Transcript WHO_drugs_vaccines_bioinformatics

Bioinformatics and Malaria: How can the computer help in
vaccine and drug design against Malaria?
The worldwide Malaria threat:
-
2 billions live at risk of malarial infection
500 million individuals get infected per year
2-3 millions die due to P. falciparum infections
Resistance is found against virtually all
commercially available drugs
- Vectors become resistant against pyrethroids
- The only, highly functional vaccine to date is the
administration of irradiated sporozoits
- BUT, new, very promising drugs are in development
(monkey trials/clinical trials)
Three different organism interact in malarial infections
2900 Mb
25-30 Mb
280 Mb
from Good & Doolan 1998
Differing stages, different target structures
from Good & Doolan 1998
Knowing the genomes/transcriptomes of all involved species....
H. sapiens
P. falciparum
A. gambiae
... reveal structures at which an interference can take
place, and this is a necessary a “computer job”
Part 1: Bioinformatics + drug target finding
Acalcidosome
Licensed drugs: Quinine derivates, pyrimethamines
Artemsisin drugs
Known “obvious” drug targets, for which some drugs are
already available
Olliaro & Yuthavong 2001
The DOXP pathway example
- In plants, isoprenoid precursors are synthesized via the DOXP
pathway (in the chloroplast), in mammalians via the
mevalonate pathway (in the cytosol)
- Fosmidomycin is a potent inhibitor of the plant DOXP
reductoisomerase
BLAST and alignment analysis of some DOXP reductase genes
identified a candidate P. falciparum sequence
Jooma et al. 1999, Science
Work hypothesis of Jooma and cols.:
- Is the already tested drug (non-toxic in human use)
Fosmidomycin active against Malaria blood stages which
synthesize a lot of isopentenyl precursors?
In vitro cultures of different strains of P. falciparum were
effectively inhibited...
Jooma et al. 1999, Science
...and mice infected with lethal P. vinckei were cured at
very low doses of either Fosmidomycin or its derivate
Jooma et al. 1999, Science
Advantageous would be the automated identification of
all metabolic enzymes in Plasmodium, and the automated
assignment of all known inhibitors to these enzymes
Pf metabolic
enzymes
High-throughput
screening
Inhibitor
database
Even drugs that block both human and plasmodial enzymes
can by considered, if the human enzyme is not active/present
in the tissues where the drug is bio-available
SAGE/Microarray data
bank of human tissues
SAGE/Microarray data
of blood stage plasmodium
Drug data bank
Science 295, 15/02/2002, p 1311-15
Compounds which are weak inhibitors may be modified
by combinatorial chemistry in silico if the target structure
(3-dimensional!) is known, minimizing the number of
potential test compounds
Target structure
Z
X
N
H
C
Y
A major drawback of alignment-based drug target search
is that some (how many?) enzymes are missed
1
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ONE BEER FOR
THE ONE WHO FINDS
TELOMERASE!
Hoffman et al., Nature 2002
Part 2:
Bioinformatics and vaccine research
Is a Malaria vaccine feasible?
60
Co
Protection
What are known candidate structures:
- anti-infection: CSP, SSP2, STARP, SALSA
- anti-hepatic stages CSP, SSP2, LSA1, LSA3, EXP1,
STARP, SALSA
- anti-merozoite: MSP1-4, PfEBA-175, DBP(Pv), AMA1
SERA, GLURP,Pf155-RESA, RAP1, RAP2
- anti-IRBC: PfEMP1, RIFIN, Pf322
GPI
- anti-infective stages: Pfs25, Pfs28, Pfs45/48, Pfs230
Richie and Saul, Nature 2002
Rappuoli 2001
Curr. Opin. Microbiol.
Rappuoli 2001
Curr. Opin. Microbiol.
Suggestion of
Hoffmann et al.
(Nature Medicine 4,
1998, p 1351-53)
In the case of blood stage vaccine candidates:
identify expressed genes
cDNA, EST data bank
2. Are they surface-expressed (either merozoite or IRBC)?
3. Express as rec. protein or deliver directly
as a DNA vaccine in the rodent system
4. Find homologue in P. falciparum/vivax
5. Test efficacy in in vitro reinvasion assays and in the
monkey model
6. Volunteer trials
Identified antigens must be checked for strain varying
polymorphisms, these polymorphism must be represented
in a anti-blood stage vaccine
Protective
epitope
Variants in strains
A
B
C
Candidate protein X
D
By genome scanning, many novel candidate protein
domains potentially important in cell-cell interaction
were found
Trends in Parasitology 17 (5), p 297-99
- An important antibody target are the erythrocyte
surface-exposed antigens PfEMP1 and perhaps RIFIN
and STEVOR (P. falciparum) and VIR (P. vivax)
DBL
CIDR
DBL
DBL
ATS
PfEMP1: Highly polymorphic, 50 copies per genome, 1
is expressed per trophozoite stage parasite, mediate
cytoadherence which can promote severe disease
Step1: Exploring the endless: Sequencing 500 var genes from
Amazonian isolates
Full length var genes
DBL
DBL
DBL
“Pathoarray”
CIDR
Patient data (disease
severity)
Step 2: Checking the expressed repertoire against the
Pathoarray
Patient samples
(var - cDNA)
Multiplex-PCR with
domain-specific/
degenerated oligomixes
Patient data (disease
severity)
Definition of “severe” or
“non-severe” var domains
Step 3: Checking the immune response: Is there a
anti-severe disease response?
Patient samples
(Plasma)
Anamnestic
data
Elisa
Vaccine
subunit
candidate
Peptide array
Drawbacks in the genomic approach to vaccines
- Some structures may be lost because the prediction
program (HexExon, Glimmer M, PHAT) did not recognize
the coding region (see drug targets, too) of a potential
antigen
- What if the highly effective vaccine target is a
glycosid rest? --> SEE GPI!!!
Further reading:
From genomics to vaccines: Malaria as a model system
(Nature medicine 4, 1351 f, 1998)
Plasmodium, human and Anopheles genomics and Malaria
(Nature 415, 702, this nature issue is particularly interesting, 2002)
An overview of chemotherapeutic targets for antimalarial drug discovery
(Pharmacol. Ther. 81, 91, 1999)
Progress and Challenges for Malaria vaccines
Nature 415, 694