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Computational prediction of anti HIV‐1 peptides andin vitroevaluation of anti HIV‐1 activity of HIV‐1 P24‐derived peptides

 

作者: Naghmeh Poorinmohammad,   Hassan Mohabatkar,   Mandana Behbahani,   Davood Biria,  

 

期刊: Journal of Peptide Science  (WILEY Available online 2015)
卷期: Volume 21, issue 1  

页码: 10-16

 

ISSN:1075-2617

 

年代: 2015

 

DOI:10.1002/psc.2712

 

关键词: anti‐HIV‐1 peptides;machine learning approach;support vector machine;P24 protein

 

数据来源: WILEY

 

摘要:

The world is entering the third decade of the acquired immunodeficiency syndrome (AIDS) pandemic. The primary cause of the disease has known to be human immunodeficiency virus type I (HIV‐1). Recently, peptides are shown to have high potency as drugs in the treatment of AIDS. Therefore, in the present study, we have developed a method to predict anti‐HIV‐1 peptides using support vector machine (SVM) as a powerful machine learning algorithm. Peptide descriptors were represented based on the concept of Chou's pseudo‐amino acid composition (PseAAC). HIV‐1 P24‐derived peptides were examined to predict anti‐HIV‐1 activity among them. The efficacy of the prediction was then validatedin vitro. The mutagenic effect of validated anti‐HIV‐1 peptides was further investigated by the Ames test. Computational classification using SVM showed the accuracy and sensitivity of 96.76% and 98.1%, respectively. Based on SVM classification algorithm, 3 out of 22 P24‐derived peptides were predicted to be anti‐HIV‐1, while the rest were estimated to be inactive. HIV‐1 replication was inhibited by the three predicted anti‐HIV‐1 peptides as revealedin vitro, while the results of the same test on two of non‐anti‐HIV‐1 peptides showed complete inactivity. The three anti‐HIV‐1 peptides were shown to be not mutagenic because of the Ames test results. These data suggest that the proposed computational method is highly efficient for predicting the anti‐HIV‐1 activity of any unknown peptide having only its amino acid sequence. Moreover, further experimental studies can be performed on the mentioned peptides, which may lead to new anti‐HIV‐1 peptide therapeutics candidates. Copyright © 2014

 

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