HiTel launch

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MGMS 25th Anniversary Meeting
Working with proteins Roderick E Hubbard

• 13th March 2007

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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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1980
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1980
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1982
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1982
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1982
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1982
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1983
PERQ computer Metheus colour
Evans and Sutherland PS300
raster
graphics (shared)
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1985
Evans and Sutherland PS300 (130k)
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1982 - 1986
Evans and Sutherland PS300 Vector
graphics Continual refresh from data network Host
/ graphics connection Programming a challenge
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1982 - 1986
1982 1986 Evans and Sutherland PS300 Vector
graphics Continual refresh from data network Host
/ graphics connection Programming a
challenge Dot surfaces
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1982 - 1986
1982 1986 Evans and Sutherland PS300 Vector
graphics Continual refresh from data network Host
/ graphics connection Programming a
challenge Dot surfaces Mesh surfaces
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1986
Silicon Graphics Raster graphics
workstation 65k First SG imported into Europe
!!
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1986
Raster graphics workstation Fast computing behind
space filling graphics More memory Cheaper
disks Menu systems Interactive modelling
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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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1988
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1990
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1991
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1993
By the mid-1990s, molecular graphics equipment
available to all reasonably funded laboratories.
Workstation for around 5k
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An excursion into virtual reality
1992-4
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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining and analysing structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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Determining protein structures

• Advances in protein production, crystallisation,
  x-ray sources, data processing, structure
  solution and refinement
• Complemented by advances in streamlined packages
  for solving and refining structures gt high
  throughput crystallography

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ER Ligands
Raloxifene (RAL) Antagonist in breast and uterine
tissue but agonist in bone and heart Licensed for
treatment of osteroporosis
17b-Oestradiol (E2) most potent, endogenous
oestrogen (Kd 0.1nM) promotes cell proliferation
in female reproductive tissues plays an important
role in maintenance of cardiovascular system,
bone and brain in both sexes
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Cell Biology of Estrogen Action
CELL MEMBRANE
CYTOPLASM
NUCLEUS
Receptor held in inactive Heat Shock Protein
complex
DNA
Gene
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Molecular Biology of Estrogen Action
Estrogen receptor (ER) binds to response element
(ERE) and recruits co-activators / co-repressors
that instruct a series of large multi-protein
complexes to
A
ER
ER
Polymerase
TAFs
complex
TBP
DNA
ERE TATA
B
ER
ER
Polymerase
TAFs
complex
TBP
DNA
ERE TATA
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Structural Biology of the Estrogen Receptor (ER)
Receptor has a distinctive domain structure with
a DNA binding domain (DBD) and Ligand Binding
Domain (LBD)
AF-1 (a) DNA binding
ligand / AF-2
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Protein Crystallography
Crystal
Diffraction
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Examples of analysis ER story
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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining and analysing structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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Protein Science, (1998) 7, 1359 1367
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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining and analysing structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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Virtual Screening - rDock
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Virtual Screening - rDock

• Contributions to success
• Quality of docking library (diversity,
  properties)
• Target model conformation / solvent
• Docking performance
• Post-screening selection of compounds for assay

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Hit Generation Hsp90

• rDock
• 807 compounds purchased
• Found 10 hits (lt20mM)
• Included known hit four other members of same
  series
• ? indicative SAR (5-150 mM)
• 2 other classes of compounds

rDock class 2 rDock class 3 (0.9mM) gt
backup (6mM) oral candidate
lead (5mM) gt clinical candidate
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Lead Optimisation

• High Throughput X-ray gt rapid structural
  information

• Understand details of binding mode
• Identify potential interactions to improve
  potency
• Structure(s) in homologues -gt selectivity
• Identify regions where modifications can be made
• e.g overcome physicochemical properties ADMET
  issues
• Challenge of incorporating true drug-like
  properties

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PDK1 hits from fragments
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PDK1 hits from fragments
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PDK1 hits from fragments
Side chain occupies solvent accessible pocket in
hinge cleft find compounds containing SeeD and
hydrophobic side chain
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PDK1 hits from fragments
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PDK1 hits from fragments
Chemistry around side chains to explore affinity
and solubility
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PDK1 hits from fragments
Structures of 81903, 48319 and 49537 bound to PDK1
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PDK1 hits from fragments

• Synergy between high throughput crystallography,
  NMR, modelling, medicinal chemistry

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Working with Proteins a personal per (and
retro) spective

• The Past
• What was a driver for MGMS?
• Life before and after 1983
• The Past and Present
• Hardware developments, 1987 2007
• Methods developments, 1987 2007
• Determining and analysing structure
• Predicting structure, conformation, mechanism and
  interactions
• Structure-based drug discovery
• The Future
• Priorities for the next decade

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Priorities for next 10 years

• Graphics and computational hardware
• Will continue to get faster, year on year
• Will enable new science, but not the barrier

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Priorities for next 10 years

• Modelling protein conformation, mechanism and
  interactions
• Experimental data will inform empirical methods
• Computing power will allow increased use of more
  advanced models MM-PBSA, QM-based
• Challenge remains entropy and its effects
  experiments report on ensembles

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Priorities for next 10 years

• Structure-based drug discovery
• Interface between structure, modelling and
  chemistry in design of synthetically tractable
  compounds
• Experimental data will improve empirical scoring
• Models to predict / design drug-like properties

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Acknowledgements

• York
• Leo Caves
• Andy Raine
• Tom Oldfield
• Mike Hartshorn
• Gaby Kuschert
• Dave Edwards
• Karen Hand
• Richard Greaves
• Chandra Verma
• Pawel Herzyk
• Steph Makins
• Edward Croft
• Sarah Done
• Ollie Barker
• Ana Rodrigues
• Tom Davies
• Derek Smith
• Craig Elliott

• Vernalis
• Lisa Wright
• Alan Surgenor
• James Murray
• Pawel Dokurno
• Christine Richardson
• Nicolas Foloppe
• Ijen Chen
• Xavier Barril
• Martin Drysdale
• Lee Walmsley
• Ben Davis
• Heather Simmonite
• Christophe Fromont
• Brian Dymock
• Paul Brough
• Harry Finch
• David Knowles

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1959