Combinatorial protein domain hunting to facilitate drug discovery
Submitting InstitutionsUniversity College London,
Unit of AssessmentBiological Sciences
Summary Impact TypeTechnological
Research Subject Area(s)
Biological Sciences: Biochemistry and Cell Biology
Summary of the impact
Combinatorial Domain Hunting (CDH) technology is a technique for
producing fragments of proteins that are soluble and tractable for
biophysical analysis. It was developed between 1999 and 2008 at Birkbeck
College, in the laboratory of Dr Renos Savva. This technology was patented
in 2001 and the biotech company Domainex Ltd was then formed to
commercialise it. In 2007, Domainex merged with a UCL spinout company, NCE
Discovery Ltd. The company has attracted over £3m in investment and
employs about 31 people. In addition to its contract research programme,
it has developed an in-house drug discovery programme utilising CDH. Early
in 2012 a patent was filed on a series of inhibitors of the protein
kinases IKK03b5 and TBK1, which are validated drug targets for cancer and
inflammation, and the first of these are expected to begin clinical trials
Drug discovery programmes rely on the availability of protein targets for
drugs in pure, soluble forms and in relatively large (gram) quantities.
There are often difficulties with producing such proteins. Protein
truncation can overcome these, but limited proteolysis is not always
applicable and bioinformatics-informed truncation may be inaccurate and
unsuccessful, or resource-intensive. The technology of combinatorial
domain hunting (CDH), developed by Renos Savva and his co-workers at
Birkbeck College (Department of Biological Sciences) between 1999 and
2008, reliably produces stable, soluble truncated protein fragments
through exhaustively sampling expression of random fragments of the
encoding gene [1, 2]. These fragments bind ligands and are
suitable for structural studies, including X-ray crystallography.
CDH involves subjecting a sequence of DNA that corresponds to a
protein-coding gene to an enzymatic process leading to multiple
double-strand breaks in the DNA, and thence to a pool of randomly
truncated variants. Fragments of the desired approximate size are selected
using electrophoresis and cloned to form a library for parallel
recombinant protein production in E. coli. Detection at various
stages is via a short peptide fusion tag on every variant, which also
assists purification. Promising samples are then scrutinised using more
robust biophysical methods.
In practice, tens of thousands of gene fragments will be expressed within
each project, and these will be whittled down within a period of about
three months to give up to 20 protein fragments that are soluble and
tractable to further analysis, and that may provide suitable targets for
downstream drug discovery. These will often cover different parts of the
original protein, perhaps sampling different domains with different
binding sites and functionalities, increasing the scope of downstream
projects to discover small-molecule binders with a range of
pharmaceutically interesting properties.
As a proof of principle, CDH was applied to p85a, successfully
identifying soluble and highly expressed constructs encapsulating all its
known globular domains, and immediately suitable for downstream
applications . A valuable extension of combinatorial domain
hunting, CDH2, enables empirical discovery of stable
protein-protein core complexes. CDH2 was demonstrated ab
initio using a previously well-characterized Hsp90/Cdc37 complex .
Without using a priori information, the isolation of stable
protein-protein complexes, suitable for further analyses was demonstrated.
This resource-efficient process can provide protein complexes for
screening of compounds designed to modulate protein-protein interactions,
thus facilitating novel drug discovery.
After testing the technology in concept, a patent was filed that also
covered the later implementation of the technology, CDH2 .
This patented technology led to the spin-out of Domainex Ltd in 2001,
initially as a contract research company for drug discovery.
References to the research
 Prodromou C, Savva R, Driscoll PC. DNA fragmentation-based
combinatorial approaches to soluble protein expression Part I. Generating
DNA fragment libraries. Drug Discov Today. 2007 Nov;12(21-22):931-8. http://dx.doi.org/10.1016/j.drudis.2007.08.012
 Savva R, Prodromou C, Driscoll PC. DNA fragmentation based
combinatorial approaches to soluble protein expression Part II: library
expression, screening and scale-up. Drug Discov Today. 2007
 Reich S, Puckey LH, Cheetham CL, Harris R, Ali AA, Bhattacharyya U,
Maclagan K, Powell KA, Prodromou C, Pearl LH, Driscoll PC, Savva R.
Combinatorial Domain Hunting: An effective approach for the identification
of soluble protein domains adaptable to high-throughput applications.
Protein Sci. 2006 Oct;15(10):2356-65. http://dx.doi.org/10.1110/ps.062082606
 Maclagan K, Tommasi R, Laurine E, Prodromou C, Driscoll PC, Pearl LH,
Reich S, Savva R. A combinatorial method to enable detailed investigation
of protein-protein interactions. Future Med Chem. 2011 Mar;3(3):271-82. http://dx.doi.org/10.4155/fmc.10.289
 Patent for CDH and CDH2: WO 03/040391 Method for producing and
identifying soluble protein domains. Driscoll P., Savva R., McAlister M.,
Pearl L., Prodromou C. Filed 8 November 2002; granted in Australia
(2002341204), the EU (02 774 994.4), Canada (2465377), and Japan
(2003-542637), and pending in the USA (10/494,895).
BBSRC Exploiting Genomics Initiative Postdoctoral Project Grant (02/2003
• Microarrays to soluble proteins: exploitation of expression profiling
through high throughput protein production at the BCSB.
• Awarded value: £1,337,456.
• Dr R. Savva (Co-applicant) acting as lead scientist/ supervisor.
In collaboration with Professor. P.C. Driscoll (Principal Applicant) UCL,
and Professor L. H. Pearl (Co-applicant) ICR Chester Beatty Labs, Fulham
Details of the impact
Domainex Ltd was incorporated as a private company in December 2001 to
exploit the innovative technology of combinatorial domain hunting
developed in the Savva laboratory for drug discovery purposes. The patent
protecting this technology has now been granted in Australia, the EU,
Canada, and Japan, and is pending in the USA. Domainex has received over
£5m in private investment, contracts and grant funding in the 11 years
since it was established. The most recent investment round closed in June
2010 with the raising of around £1.3m from Longbow Capital, The Capital
Fund (managed by YFM Venture Finance), Bury-Fitzwilliam and from Takeda
Research Investments [a].
Domainex was originally set up as a fee-for-service drug discovery
company and, following an initial investment of £250,000 from the
Bloomsbury Bioseed Fund, the first company employees were hired in 2002 to
develop the CDH technology into a process that could be offered
commercially via this model. Since then a number of medium and large
biotechnology, agrochemical, and pharmaceutical companies have placed
contracts of ~£30,000 to >£100,000 for CDH studies; this still forms
part of Domainex's work and helps fund the in-house drug discovery. By
2007, contractual milestones with the founder institutions were met, and
Domainex personnel moved to an incubator lab at the London Bioscience
Innovation Centre (LBIC) in Camden. A £1m trigger point in the company's
revenues resulted in the transfer of IP to Domainex, and an accrued
overheads payment of £78,000 to the host department at Birkbeck [b].
In 2007, a merger with the chemistry contract research organisation, NCE
Discovery, greatly expanded the remit of in-house research at Domainex by
allying the core CDH technology with state-of-the-art medicinal chemistry
expertise. This enabled the company to initiate internal drug discovery
programmes with the aim of reaching the lead optimisation stage before
seeking to partner, or outsource, for toxicology and clinical trials of
lead molecules. Following the merger, Domainex relocated to the Cambridge
Science Park. It moved to larger premises on the same site in mid-2011,
doubling its space, increasing its capacity for in-house medicinal
chemistry and drug discovery, and enabling it to expand its staff to the
present size. Late in 2009, Takeda Ventures, Inc., the corporate venture
arm of Takeda Pharmaceutical Company Limited, took an interest on the
Domainex board through acquiring an 8% stake during an investment round.
The company's primary investors are now Longbow Capital and YFM Equity
Partners; previous funders include The Capital Fund, and founder
scientists and institutions also remain stakeholders.
Domainex is now a thriving and successful small biotech company employing
about 30 people, mainly highly skilled scientists engaged in molecular
biology, biochemistry, computational and medicinal chemistry. It thus
makes a significant contribution to the local and national economy. It had
a turnover of £1.95m for the year ended 30 April 2012, up from £82,000 in
the year to 30 April 2008 [c].
Client companies and partners from the period 2008-13 include Ark
Therapeutics, Syngenta, ICR, and Sigma Aldrich [d]. Domainex was
also a partner on the EU Framework 6 Spine II Complexes consortium
2006-2009 [e] and has received grants from public bodies including
the Technology Strategy Board [f]. One major scientific
achievement of such collaboration was the structure of a CDH-optimised
protein kinase in complex with lead compounds from the pharmaceutical
company UCB [g].
The in-house drug discovery programme has initially centred on proteins
that are considered to be useful targets for oncology and
anti-inflammatory drugs and is now producing candidate compounds. The most
advanced programme in the pipeline focuses on two closely related kinases,
TANK-binding kinase 1 (TBK1) and IkappaB kinase epsilon (IKK03b5). This
has yielded patented inhibitors [h] that are now in the lead
optimisation stage. Domainex is seeking partners within the pharmaceutical
industry for the clinical development of these compounds, having raised
£4m by end August 2013 [i]. The first are expected to be nominated
as candidate drugs in 2014 and to enter Phase I in 2015. Another patent
has been filed on the synthetic lethality of TBK1/IKK03b5 inhibitors and
other oncogenes, which includes the use of these oncogenes as biomarkers
and in combination therapies. The company also has an active programme
targeting a number of lysine methyltransferases, enzymes that are involved
in the epigenetic regulation of gene expression and that are known to play
a part in cancer development. Inhibitors of these enzymes are currently at
the lead optimisation stage.
Domainex has received several accolades both for its innovative
technology and for its proactive work on promoting collaborations between
academia and industry. The most recent of these was the 2010 Genesis Life
Science Innovation and Enterprise Programme Of The Year Award [j].
Sources to corroborate the impact
[b] All company details can be verified by the CEO, Domainex. Contact
[c] Financial Statements for year ended 30th April 2008 and year ended
30th April 2012. Copies available upon request.
e.g. Sigma-Aldrich collaboration:
Meier C, Brookings DC, Ceska TA, Doyle C, Gong H, McMillan D, Saville GP,
Mushtaq A, Knight D, Reich S, Pearl LH, Powell KA, Savva R, Allen RA.
Engineering human MEK-1 for structural studies: A case study of
combinatorial domain hunting. J Struct Biol. 2012 Feb;177(2):329-34. http://dx.doi.org/10.1016/j.jsb.2012.01.002.
[h] Patent covering IKK03b5 inhibiting compounds: WO 2012/010826
Pyrimidine compounds as inhibitors of protein kinases IKK epsilon and/or
TBK-1, processes for their preparation, and pharmaceutical compositions
containing them. Perrior T.R., Newton, G.K., Stewart M.R., Aqil, R. Filed
26 January 2012. http://w.pat.tc/WO2012010826A1