Download Finding Multiple Protein Targets of a Ligand by Computer

Finding Multiple Protein Targets
of a Ligand by Computer
l Potential Application:
n Identification of unknown and secondary therapeutic
targets of drugs, drug leads, natural products.
n Prediction of protein targets related to side effect
and toxicity.
n Ligand-protein interactions in pathways etc.
l Methodology:
n Ligand-protein inverse docking
Why study
protein targets
of a molecule?
I. Therapeutic Targets
Nature 396, 15 (1998)
Why study protein targets
of a molecule?
II. Side effect and toxicity
Abstract From Medline
http://igm.nlm.nih.gov/
Why study protein targets
of a molecule?
Detection of side effect and toxicity
in early stages of drug discovery
l Most drug candidates fail
to reach market
l Side effect and toxicity is
an important reason.
l Money ($350 million per
drug) and time (6-12 years
for a drug) has been
wasted on failed drugs.
Drug Candidates
in Different Stages of Development
Majority of Them Fail to Reach Market
Clin Pharmacol Ther.
Ther. 1991; 50:471
Drug Discov Today 1997; 2:72
Why study
protein targets
of a molecule?
III. Drugs from Natural
Products
From natural products
to therapeutic drugs
TIPS, May 1999, 20:190
§
§
Screening
New drug design
Why study protein targets
of a molecule?
IV. Applications in pathways
EGF Pathway
From Signaling Pathway Database
http://www.grt.kyushu-u.ac.jp/spad/
Strategy
Existing Methods:
New Method:
Given a Protein,
Find Putative Binding Ligands
From a Chemical Database
Given a Ligand,
Find Putative Protein Targets
From a Protein Database
Compound Database
Protein Database
Compound 1
...
Compound n
Protein 1
...
Protein n
Protein
Ligand
Successfully Docked Compounds
as Putative Ligands
Successfully Docked Proteins
as Putative Targets
Science 1992;257: 1078
Feasibility
Proteins
l Database: >12,000 3D structures in PDB.
l Protein diversity: 17% in PDB with unique sequence.
l Development of structural genomics: 10,000 unique proteins within 5
years.
Ann. Rev. Biophys. Biomol. Struct. 1996; 25:113
Nature Struct. Biol. 1998; 5:1029
Method
l Ligand-protein docking docking algorithms capable of finding binding
conformations.
Proteins. 1999; 36:1
Computers
l Increasing performance (docking of 100,000 compounds in days).
l Decreasing cost (Linux PC, Multi-processor Machine)
How to Model Ligand-Protein Binding?
Learn from the Mechanism
of Ligand-Protein Binding
Ligand Binding Site
Ligand binding mechanism
.
.
.
.
.
How to Check Chemical Complementarity ?
Potential Energy Description:
Optimization and Scoring Functions in
Ligand-Protein Docking
Potential Energy Description:
Conformation
change
Low energy
conformation
Energy Functions
n Chemical bonds
n Hydrogen bonding
n van der Waals interactions
n Electrostatic interactions
n Empirical solvation free energy
V = Vbonds +
Σ H bonds [ V0 (1-e-a(r-r0) )2 - V0 ] +
Σ non bonded [ Aij/rij12 - Bij/rij6 + qiqj /εεr rij] +
Σ atoms i ∆σi Ai
Modeling Strategy for
Ligand-Protein Docking
Receptor Cavity Model
Ligand-Protein Docking Algorithm
Geometric considerations
Docking Evaluation (Chemical Complementarity)
Structure optimization to release bad contacts
Evaluation of ligand-protein interaction energy
Science 1992;257: 1078
Strategy for
Ligand-Protein Inverse Docking
Ligand
Automated Process
to inversely dock a ligand to each entry in
a Built-In Biomolecular Cavity Database
Successfully Docked Proteins
and Nucleic Acids
Putative Targets of Ligand
Therapeutic Targets
Side-Effect and toxicityTargets
Metabolism, Signalling etc
Automated Protein Targets Identification Software
INVDOCK
Ligand
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Automated Process to inversely dock the Lignad to each entry in
a Built-In Biomolecular Cavity Database (10,000 Protein and Nucleic Acid Entries)
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Step 1: Vector-based docking of a ligand to a cavity
Step 2: Limited conformation optimization on the ligand and side chain of biomolecule
Step 3: Energy minimization for all atom in the binding site
Step 4: Docking evaluation by molecular mechanics energy functions and comparison with other ligands
Successfully Docked Proteins and Nucleic Acids
as Putative Targets of a Ligand
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Potential Applications:
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Protein function, Proteomics, Ligand transport, Metabolism
Therapeutic Targets, Side-Effects, Metabolism, Toxicity
Function in Pathways
INVDOCK Cavity Models
HIV-1 Protease
INVDOCK Cavity Models II
Estrogen
Receptor
INVDOCK Testing Results
The docked (blue) and crystal (yellow) structure of ligands in some PDB
ligand-protein complexes. The PDB Id of each structure is shown.
INVDOCK Testing Results II
Comparison of docked structure of 4H-tamoxifen (blue ball-and-stick structure) with the crystal
structure of estrogen (yellow stick structure) in protein estrogen receptor (PDB Id: 1a52). For
comparison, the docked structure of estrogen (red line-drawing structure) is also included.
INVDOCK Testing Results III
Molecule
Docked Protein
PDB
Id
RMSD
Description of Docking Quality
Energy
Match
Indinavir
Xk263 Of Dupont
Merck
HIV-1 Protease
1hsg
1.38
-70.25
Match
HIV-1 Protease
1hvr
2.05
-58.07
Match
Vac
Folate
HIV-1 Protease
Dihydrofolate Reductase
4phv
1dhf
0.80
6.55
-88.46
One end match, the other in
different orientation
-46.02
Match
5-Deazafolate
Dihydrofolate Reductase
2dhf
1.48
-65.49
Match
Estrogen
Estrogen Receptor
1a52
1.30
-45.86
Complete overlap, flipped along
INVDOCK Testing Results IV (a)
Tamoxifen is a famous
anticancer drug for
treatment of breast
cancer.
It was approved by FDA in
1998 as the 1st cancer
preventive drug.
30 million people are
expected to use it.
Vitamin E is a widely used
supplement.
Many experimental
studies have indicated its
therapeutic effect to a
number of diseases.
INVDOCK Testing Results IV (b)
Aspirin is a famous
antiinflammatory drug.
It is called as a “wonder
drug” because of its
multiple therapeutic
effects.
Vitamin C is a widely used
supplement.
Many experimental
studies have indicated its
therapeutic effect to a
number of diseases.
INVDOCK Identified Protein Targets
For an Anticancer Drug Tamoxifen
PDB Id
Protein
Experimental Findings
1a25
1a52
1bhs
1bld
1cpt
1dmo
Protein Kinase C
Estrogen Receptor
17beta Hydroxysteroid dehydragenase
Basic Fibroblast Growth Factor
Cytochrome P450-TERP
Calmodulin
Secondary Target
Drug Target
Inhibitor
Inhibitor
Metabolism
Secondary Target
Tamoxifen is a famous anticancer
drug for treatment of breast cancer.
It was approved by FDA in 1998 as
the 1st cancer preventive drug.
30 million people are expected to
use it.
INVDOCK Testing Results :
PDB
Putative Protein Target
1a52
Estrogen Receptor
1akz
Uracil-DNA Glycosylase
1ayk
Collagenase
1az1
Aldose Reductase
1bnt
Carbonic Anhydrase
1boz
Dihydrofolate Reductase
Experimental Finding
putative targets of 4H4H -tamoxifen
Target
Status
Clinical Implication
Ref
Drug target
Confirmed
Treatment of breast cancer
36
Inhibited activity
Confirmed
Tumor cell invasion and
cancer metastasis
38
Decreased level
Combination therapy for
cancer
43
INVDOCK Testing Results :
PDB
Putative Protein Target
Experimental Finding
1a27
17β-Hydroxysteroid-Dehydrogenase
Stimulated Activity
1az1
Aldose Reductase
Increased Level
putative targets of vitamin E
Target
Status
Clinical Implication
Testicular Steroidogenesis
Treatment Of Cataract Development
1bm
k
Map Kinase P38
1crr
C-H-Ras P21 Protein
Improved Cancer Therapy
Decreased H-Ras Expression
INVDOCK Testing Results V
Compound
Putative Targets
Identified
Experimentally
Confirmed
Experimentally
Implicated
4H-Tamoxifen
17
4
4
Aspirin
52
4
16
Vitamin C
46
4
9
Vitamin E
26
2
11
INVDOCK Testing Results VI
Chinese
Natural Product
Compound
Putative CancerRelated Targets
Identified
Experimentally
Confirmed or
Implicated
Acronycine
12
3
Allicin
15
2
Baicalin
17
3
Catechin
16
3
Emodin
9
4
Conclusions
l Ligand-protein inverse docking is
useful in probing putative targets
of a molecule.
l Potential applications in
identification of therapeutic, side
effect, toxicity targets of drugs,
drug leads, natural products; and
in determination of pathways.
l Application potentials increase
with advances in structural and
functional genomics.