pharmaceutical proteomics non-clinical studies subcommittee of the advisory committee for...
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Pharmaceutical Proteomics
Non-Clinical Studies Subcommittee of theAdvisory Committee for Pharmaceutical Science
US Food and Drug AdministrationMarch 9, 2000
Leigh Anderson, Ph D.CEO, Large Scale Proteomics Corp.
Why Proteins?Roles of Proteome, Transcriptome, Genome
Genome (all genes): What could happen
Transcriptome (all mRNA’s): What might be happening
Proteome (all proteins): What is
happening
Molecular Technologies and Biological Function
?
??Microarrays
(Affymetrix, Incyte)
Proteomics(LSP, OGS)
Diagnosis,Pharmacology,
Toxicology
Genomics,SNPs
Protein Structure
Change (PTM)
Protein Abundance
Change
mRNA Abundance
Change
Functional Change
Genomic Difference
DNA Microarrays Will Not Suffice to Monitor Pre-Clinical Markers
• Human Liver (LSP and Incyte)
– Correlation <0.5
– Different populations of gene products
• 60 Human Cell Lines (Tew, et al.)
– Correlation = 0.43
• Human Serum Proteins (Kawamoto, et al.)
– Correlation (without albumin) is < 0
• Yeast (Gygi, et al.)
– Correlation (subset) = 0.36
Protein and mRNA Abundances Are Poorly Correlated:
• Serum
• Urine
Important Sample Types Contain No Useful mRNA
Protein (2D) vs mRNA (RTI) Abundance in Human Liver
1000 10000 100000 1000000
0.0001
0.001
0.01
0.1
1
CPSACTB
HSP60
PDI
BIP
CRTC
F1ATPB
ACTG
HSC70
CYB5
ENPL
GR75
PYVC
HSP70
TBB1
VIME
TPM
NP450R
TBA1
HSP90
COX-II
LAMR
LAMB
Protein Abundance (CB stained 2-D gel)
MessageAbundance
(% of clones in RTI)
Not detected by RTI
1 clone
2 clones
R= 0.48
LSP/Incyte 9/27/96
Replotted from data in: Glutathione-associated enzymes in the human cell lines of the National Cancer Institute Drug Screening Program. Tew KD, Monks A, Barone L, Rosser D, Akerman G, Montali JA Wheatley JB, Schmidt DE Jr.,
Mol Pharmacol (1996 Jul) 50(1):149-59
Protein vs mRNA for GST in 60 Human Cell Lines
0.1
1.0
10.0
100.0
1000.0
0.1 1.0 10.0 100.0
GS
T
mR
NA
(n
mo
l mR
NA
/mg
pro
tein
)
Lung
Ovarian
CNS
Leukemia
Prostate
Renal
Melanoma
Breast
Colon
R=0.43
GSTProtein (g GST/mg protein)
The protein abundance fingerprint is affected by:
• Perturbations around a “normal” state– Disease states– Treatment effects (e.g., drugs)
• Therapeutic• Toxic
• Progressive change in the “normal” state– Differentiation (e.g., cell type differences)– Evolution of the species
Drug Targets Are Proteins
The top 10 drugs in U.S. sales in 1995 bind to enzymes, receptors and channels in approximately equal proportions
Tradename Generic name$b in U.S.
sales Site of action Enzyme Receptor Channel
1 Zantac ranitidine 2.145 histamine H2 receptor X
2 Prozac fluoxetine 1.472 serotonin re-uptake ?
3 Prilosec omeprazole 1.191 H+/K+ ATPase X
4 Procardia XL nifedipine 1.101 Ca channel X
5 Epogen erythropoietin .964 epo receptor X
6 Zoloft sertraline .894 serotonin re-uptake ?
7 Vasotec enalapril .858 angiotensin converting enzyme
X
8 Mevacor lovastatin .849 HMG CoA reductase X
9 Cardizem CD diltiazem .758 Ca channel X
10 Premarin conj. estrogens .711 estrogen receptor X
Drug Mechanisms Involve Changes in Gene RegulationImplemented at the Protein Layer
Receptor Binding
SignalTransduction
Enzyme Inhibition
Drug Effects
NuclearEvents
mRNA's
Toxicology
Feedback
Proteins
NuclearEvents
mRNA'sPrecursorAccumulation
Product Deficit
Pharmacology
Toxicology
Proteins
Feedback
Pharmacology
Large ScaleProteomics
Technology for Marker Discovery
Components of the ProGEx™ Proteomics Technology Platform
• Experiment design, sample generation, fractionation and preparation
• 2-D gels: High-throughput, high-resolution
Protein “Chips”
• Mass spectrometry: high-throughput protein identification/characterization
• Software: data acquisition, DB management and mining
LSP Advanced Fractionation Technologies
• Tissue dissection
• Cell type separations
• Subcellular fractionation
• Multidimensional fractionation methods
– Chromatography
– Microbanding centrifugal methods
Annexin V
SMP-30CK-I-19
Actin ActinActin
Cholangiocytes Hepatocytes Unfract. Liver
Rare vs Predominant Cell Types in a Tissue:Cholangiocyte and Hepatocyte Protein Differences
Data from “Cholangiocyte specific rat liver proteins identified by establishment of a two-dimensional gel protein database and their role in cytoprotection”. Tietz et al. Electrophoresis, in press.
LSP 2-D Gel Technology
High-throughput• Proprietary large scale automation• Modular-replicatable systems
Reproducible• Sample preparation• Reagent standardization• Computer-controlled systems, data logging
Ultra-sensitive quantitation• Proprietary fully automated silver stain• Colloidal Coomassie Blue• Fluorescence
High Resolution• Resolution measure > 40,000• Near-gaussian spot shapes
Each spot is a distinct protein type (defined by its position)Each spot can by quantitated to yield protein abundance
A 2-D Gel is Equivalent to Thousands ofSpecific Protein Tests Done at Once
F1ATPase
Actin
Albumin
ER-60
LSP Mass Spectrometry
High-throughput MALDI• DE-STR • Automated data flow• Automated sample prep
Automated LC/MS/MS• QTof, LCQ• Sequest/Masscot searching• Sequence generation
Automated Protein Excision/Processing• 10 spots/min• Delivers to 96/384-well plates• Coupled to Kepler database• Robotic digest processing
Identification of Protein Spots by Mass Spectrometry
Scan and analyze gel Cut spots
Same gel: 200 spots cutSilver-stained gel
Digest in96-well plates
0
10000
20000
30000
40000
Co
un
ts
1000 1500 2000 2500 3000
709
.36
33
864
.35
29
977
.45
889
83.5
267
103
0.1
111
082.
495
109
8.5
071
118.
55
128
5.7
511
354.
759
138
6.8
021
430.
732
151
0.8
561
558.
805
171
1.7
53
180
6.8
761
820.
88
195
0.0
021
987.
052
207
8.0
46
225
9.1
142
321.
22
269
4.2
31
Tp
frag
men
t
MALDI-TOF LC-MS/MS + Sequest
LSP Bioinformatics
Kepler™ System• Automated image analysis• Statistical analysis• 15 years proprietary development and use
Newton™ DB Mining• Database-wide queries• Comparison of complex effects• Distance/similarity of effects
Integrated Laboratory Database
Relational Database Architecture• ~20,000 analyses currently on-line
Organization of Proteomics Results Related to Pharma Development: MAP™ and MED™ Databases
ProGEX™ Proteomics PlatformSample Generation, 2-D Gel Analysis,
Kepler Bioinformatics, MS Identification
Drug EffectsDisease ModelsKnockouts
DiseaseGenetics
Human Ex Vivo
Rodent Ex VivoHuman In Vitro
MED™Molecular Effects of
Drugs DatabaseMAP™Molecular Anatomy
and Pathology Database
DB Mining: surrogate markers, mechanisms, targets
Class Generic name Tradename
1 5-alpha-reductase inhibitor Finasteride Proscar
2 ACE inhibitor Captopril Capoten
3 Enalapril Maleate; MK421 Vasotec
4 Acne product Isotretinoin Accutane
5 Adrenal steroid inhibitors Aminoglutethimide Cytadren
6 Alzheimer's treatment Tacrine HCl Cognex
7 Analgesic Acetaminophen Tylenol
8 Androgen Stanozolol Winstrol
9 Anesthetic Halothane Fluothane
10 Anti tuberculosis Isoniazid Nydrazid
11 Antibiotic Tetracycline Hydrochloride Sumycin
12 Chloramphenicol Chloromycetin
13 Erythromycin estolate Ilosone
14 Anticonvulsant Valproic Acid Depakene
15 Antiestrogen, nonsteroidal Tamoxifen Nolvadex
16 Antifungal Ketoconazole Nizoral
17 Antineoplastic Amethopterin (MTX) Methotrexate
18 Antiviral Zidovudine (AZT) Retrovir
19 Acyclovir Zovirax
20 Ca channel blocker Amlodipine Besylate Norvasc
21 Isradipine DynaCirc
22 Verapamil HCl Calan SR
23 Carbonic anhydrase inhibitor Methazolamide Neptazane
24 Diuretic (K-sparing) Spironolactone Aldactone
25 Estrogens Conjugated estrogens Premarin Oral
26 Gall stone dissolution Chenodeoxycholic acid Chenix
27 Gout remedy Allopurinol Zyloprim
28 Immunosuppressant Cyclosporine Sandimmune
29 Tacrolimus (FK506) Prograf
30 Azathioprine Imuran
31 Lipd-lowering agent Probucol Lorelco
32 Gemfibrozil Lopid
33 Lovastatin Mevacor
34 Simvastatin Zocor
35 Fluvastatin Lescol
36 Niacin (nicotinic acid) Nicolar
37 Pravastatin sodium Pravachol
38 Nicotine delivery system Nicotine (transdermal) Nicoderm
39 NSAID Diclofenac Voltaren
40 Oxaprozin Daypro
41 Piroxicam Feldene
42 Naproxen Aleve
43 Psychoactive Alprazolam Xanax
44 Diazepam Valium
45 Fluoxetine Hydrochloride Prozac
46 Triazolam Halcion
47 Rheumatoid arthritis disease-modifier
Hydroxychloroquine Plaquenil
48 Sulfasalazine Azulfidine
49 Penicillamine Cuprimine
50 Skeletal muscle relaxants Dantrolene Dantrium
51 Thyroid replacement Levothyroxine Sodium Synthroid
Molecular Effects of Drugs™ (MED™) Database
LSP conducts an ongoing program examining the mechanisms
(therapeutic and toxic) of marketed pharmaceuticals, of which >50 have been studied
so far
Part of LSP's Rodent Molecular Effects Database
Successful Preclinical Marker Studies
• Monitor Therapeutic vs Toxicity Mechanisms• Cholesterol-lowering agents
• Compare Compound Mechanisms via SAR • PPAR nuclear receptor
• Recognize Mechanism Similarity Across Classes • 1,3-DT-2-T & Piroxicam
• Relate Toxic & Therapeutic Mechanisms • Cyclosporine Nephrotoxicity
• Detect Covalent Protein Adducts • Methapyrilene
• Detect Protein Phosphorylation• APAP vs AMAP Nuclear Effect
These studies are described in LSP scientific publications
Cholesterol Metabolism HMG CoA Reductase Inhibitors: Therapeutic vs toxicity mechanisms
• A tightly regulated pathway affecting a relatively small number of proteins
• Upregulated by lovastatin via inhibition of HMG CoA reductase
• Upregulated by cholestyramine via sequestration of bile acids
• Downregulated by high cholesterol diet (5%)
High Cholesterol (5%)
Control
Cholestyramine (1%)
Lovastatin (0.075%)
Lovastatin + Cholestyramine
Master 5 animals/group
Regulation of Liver Cytosolic HMG-CoA Synthase by Treatments Affecting Blood Cholesterol
21 Protein Spots AreAffected Through theCholesterol Pathway
6 Low Abundance Spots Are Strongly Induced
Cytosolic HMG CoA Synthase
Mitochondrial HMG CoA Synthase (fragment)
23kd Morphine- binding Protein (104)
PP strong- responder (367)
Effects of Cholesterol-Lowering Drugs in Rat Liver
Peroxisome Proliferators: SAR on PPAR
• Bind to PPAR Nuclear Receptors
• Trigger Induction of Fatty Acid Metabolism (etc? )
• Occur in Numerous Disparate Structural Classes
• Produce Liver Tumors in Rats
• No Apparent In Vivo Genotoxicity
A collaboration with Eli Lilly
OC
HO CH2
H2C
CH3
CH2
H2C
CH2
CH2
C
HN
N
N
N
O
H3C
C
HO CH2
H2C
H2C
CH3
O
H3C OH2C
C
HN
N
N
N
NH
N
N
H3C CH3
Cl
S CH2
C
O
O
WY14643
LY171883
LY163443*
-
C
O
O
H2C
CH
H2C
CH2
H2C
CH3
CH2
H3CC
O
O
CH2
CH
CH2
H2C
CH2
CH3
CH2
H3C
OCl
O
C
C
H3C CH3
O
O
C
C
H3C CH3
O
O
DEHP
Clofibric Acid
Nafenopin
-
-
Peroxisome Proliferators and Related Compounds*
SAR Comparison of Drug Effects by Quantitative Proteomics
The effects of peroxisome proliferators on protein abundances in mouse liver. Anderson, N.L., Esquer-Blasco, R., Richardson, F., Foxworthy, P. and Eacho, P. Toxicology and Applied Pharmacology, 137, 75-89, 1996.
OneCompound
200150
10090
8070
60
50
40
30
20
15
4.5 5.0 5.5 6.0 6.5 7.0
Cyt. b5
Actin
CPS
163
Albumin
HSP-60
MUP
CA-IIISMP-30
Calreticulin
SOD
Effects of Peroxisome Proliferators in Mouse LiverNafenopinWY14,643LY171,883LY163,443DEHPClofibrate
>10 1.25
1
2
0.25<10 0.5
0.8
4
P <0.000001P <0.00001
P <0.001P <0.0001
HSP-90
NP450R
SAR Comparison of Drug Effects by Quantitative Proteomics
The effects of peroxisome proliferators on protein abundances in mouse liver. Anderson, N.L., Esquer-Blasco, R., Richardson, F., Foxworthy, P. and Eacho, P. Toxicology and Applied Pharmacology, 137, 75-89, 1996.
200150
10090
8070
60
50
40
30
20
15
4.5 5.0 5.5 6.0 6.5 7.0
Actin
CPS
163
Albumin
HSP-60
MUP
CA-IIISMP-30
Calreticulin
SOD
Effects of Peroxisome Proliferators in Mouse LiverNafenopinWY14,643LY171,883LY163,443DEHPClofibrate
>10 1.25
1
2
0.25<10 0.5
0.8
4
P <0.000001P <0.00001
P <0.001P <0.0001
HSP-90
NP450R
TwoCompounds
SAR Comparison of Drug Effects by Quantitative Proteomics
The effects of peroxisome proliferators on protein abundances in mouse liver. Anderson, N.L., Esquer-Blasco, R., Richardson, F., Foxworthy, P. and Eacho, P. Toxicology and Applied Pharmacology, 137, 75-89, 1996.
SixCompounds
200150
10090
8070
60
50
40
30
20
15
4.5 5.0 5.5 6.0 6.5 7.0
Actin
CPS
163
Albumin
HSP-60
MUP
CA-IIISMP-30
Calreticulin
SOD
Effects of Peroxisome Proliferators in Mouse LiverNafenopinWY14,643LY171,883LY163,443DEHPClofibrate
>101.25
1
2
0.25<10 0.5
0.8
4
P <0.000001P <0.00001
P <0.001P <0.0001
HSP-90
NP450R
A= ControlB= LY163,443C= LY171,883 D= DEHPE= Clofibric acidF= WY14,643G= Nafenopin
Peroxisome Prolferators: 6 Compounds Compared Over 107 Selected Protein SpotsThe effects of peroxisome proliferators on protein abundances in mouse liver. Anderson, N.L., Esquer-Blasco, R., Richardson, F., Foxworthy, P. and Eacho, P. Toxicology and Applied Pharmacology, 137, 75-89, 1996.
AAA
AAA
A
A
A
AA
A
A A
A
B
B
B
BB
B
C
C
C
C
CCD
DD
DD
DE
EE E
EE
FF
FF
F
F GG
GG
G
G
Peroxisome proliferation response
LY163,443 response
Drug Mechanisms via Quantitative Proteomics:Patterns of Change in >100 Proteins Can Be Evaluated
to Reveal Mechanistic Similarities and Differences
Each symbol representsthe liver protein patternof an individual mouse
Dithiolethiones: Phase II enzyme induction, mechanism similarity across classes
SS
N
H3C
SOltipraz (parent)
SS
S
O
H3CAnethole Trithione
SS
S
1,2-Dithiole-3-thione
S
SS
1,3-Dithiole-2-thione
OC
CC
CO
CH3
O
H3C
O
Dimethyl fumarate
A collaboration with Division of Cancer Prevention and Control, Chemopreventive Investigational Drug Unit, US National Cancer Institute
o2 Group 15: Oltipraz (control)
O2 Group 16: Oltipraz (442umol)
a Group 17: ANTT (control)
A Group 18: ANTT (442umol)
m Group 19: DMF (control)
M Group 20: DMF (442umol)
r Group 21: 1,3-DT-2-T (control)
R Group 22: 1,3-DT-2-T (442umol)
w Group 23: 1,2-DT-3T (control)
W Group 24: 1,2-DT-3-T (442umol)
o2
o2
o2
o2
o2a a
aa a
m
m
m
mm
r
r
r
r r r
ww
w
wwO2
O2O2
O2
O2AA
AAA
M
M
MM
R
R
RR
R
W
W
W
W
-4 -3 -2 -1 0 1 2
FACTOR2: Potency as Phase II Enzyme Inducer
-2
-1
0
1
2
3
4
FA
CT
OR
1: P
oten
cy W
ith
Res
pect
to M
echa
nism
“R
”
Effects of Chemoprevention Compounds in Rat Liver: Two Mechanisms Are Detected Among the Dithiolethiones
Principal Components Analysis of Data on 81 Spots
Controls
Each symbol is an individualanimal’s protein expression pattern
o1 Group 1: Oltipraz 21 days in feed + 2 days recovery controls
i Group 2: Ibuprofen 21day feed control
f Group 3: DFMO 21day feed control
h Group 4: 4-HPR 21day feed control
cp Group 5: Carbenoxolone and Piroxicam 21day feed control
gd Group 6: Ca glucarate and DHEA analogue 21day feed cntrl
O1 Group 7: Oltipraz 21 days in feed + 2 days recvry 100mg/kg
I Group 8: Ibuprofen 21day feed MTD
F Group 9: DFMO 21day feed MTD
H Group 10: 4-HPR 21day feed MTD
C Group 11: Carbenoxolone 21 day feed MTD
P Group 12: Piroxicam 21 day feed MTD
G Group 13: Ca glucarate 21day feed MTD
D Group 14: DHEA analogue 21day feed MTD
o2 Group 15: Oltipraz (control)
O2 Group 16: Oltipraz (442umol)
a Group 17: ANTT (control)
A Group 18: ANTT (442umol)
m Group 19: DMF (control)
M Group 20: DMF (442umol)
r Group 21: 1,3-DT-2-T (control)
R Group 22: 1,3-DT-2-T (442umol)
w Group 23: 1,2-DT-3T (control)
W Group 24: 1,2-DT-3-T (442umol)
o1o1
o1o1o1
o1o1
o1
i
iii i
f
f
f
f
f
h h
hh
h
hcp cp
cp
cp cp
gd
gd
gd
gd
gd
O1O1
O1 O1O1
II
II
I
I
I
I
I
FF
F
F
F
FF
F
H
HH H
HH
H
H HHCCC
C
C
C
P
P
P
P
PP
P
G
G
GGGG
GGGG DD
DD
D
D
o2
o2
o2
o2
o2a a
aa a
m
m
m
mm
rr
r
r r r
ww
w
wwO2O2O2
O2
O2AA
AAA
M
MM
M
R
R
RR
R
W
W
W
W
-4 -3 -2 -1 0 1 2
-3
-2
-1
0
1
2
3
4
FACTOR2: Potency as Phase II Enzyme Inducer
FA
CT
OR
1: P
oten
cy W
ith
Res
pect
to M
echa
nism
“R
”
Effects of Chemoprevention Compounds in Rat Liver:Mechanism “R” Is Shared With Piroxicam
Principal Components Analysis of Data on 81 Spots
Cyclosporin:Markers of Mechanism-Specific Toxicity
• Potent immunosuppressive drug
• Used to prevent organ graft rejection
• Produces dose-limiting adverse side effects in kidney (tubular toxicity, kidney calcification, renal dysfunction)
• Pathogenesis unclear
A collaboration with Novartis Pharma
Kidney Protein Effects of CsA:Major Downregulation of Spot 75
CsA 15mg/kg/d 12days
CsA 50mg/kg/d 12 days
Arrow Plot here!
Mitochondrial:
67 Cytochrome C oxidase
peptide II
Cytosolic:
75 Calbindin 28kD
96 Senescence marker
protein 30
109 a-2U-globulin
119 Tropomyosin
6775
96
109
119
Cyclosporine A decreases the protein level of the calcium-binding protein calbindin-D 28kDa in rat kidney. Steiner, S., Aicher, L., Cordier, A., Raymackers, J., Meheus, L., Esquer-Blasco, R., and Anderson, N.L. Biochem. Pharmacol., 51, 253-258, 1996.
Control kidney immuno-stained for calbindin d28
CsA-treated kidney immuno-stained for calbindin d28, showing calcium deposits
Histological Effects of CsA Treatment in Rat Kidney
Cyclosporine A decreases the protein level of the calcium-binding protein calbindin-D 28kDa in rat kidney. Steiner, S., Aicher, L., Cordier, A., Raymackers, J., Meheus, L., Esquer-Blasco, R., and Anderson, N.L. Biochem. Pharmacol., 51, 253-258, 1996.
0
20
40
60
80
100
120
140
160
180
200
Control CsA FK-506 Rapamycin PSC-833
% o
f C
ontr
ol r
enal
cal
bind
in
10 days31 daysCsA, SDZ PSC 833: 50mg/kg/day
FK-506, Rapamycin: 5mg/kg/day
Drug-Effects on Renal Calbindin Levels
Methapyrilene:
• Histamine H1 receptor antagonist• Formerly used in many OTC and prescription
medications• Produces liver tumors in rats• No apparent In vivo genotoxicity• Causes proliferation of mitochondria
H2C
N
H2C
CH2
N
CH 3
N
CH 3
S
Methapyrilene H2C
N
H2C
CH2
N
CH 3
NO
CH3
Pyrilamine
Non-genotoxic liver carcinogen, novel covalent protein modifications
A collaboration with Eli Lilly
Methapyrilene Treatment Results in Charge Modification of Four Major Mitochondrial Proteins
1,000ppm MPYControl
grp75
HSP60
F1 ATPase beta
Carbamyl phosphate synthase
Protein Modification Correlates with Tumorigenicity
for Methapyrilene
Charge Modification
In vivo
In vitro
In vivo
Rat
-0.96
-0.81
Mouse
-0.14
-0.33
Human
-0.11Index
+
1 week
48 hr
Mitochondrial ProteinNA
Tumorigenicity
Strengths of Quantitative Proteomics
• Informative protein markers have been found for:– Disease states– Treatment effects (e.g., drugs)
• Therapeutic• Toxic
• Global analysis of marker patterns has:– Classified mechanisms and disease states– Allowed more sensitive detection than obtained with
single markers