Nucleobase sequence based building up of reliable QSAR models with the index of ideality correlation using Monte Carlo method

Abstract

This study describes in silico designing of aptamers against the influenza virus using Monte Carlo method. Aptamers are short, single-stranded oligonucleotides and these bind to an ample range of biologically important proteins which are related to many disease conditions. The affinities and specificities of aptamers are comparable to antibodies. In the medicinal chemistry, quantitative structure-activity relationship (QSAR) is an important skill which is used for drug design and development. To study the inhibitory activity of aptamers, we have developed QSAR models based on Monte Carlo method. The nucleobase sequence descriptors B_k, BB_k and BBB_k are used to generate the QSAR models. A number of statistical benchmarks together with index of ideality of correlation (IIC) is considered to validate the build QSAR models. Data set of 98 aptamers is divided into four random splits. The statistical criteria R² = 0.8711 and CCC = 0.9207 of the validation set of split 3 are best, so the build QSAR model of split 3 is the paramount model. The aptamer fragment responsible for the promotors of endpoint increase and decrease are also determined. These fragments are applied to design new nine aptamers from the lead aptamer APT01.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aptamers
• influenza virus
• QSAR
• IIC
• nucleobase sequence

Acknowledgments

The authors are thankful to Dr Andrey A. Toropov and Dr Alla P. Toropova for providing CORAL software. The authors are also thankful to the authorities of respective universities for providing infrastructure.

Disclosure statement

The authors declare no conflicts of interest.