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Functional consequence of SNPs on the Tuberculosis drug metabolising enzyme, human arylamine N-acetyltransferase 1

Abstract
Background
The human arylamine N-acetyltransferase 1 (NAT1) plays a vital role in determining the duration of action and pharmacokinetics of amine-containing drugs such as para-aminosalicylic acid used in clinical therapy, as well as influencing the balance between detoxification and metabolic activation of these drugs. Single nucleotide polymorphisms (SNPs) in this enzyme are continuously being detected and show inter-ethnic and inter-individual variation. Administrating tuberculosis (TB) treatment in the absence of genotypic information for drug metabolizing enzymes can limit the successful eradication of the disease from a patient. Recent studies have shown that loss of H-bonds affects protein function.

Results: In this study, the eects of 11 novel non-synonymous SNPs (nsSNPs) on the structure and function of NAT1 was tested computationally using SIFT and POLYPHEN-2 algorithms and structural analyses methods including loss of hydrogen-bonding, stability calculation, solvent accessibility and sequence conservation. Four out of 11 nsSNPs (Q210P, D229H, V231G and V235A) were predicted to aect protein function using both algorithms. Two of these four SNPs showed a loss of 2-4 hydrogen bonds and in most cases a destabilized protein structure. Another two SNPs (F202V, N245I) were predicted to aect protein function using both algorithms but without any loss of hydrogen-bonds. Three additional nsSNPs (T240S, S259R, T193S) were predicted to be benign with either a loss of three hydrogen bonds or no loss of hydrogen-bonds. The remaining two nsSNPs (E264K and R242M) showed conflicting results between SIFT and POLYPHEN-2 and both cases showed stable Gibbs free energy. No correlation could be identified between the predicted functional eects from SIFT and POLYPHEN-2, and the stability calculations and the hydrogen-bonding analyses. However, the structural effects of modifying an amino acid together with the conficting results from both algorithms warrant experimental testing to resolve the consequences of these 11 novel nsSNPs on NAT1.

Conclusion: The nsSNPs that aect protein function and/or have a destabilized structure provides a prioritized list of SNPs that will be tested in the laboratory by creating a SNP construct that will be cloned into an expression vector. These ndings will inform a strategy of incorporating genotypic data (i.e, functional SNP alleles) with phenotypic information (slow or fast acetylators) to better prescribe effective tuberculosis treatment.



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