Western blotting (protein immunoblotting) is an analytical technique used to identify and locate specific proteins in a sample of tissue homogenate or extract, based on their ability to bind to specific antibodies.
Onion (Allium Cepa) Genotoxicity Test
Laboratory of Ecotoxicology and LCA
Department of Environmental Chemistry, ICT Prague
References:
1. FERETTI, D., ZERBINI, I., ZANI, C., CERETTI, E., MORETTI,M.,MONARCA, S. (2007): Allium cepa chromosome
abberation and micronucleus tests applied to study genotoxicity of extracts from pesticide-treated vegetables and
grapes. Food Addit. Contam. 24 (6): 561-572.
2. RANK, J., NIELSEN, M.H. (1997): Allium anaphase-telophase genotoxicity assay. Department of Environment,
Technology and Social Studies, Roskilde University, Denmark.
Design of fragment screening libraries (IQPC 2008)Peter Kenny
These were the slides that I used for the 2008 IQPC compound libraries conference which was the first external lecture on fragment screening libraries.
Fragment screening library workshop (IQPC 2008)Peter Kenny
I also ran a workshop on selection of compounds for fragment screening just before the 2008 IQPC compound library conference and these are the slides I used.
Western blotting (protein immunoblotting) is an analytical technique used to identify and locate specific proteins in a sample of tissue homogenate or extract, based on their ability to bind to specific antibodies.
Onion (Allium Cepa) Genotoxicity Test
Laboratory of Ecotoxicology and LCA
Department of Environmental Chemistry, ICT Prague
References:
1. FERETTI, D., ZERBINI, I., ZANI, C., CERETTI, E., MORETTI,M.,MONARCA, S. (2007): Allium cepa chromosome
abberation and micronucleus tests applied to study genotoxicity of extracts from pesticide-treated vegetables and
grapes. Food Addit. Contam. 24 (6): 561-572.
2. RANK, J., NIELSEN, M.H. (1997): Allium anaphase-telophase genotoxicity assay. Department of Environment,
Technology and Social Studies, Roskilde University, Denmark.
Design of fragment screening libraries (IQPC 2008)Peter Kenny
These were the slides that I used for the 2008 IQPC compound libraries conference which was the first external lecture on fragment screening libraries.
Fragment screening library workshop (IQPC 2008)Peter Kenny
I also ran a workshop on selection of compounds for fragment screening just before the 2008 IQPC compound library conference and these are the slides I used.
Design of fragment screening libraries (Feb 2010 version)Peter Kenny
I have lectured on design of fragment screening libraries a number of times and, to be honest, my material is getting a bit dated. This presentation is from Feb 2010 when I was visiting CSIRO and the photo in the title slide was taken in Tierra del Fuego.
This lecture outlines the different strategies for finding a fragment hit and the subsequent elaboration strategies used in order to increase potency to develop a lead compound in drug discovery.
Drug discovery take years to decade for discovering a new drug and very costly
Effort to cut down the research timeline and cost by reducing wet-lab experiment use computer modeling
Others have done the work. Some have used the work. I have spoken only on behalf of their behalf.
At an INTEGRATE AMR networking meeting, Warwick Medical School's Dr Esther Robinson brought home just how serious a problem antimicrobial resistance poses from a clinician's perspective.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
1. 1
Fragments for drug discovery
and chemical biology
Rod Hubbard
YSBL, York,
Vernalis, Cambridge
Warwick, Sep 2016
For slides – roderick.hubbard@york.ac.uk
2. 2
Finding small molecule hits
• Trying to find compounds that bind to target
• Compounds need to have required shape and chemistry
• High Throughput Screening
• Compounds decorated in the wrong way
• Particularly a problem with new target classes
Target
Hit
3. 3
• Hits from fragments
• Find small parts that bind – usually biophysical screen
• Then grow or merge fragments to create hit compound
• Usually structure-guided design
Why fragments?
Hit
Target
Screen Structure
guided
design
4. 4
Why fragments?
• Hits from fragments
• Find small parts that bind
• Then grow or merge fragments to create hit compound
• Can also generate ideas
• Deconstruct other hits to optimise key interaction motifs
• Suggest interactions to exploit in hit / lead optimisation
• Scaffold hopping
Hit
Target
5. 5
Overview
• Requirements for fragment-based discovery
• Examples of drug discovery
• Hsp90
• Examples of chemical biology
• Using fragments to explore binding
• Enzyme activators
• Probing the bacterial replisome
Warwick, Sep 2016
6. 6
Why are fragments different?
• A fragment is just a small weak hit
• Requires assay(s) that can detect binding reliably
• Methods for evolving fragments (libraries and/or design)
• Design of library includes constraints of assay / evolution
Affinity
10mM 1mM 100mM 10mM 1mM
Fragments MW 110-250
Scaffolds MW 250-350
Lead Compounds
Hit Compound MW 250-500
Warwick, Sep 2016
7. 7
Screening fragment libraries
• Different experimental approaches have different
strengths and limitations
Warwick, Sep 2016
Affinity
10mM 1mM 100mM 10mM 1mM
Fragments MW 110-250
Scaffolds MW 250-350
Lead Compounds
X-Ray crystallography
Ligand-observed NMR
Surface Plasmon Resonance (SPR)
Enzyme / binding assays (HCS)
Isothermal Titration Calorimetry (ITC)
Hit Compound MW 250-500
Protein-observed NMR
Differential scanning fluorimetry (DSF / TSA)
Hubbard & Murray (2011), Meth Enzym, 493: 509; Meiby et al (2013) Anal Chem 85: 6756
Mass spectrometry (MS)
Weak Affinity Chromatography (WAC)
8. 8
Optimise fragment
Fragment to hit :
SAR by catalog
off-rate screening
-5
0
5
10
15
20
25
30
-50 0 50 100 150 200 250 300
RU
Response
Time s
Cycle: 95 VER-00082099i 50 nM
Fitted Cycle: 95 VER-00082099i
Cycle: 96 VER-00082099i 500 n
Fitted Cycle: 96 VER-00082099i
Cycle: 97 VER-00082099i 5000
Fitted Cycle: 97 VER-00082099i
-4
-2
0
2
4
6
8
-100 -50 0 50 100 150 200 250 300
RU
Response
Time s
Cycle: 103 VER-00055030l 50 n
Fitted Cycle: 103 VER-00055030l
Cycle: 104 VER-00055030l 500
Fitted Cycle: 104 VER-00055030l
Cycle: 105 VER-00055030l 5000
Fitted Cycle: 105 VER-00055030l
Characterisation
X-ray or NMR
guided model
The process
Warwick, Sep 2016
Hubbard et al (2007), Curr Topics Med Chem, 7: 1568 Hubbard and Murray (2011), Methods Enzym, 493: 509
Target
Optimise fragment
Hits
Competitive
NMR screenFragment Library
~ 1500 compounds
Ave MW 190
Design, Build & Test
N
N SNH2
O
N
H
Cl
Cl
O
N
N
O
OH
OH
O
N
H
N O
NN
NH2
O
OMe
NN
NH2
S
N
H
O
N
N
N
NH2
Cl
ClN
SNNH2
NH2
N
NH2
O
OEt
Virtual screen; literature;
library screenScreen by SPR, DSF, WAC,
biochem assay, Xray
Drug?
9. 9
Finding fragments
• Finding fragments that bind is not difficult
• A good way of assessing target “ligandability”
• Low hit rate can indicate difficult to progress
• See also Hajduk (2005) J Med Chem, 48, 2518
• Low hit rates from catenin, Pin1 and Hsp70 ATP site
Updated from Chen & Hubbard (2009), JCAMD, 23: 603
0%
1%
2%
3%
4%
5%
6%
7%
8%
0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4
Dscore
Class1hitsrates
Low hit rates (< 2%)
High hit rates (> 2%)
Kinases
high hit rate
1Calculate druggability
Validatedhitrate
Ligandability calculated from structure (DScore)
Validated
hit rate
from a
ligand-
observed
NMR
screen
protein-protein interaction
targets – varying hit rates
Poor targets
10. 10
Overview
• Requirements for fragment-based discovery
• Examples of drug discovery
• Hsp90
• Examples of chemical biology
• Using fragments to explore binding
• Enzyme activators
• Probing the bacterial replisome
Warwick, Sep 2016
11. 11
Pre-Clinical Clinical Trials
Drug Discovery
Warwick, Sep 2016
Discovery
I II III
Patient
Target Hit ID
H2Ls
Lead
Optimisation
Good Idea
Hit Compound
Lead Compound
Clinical Candidate
Drug
Medicine
12. 12
Hsp90 – the Target
• Hsp90 function is complex involving protein dimerisation and
association to other chaperones and co-factors
GM
Geldanamycin – a
fungal natural
product
Hsp90 requires ATP to function (via hydrolysis to ADP)
Kamal et al (2004) Trends in Mol Med 10: 283
13. 13
Hsp90: Fragment screen
• Targetting the N-terminal domain – an ATPase
• FBLD programme began in early 2002
• - screened library of 729 fragments by NMR
• 17 fragments identified
• Crystal structures for most fragments binding to Hsp90
AmideAmino-pyrimidine Second site binder
Resorcinol
14. 14
Using fragments
• Finding fragments that bind is not difficult
• The challenge is knowing what to do with the hits
• Link, grow or merge
Screen
GROW
Warwick, Sep 2016
15. 15
Hsp90 – AUY922 story
Starting fragment Hit from SAR by
Catalogue (also MTS and VS)
• GI50 in HCT116 colon cell line
FP IC50 = 0.28mM
GI50 = 6mM
FP IC50 = 0.009mM
GI50 = 0.014mM
FP IC50 = ~1mM
D93 G97
K58
F138
L107
rCat
N
O
O
O
O
Phase II Candidate
(Novartis)
D93
G97
K58
F138
L107
Brough et al (2008) J Med Chem 51,196-218
Roughley et al (2012) Top Curr Chem , 317, 61
16. 16
Using fragments
• Finding fragments that bind is not difficult
• The challenge is knowing what to do with the hits
• Link, grow or merge
Known Ligands
Virtual Screening hitsScreen
Detailed Design
17. 17
NN
NH2
O
OMe
VER-26734
FP IC50>5mM
NN
NH2
S
N
H
O
VER-52959
FP IC50=535mM
Fragment Evolved fragment
HSP90 – BEP800 story
N
N
N
NH2
Cl
ClN
N
O
OH
OH
O
N
H
N O
luminespib
Vernalis Phase II candidate (FBLD
/ SBDD derived)
VER-41113
FP IC50=1.56mM
Virtual Screening Hit
VER-45616
FP IC50=0.9mM
SNNH2
NH2
N
NH2
O
OEt
Virtual Screening Hit
Brough et al (2009) J Med Chem 52,4794-4809
Roughley et al (2012) Top Curr Chem 317, 61
D93 G97 K58
F138
L107
18. 18
N
N SNH2
O
N
H
Cl
Cl
O
N
NN
NH2
O
OMe
VER-26734
FP IC50>5mM
NN
NH2
S
N
H
O
VER-52959
FP IC50=535mM
Fragment Evolved fragment
HSP90 – BEP800 story
N
N
N
NH2
Cl
ClN
VER-82576
NVP-BEP800
FP IC50=0.058mM
KD = 0.9nM (SPR)
HCT116 GI50=0.161mM
BT474 GI50=0.057mM
N
O
OH
OH
O
N
H
N O
luminespib
Vernalis Phase II candidate (FBLD
/ SBDD derived)
VER-41113
FP IC50=1.56mM
Virtual Screening Hit
VER-45616
FP IC50=0.9mM
SNNH2
NH2
N
NH2
O
OEt
Virtual Screening Hit
Brough et al (2009) J Med Chem 52,4794-4809
Roughley et al (2012) Top Curr Chem 317, 61
19. 19
Drug leads from fragments
• Vernalis have disclosed leads for:
• kinases such as Chk1, DYRK1A, PDPK1, Pim1, Pak1, Pak4,
STK33 and PDHK
• ATPases such as DNA gyrase, HSP70 and HSP90
• protein-protein interaction targets Pin1, Mcl-1 and Bcl-2
• FAAH and tankyrase
• In recent years – clinical candidates for:
• Chk1, FAAH, Hsp90, (Bcl-2 – inspired by), Mcl-1
• Many other examples published
• Small and large pharma
• List on http://practicalfragmentsblogspotcom/.
• Some recent reviews and books
Warwick, Sep 2016
20. 20
Overview
• Requirements for fragment-based discovery
• Examples of drug discovery
• Hsp90
• Examples of chemical biology
• Using fragments to explore binding
• Enzyme activators
• Probing the bacterial replisome
Warwick, Sep 2016
21. 21
Pre-Clinical Clinical Trials
Drug Discovery
Warwick, Sep 2016
Discovery
I II III
Patient
Target Hit ID
H2Ls
Lead
Optimisation
Good Idea
Hit Compound
Lead Compound
Clinical Candidate
Drug
Medicine
22. 22
Pre-Clinical Clinical Trials
Chemical Biology
Warwick, Sep 2016
Discovery
I II III
Patient
Target Hit ID
H2Ls
Lead
Optimisation
Good Idea
Hit Compound
(Lead Compound)
Clinical Candidate
Drug
Medicine
23. 23
Overview
• Requirements for fragment-based discovery
• Examples of drug discovery
• Hsp90
• Examples of chemical biology
• Using fragments to explore binding
• Enzyme activators
• Probing the bacterial replisome
Warwick, Sep 2016
24. 24
Warwick, Sep 2016The TolB project
• A protein involved in bacterial attack / defence
• Structures determined of TolB in complex with various proteins
(collaboration with Colin Kleanthous, now in Oxford)
• Exact mechanism of action still unclear
• Crystal structure with peptide bound
• Fragment screen (thermal shift) identified fragments that bind
to the tryptophan pocket
• But also new site
25. 25
Warwick, Sep 2016The TolB project
• A protein involved in bacterial attack / defence
• Structures determined of TolB in complex with various proteins
(collaboration with Colin Kleanthous, now in Oxford)
• Exact mechanism of action still unclear
• Crystal structure with peptide bound
• Fragment screen (thermal shift) identified fragments that bind
to the tryptophan pocket
• But also new site
Sequence is conserved in this region
(not noticed before)
Mutation affects activity
26. 26
Warwick, Sep 2016Overview
• Requirements for fragment-based discovery
• Examples of drug discovery
• Hsp90
• Examples of chemical biology
• Using fragments to explore binding
• Enzyme activators
• Probing the bacterial replisome
•Warwick, Sep 2016
27. 27
Warwick, Sep 2016Bacterial orthologue – BtGH84
• Family 84 glycoside hydrolase
• 40% identity with human OGA domain
• Crystal structure available
• Low micromolar (class-wide unselective)
inhibitors developed previously
• tool compounds
• Fragment screen of 91 fragments
• Ligand observed NMR
• PUGNAc as competitor
• Investigated both competitive and non-
competitive inhibitors
PUGNAcThiamet G
Darby et al Angew Chemie (2014) 53:13419
28. 28
Warwick, Sep 2016
• Non-competitive fragment M1E05 enhances BtGH84 activity
• Confirmed with alternative substrate, many controls
• Activation is concentration dependent
• Increases the Vmax
app and reduces the Km
app - 2.5 mM to 1.3 mM
BtGH84 is activated by a fragment
M1E05
Darby et al Angew Chemie (2014) 53:13419
29. 29
Warwick, Sep 2016BtGH84 is activated by a fragment
• Non-competitive fragment M1E05 enhances BtGH84 activity
• Confirmed with alternative substrate, many controls
• Activation is concentration dependent
• Increases the Vmax
app and reduces the Km
app - 2.5 mM to 1.3 mM
• Assay, NMR and ITC confirm that M1E05 affects PUGNAc binding
M1E05
Darby et al Angew Chemie (2014) 53:13419
30. 30
Warwick, Sep 2016BtGH84 is activated by a fragment
• Non-competitive fragment M1E05 enhances BtGH84 activity
• Confirmed with alternative substrate, many controls
• Activation is concentration dependent
• Increases the Vmax
app and reduces the Km
app - 2.5 mM to 1.3 mM
• Assay, NMR and ITC confirm that M1E05 affects PUGNAc binding
• Higher activity (200µM) compounds identified (see paper)
• Non-essential activator kinetics suggests mechanism
• Compounds stabilise folding of loop required for catalysis
• Better compounds required for probing GlcNAc status in cells
• But possibilities for industrial / bioprocessing enzymes
• Investigating covalent tethering of activators (it works !!)
M1E05
Darby et al Angew Chemie (2014) 53:13419
31. 31
Warwick, Sep 2016Overview
• Requirements for fragment-based discovery
• Examples of drug discovery
• Hsp90
• Examples of chemical biology
• Using fragments to explore binding
• Enzyme activators
• Probing the bacterial replisome
32. 32
Warwick, Sep 2016Fragnet
• EU ITN funded from March 2016
• 15 advanced PhD students employed across Europe to be
trained in the methods of fragment based discovery
• Students in academic beneficiaries: VUA, Amsterdam, University of York,
University of Barcelona, Hungarian Academy of Sciences
• Students in beneficiaries: Novartis, Switzerland, Vernalis, UK; Beactica,
Sweden; Zobio, Holland
• Partners: GSK, UK, Iota, UK, Roche, Switzerland, Servier, France
• About 60% of the projects are developing methods
• Computational, novel synthesis, covalent targetting
• A couple of the applications are antimicrobial
• One of which is the bacterial replisome work at York
•
33. 33
Warwick, Sep 2016Bacterial replisome
• A collection of proteins / complexes that together replicate DNA
in bacteria
• Peter McGlynn at York able to reconstitute in vitro
34. 34
Warwick, Sep 2016Bacterial replisome
• A collection of proteins / complexes that together replicate DNA
in bacteria
• Peter McGlynn at York able to reconstitute in vitro
• Screen of 1000 member York library for inhibition of DNA
synthesis – a pseudo phenotypic screen
• Identified DNA intercalators through topoisomerase assay
• Now running functional assays to identify possible mechanisms
• Crystal structures available for many of the components / sub-
complexes
• Target identification underway
