal Mackernan, University College Dublin

Abstract

The power of advanced simulation combined with statistical theory , experimental know-how and high performance computing is used to design a protein based molecular switch sensor with remarkable sensitivity and significant industry potential. The sensor technology has applications across commercial markets including diagnostics, immuno-chemistry, and therapeutics.

 

Continue reading…

Share