KNOWLEDGE OF MALARIA BY USING DATABASES AND

BIOINFORMATICS
G.Devala Rao, U. Chandra Teja, CH.Siva Reddy, S.Sasi Mounika, N.K.D.Devi
KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh.

Malaria has been a problem in India for centuries. Details of
this disease can be found even in the ancient Indian medical
literature like the 'Charaka Samhita'.
WHO estimates that there were 216 million cases of malaria in
2010 resulting in 655,000 deaths (roughly 2000 deaths every day).

Nearly all prophylaxis and therapeutic intervention has been
based on traditional medicines like quinine, paraquine,
chloroquine, antifolates like sulphones and sulphonamides;
pyrimethamine and proguanil, etc.
Resistance to these drugs poses a threat to control on morbidity
and mortality of malaria.
The development of new anti-malarials and improvement of
existing ones has therefore become crucial in controlling the
disease burden.
Till now...,

What comes first is...
The Choice of good targets that make the drugs most effective
against the parasite...
An ideal target -

Is essential for the survival of the organism.

Is located at a critical step in a biochemical pathway.

Makes the organism vulnerable.

Has low potential for development of drug resistance.

Lacks alternative pathways which circumvent the target.

Must differ significantly from any analogous process in

the host.

The challenge of identifying good drug targets will rely on
integration of disparate data from high-throughput
technologies such as genome and DNA sequencing,
microarrays, proteomics, structural genomics and metabolic
networks.
This integration requires mining databases using
bioinformatics tools to detect patterns that make parasite
determinants stand out as candidates for drug discovery.

Bioinformatics is a branch of biological science that deals with the
study of methods for storing, retrieving and analyzing biological
data.
What is Bioinformatics...
It generates new knowledge that is useful in such fields as drug
design and development of new software tools to create knowledge
that can be accessible from anywhere in the world.
Major research areas of Bioinformatics include Sequence analysis,
Genome annotation, Computational evolutionary biology, Analysis
of gene expression and regulation, Comparative genomics, etc.


Bottle-necks for Research on malaria...

Plasmodium spp possess a complex multistage life cycle that

involves both a vertebrate and invertebrate host and where much of the
life cycle of the parasite is not accessible to study.

Although P. falciparum blood stages can be cultivated in vitro, and

over 109 parasites can be recovered from moderate cultivation systems,
other parasite stages can be obtained only in much smaller quantities.
For example, only 107 P. falciparum sporozoites can be ob tained from
over 1000 hand-dissected mosquitoes, and the numbers of liver-stage
parasites that can be harvested in vitro are orders of magnitude lower.

A further complication with functional analysis of P. falciparum is

the lack of a robust transfection system.
Unlike the case for many bacterial and yeast systems, there are technical
hurdles that will make gene and protein expression measurements in
Plasmodium problematic.

Biological systems often possess redundant systems.
For example, Plasmodium spp have the ability to synthesize PABA de
novo or take up preformed PABA from the host.
Therefore, parasite enzymes that are involved exclusively with PABA
synthesis would be poor choices as drug targets.

Thus, for drug development, it will probably be necessary to

identify complete sets of pathway proteins from a particular parasite
stage to have the best chance of discovering those truly critical drug
targets.
Despite of these difficulties in the functional analysis of Plasmodium
genome, several technologies like DNA microarrays, the serial analysis
of gene expression (SAGE) and high-throughput proteomics are already
being applied to malaria research and are allowing unprecedented
analyses of entire organisms and cell types .

By far...,
Publication of the genome sequences of the most virulent human
malaria parasite, Plasmodium falciparum and a rodent parasite,
P. yoelii yoelii open new opportunities for intensive research to
identify critical parasite determinants encoded in the genomes
that can serve as drug targets and candidates for drug discovery
programmes.
Comparative analyses of Plasmodium genomes and genomes of
other organisms have greatly improved the identification and
assignation of putative functions to Plasmodium genes. It was
found that many of the genes perform functions that are unique
to Plasmodium.

Using sequence data from Chromosome 2, a chloroplast-like
organelle, the apicoplast were identified. One of these genes,
fabH, is predicted to encode 3-ketoacyl acyl carrier protein
synthase III, which is known to be involved in fatty acid
biosynthesis, and this led to the observation that
thiolactomycin, a known inhibitor of the bacterial ortholog
protein, inhibits P. falciparum growth in vitro.
From Chromosome 14 sequence data, another apicoplast
biochemical pathway was predicted, involving enzymes of the
non-mevalonate pathway of isoprenoid biosynthesis: deoxy-D-
xyluose 5-phosphate (DOXP) reductoisomerase and DOXP
synthase. Inhibitors of DOXP reductoisomerase suppress P.
falciparum growth and were shown to clear P. vinckei infection
in mice.

The present and Future Prognosis ...

The genomes of several different Plasmodium species have been

almost completely sequenced including those P. Falciparum & P. Vivax
and will be available to researchers world-wide.

Soon, research will focus not on the study of individual genes, but on
the complex interactions of hundreds of gene and proteins. The
complete set of proteins and genes from every stage of the parasite will
undergo scrutiny.

These enhance the ability to test the efficacy of drugs in eggrobust

model systems prior to clinical trials and clarify the relationship
between the parasite and its hosts.

The future availability of human, Plasmodium and Mosquito genome

sequences will permit comparative analysis and open the windows for
new and efficient drugs.


Identification of Unique Genes of
Parasite can be a potential target
for new drugs.
Human
Mosquito
P falciparum
Proteins that are shared by

All genomes.

Exclusively to Human & P.f.

Exclusively to Human & Mosquito.

Exclusively by P.f. & Mosquito.

Unique proteins in
Human.
P. falciparum - Targets for
anti-malarial drugs
Mosquito

As additional Plasmodium spp genomes are completed, particularly where

molecular tools, such as transfection are more robust, researchers will
undoubtedly have a clearer picture of the biology of all Plasmodium spp.

Unlike other drugs, the development of vaccines is likely to require the

identification of the complete set of proteins from the targeted parasite stages,
the characterization of epitopes within each protein and the development of the
appropriate vaccine delivery systems, which may take a while.

What Now...?
The greatest challenge faced by the molecular biology community today is
to make sense of the wealth of data that has been produced by the
genome sequencing projects.
To exploit the data for the development of vaccines and drugs, approaches
that operate on a global scale are needed.
Hence, Biological databases, the archives of consistent data that are
stored in a uniform and efficient manner, came into play. These databases
contain data from a broad spectrum of molecular biology areas.

Some of the well established databases, especially on the malaria research
are...
PlasmoDB Plasmodium genome database (http://plasmodb.org/)
P. falciparum GeneDB (http://www.genedb.org/genedb/malaria/)
Malaria Parasite Metabolic Pathways (http://sites.huji.ac.il/malaria/)
DNA replication map (http://sites.huji.ac.il/malaria/maps/dnareplication.html)
Genome database developed for P.falciparum (http://plasmocyc.stanford.edu/)
UCSF Malaria Transcriptome Database (http://malaria.ucsf.edu/)
There are efforts to produce one-stop shopping websites with many of the
functional genomic tools available.

Finally...,
Bioinformatics has changed the direction of malaria research. These
complete genomic sequence data are certain to provide the foundation
for nearly all malaria research in the next decades.
The results from these few early studies highlight the importance of
exploiting the malaria genomic sequence data for development of
antimalarial drugs.
Recent years have seen an explosive growth in biological data, which
is usually no longer published in a conventional sense, but deposited in
a database and assigned a unique identifying number for quotation in
publications.

The data itself is meaningless before analysis and the sheer volume
present makes it impossible for even a trained biologist to begin to
interpret it manually. Therefore, incisive computer tools must be
developed to allow the extraction of meaningful biological information.

!o duty is more urgent than that of returning "#A!KS

References
Internet and some Commercial Databases;
Some Articles -
* Malaria in India: The Center for the Study of Complex Malaria
in India (Acta Tropica, Elsevier)
* Progress in in silico functional genomics: the malaria Metabolic
Pathways database (TRENDS in Parasitology Vol.22 No.6 June 2006 pg-
238 to 240)
* Malaria Research in the Post-genomic Era by D.J. Carucci
* Bioinformatics and drug target selection for malaria control
(Tropical Journal of Pharmaceutical Research, June 2003; 2 (1):
123-124)