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Conf Proc IEEE Eng Med Biol Soc.
2010;2010:1836-9. doi: 10.1109/IEMBS.2010.5626439.

A signal processing-based bioinformatics approach to assessing drug
resistance: human immunodeficiency virus as a case study.

Nwankwo
N, Seker
H.

Source

Bio-Health Informatics Research Group within the Centre for Computational
Intelligence, Department of Informatics, Faculty of Technology, De Montfort
University, Leicester, LE1 9BH, The United Kingdom. [email-masked]

Abstract

Measuring drug resistance is one of the challenging and essential
pharmaceutical activities. It is a laborious and costly laboratory-based
experimentation. Various clinical and experimental analyses for measuring drug
resistance have been carried out. Results have been obtained for different types
of therapeutic agents as a consequence of changes in the amino acids
compositions in the sequence (mutation) of the organisms involved. In the same
manner, the positions of these amino acids alterations and the level of
resistance (folds) have also been experimentally identified. For example, G36S
and V38M mutation in the Human Immunodeficiency Virus (HIV) Transmembrane
glycoprotein (gp41) has been found to cause 100-fold resistance. However, there
does not seem to have bioinformatics method developed in which the amino acid
information of the proteins involved in the studies were used to computationally
assess the degree of drug resistance without involving laboratory-based
experimental procedure. The post-genomic era has witnessed the relevance of
Bioinformatics approaches in the analysis of huge biomedical data. One such
approach is the analysis of protein residues using digital signal processing
technique such as informational spectrum method (ISM). Therefore, we propose a
new bioinformatics method that is capable of assessing drug resistance without
the use of any laboratory-based experiments. This new method incorporates ISM,
sequence information of the proteins and other relevant information. By using
the ISM and EIIP amino acid scale, the
technique was applied in three classes of anti-HIV/AIDS drugs as a case study.
It is observed that the protein residues of the susceptible strains attained the
maximal peak amplitude at the consensus frequency while the resistant strains
maintained lower amplitudes. This result signifies lower contribution from the
resistant strains due to the mutation. The findings are consistent with those of
the experimental ones and therefore suggest that the approach taken can be used
to help assess drug resistance without laboratory-based experimentation. It
should also be noted that the method can be applied in other drug resistance
studies where sequence information of proteins is available and help design a
computer-aided drug resistance calculator.

PMID:

21096145

[PubMed - indexed for MEDLINE]

MeSH
Terms, Substances

MeSH Terms

Amino Acid Sequence

Anti-HIV Agents/pharmacology

Computational Biology/methods*

Drug Resistance

HIV/metabolism*

HIV Envelope Protein gp41/metabolism

HIV Envelope Protein
gp41/pharmacology

HIV Infections/drug therapy*

Humans

Lamivudine/pharmacology

Molecular Sequence Data

Mutation

Peptide Fragments/pharmacology

Phenylpropionates/pharmacology

Pyrimidines/pharmacology

Signal Processing,
Computer-Assisted

Substances

Anti-HIV Agents

HIV Envelope Protein gp41

LU 135252

Peptide Fragments

Phenylpropionates

Pyrimidines

enfuvirtide

Lamivudine

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- HSDB

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