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1. Limitations & Lessons in
the use of X-ray Structural
Information in Drug Design
Davis A.M. et.al., Drug Discov Today. 2008 Oct;13(19-20):831-41.
PRESENTED BY-
DILIP DARADE
PI/316
M.S. (Pharm)
DEPT.OF PHARMACOINFORMATICS
NIPER, HAJIPUR
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2. Drug Discovery process
 Fail Fast Fail Cheap 2

3. 3
Drug discovery through CADD
Structure-based drug design
CADD

4. Structure - function relationship
4
StructureSequence
Function

5.  Atom coordinates along with its electron density
X- ray crystallography
Protein expression
Protein isolation
Protein purification
Understanding the function
Target identification and validation
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6. Experimental Methods
X-ray crystallography
 >85 percent of the
protein structures
 Atomic detail of
proteins
 0.1 nm
 electron density of the
compound
 crystal structure is
necessary
 the same protein may
crystallize into
different crystalloid
form.
NMR Spectroscopy Electron Microscopy
 direct determination
of secondary
structures and
especially domain
movements
 the resolving power of
NMR is less
 The cost of the
experimental
implementation is high
 not for the availability
of higher molecular
masses
 Cellular architecture
shape of large
proteins molecules
 10 nm
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7. Number of structures in the PDB from 1972 - 2010. Image
courtesy of the RCSB Protein Data Bank.
Numberofreleasedentries
Year
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8. The protein structure is correct
The structure of the ligand & it’s interactions
with the protein are correct
The protein-ligand structure is relevant for
drug design
Assumptions
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9. 1. The protein structure is correct
Resolution & experience of crystallographer
Resolution high- modelling of structure having quality
Electron density
https://cdn.rcsb.org
 High resolution <1.5 Å
 Low resolution >2.5 Å
 Structure model
(including water
structure ) is
completely correct &
with high accuracy
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10. Case study
 1JSQ, 1PF4, 1Z2R for MsbA and 1S7B,2F2M for EmrE) of (ABC) transporters
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2HYD- SAV1866 1Z2R 1Z2R_2HYD_SUPERIMPOSED
PDB
Database

11. (a) Cα-trace, correct structure of the SarA protein (2FRH).
(b) Cα-trace, an incorrect model (1FZN).
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12. Lessons for modellers
The entire protein structure is modelled incorrectly are very rare. This
usually occurs only if the resolution is low and if sensible procedures
for model building, refinement and validation are dumped.
 every crystal structure, even at atomic resolution, can have
problematic parts or aspects Inspection of electron density together
with the model may help in identifying such parts(binding site,
catalytic residues, interaction, etc.).
From 1 February 2008, good practice in the validation of protein
structures:
http://xray.bmc.uu.se/embo2001/modval/.
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13. 2. The structure of the ligand & it’s interactions
with the protein are correct
Interactions of Ligand-Receptor are known, understood & correct
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14. (a)conformation of the activated (ligand-bound) state of the protein (2GWX).
(b) Identification of a bound fatty acid ligand (cis-vaccenic acid) (2BAW).
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Case study

15.  Difficulties in determining the orientation of asparagine, glutamine and histidine
sidechains & assignment of density features to water molecules.
 The density for a ligand is poor and the placement of the ligand by the crystallographer
is questionable?
 modellers can make an important contribution themselves to the structure determination
of protein–ligand complexes.
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Lessons for modellers

16. 3. The protein-ligand structure is relevant for drug design
The crystallisation conditions are relevant for drug design
1. pH effect on protein-ligand
 SARS coronavirus protease was crystallised at different
pH values and in complex with a specific inhibitor.
 The structures revealed substantial pH-dependent
conformational changes and an unexpected mode
of binding for the substrate-analogue inhibitor.
 At a pH value of 6 the structure of the monomers in
The homodimer differs (one active and other inactive
conformation) and the inhibitor binds in a different
mode to each monomer.
Case study
2. Protein flexibility
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17.  While an X-ray crystal structure of a ligand bound to its target protein is
seductive in its clarity. thermodynamics of the system may confound a simple
and straightforward interpretation based on the X-ray crystal model.
 Dissimillarity between expected structure–activity relationships and
observation from X-ray crystal structures are important.
 Combination of X-ray crystal structural information, molecular dynamics
simulations and calorimetric investigations is starting to unravel these
complexities.
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18. Can X-ray crystal structures really aid drug design?
 Used in diseases like cancer, HIV, glaucoma and hypertension.
Eg. Aliskiren
To invest in the collection of protein structural information to aid drug
design.
 potency & selectivity
Many other properties need to be built into the chemical structure that
are not directly aided and may even be hindered, by the availability of
protein structure models.
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19. Conclusions
 To prove valuable , provide a strong stimulus to chemical creativity,
through the direct visualisation of the ligand–receptor interactions.
 For users of X-ray crystal structure information, however, it is important to
realise a crystal structure is a model, a crystallographer’s partly subjective
interpretation of experimental data.
 This interpretation may be flawed, ambiguous or inaccurate in its details.
 To examine the model alongside the experimental electron density and
to put the model to the test through iterations of structure–activity work. 19

20. www.drugdiscoverytoday.com
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