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Structural characterization of plasmodial aminopeptidase: a combined molecular docking and QSAR-based in silico approaches

  • Fangfang WangEmail author
  • Xiaojun Hu
  • Bo Zhou
Original Article
  • 9 Downloads

Abstract

Aminopeptidase M1 (PfAM1) is one of the key enzymes involved in the development of new antimalarials. To accelerate the discovery of inhibitors with selective activity against PfAM1 and microsomal neutral aminopeptidase (pAPN), in the present work, the optimum comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were built based on PfAM1 and pAPN inhibitors. The results of the developed 3D-QSAR models were as follows: PfAM1/CoMFA: \( R_{\text{cv}}^{2} \) = 0.740, \( R_{\text{pred}}^{2} \) = 0.7781; PfAM1/CoMSIA: \( R_{\text{cv}}^{2} \) = 0.740, \( R_{\text{pred}}^{2} \) = 0.7354; pAPN/CoMFA: \( R_{\text{cv}}^{2} \) = 0.612, \( R_{\text{pred}}^{2} \) = 0.7318; pAPN/CoMSIA: \( R_{\text{cv}}^{2} \) = 0.609, \( R_{\text{pred}}^{2} \) = 0.7480, and the models derived from MLR, PLSR and SVR methods provided high R2 values of 0.6960, 0.6965, 0.7971 for PfAM1, 0.7700, 0.7697, 0.8228 for pAPN and Q2 of 0.7004, 0.7004, 0.5632 for PfAM1, 0.7551, 0.7566 and 0.8394 for pAPN, respectively, indicating that the developed 3D-QSAR and 2D-QSAR models possess good ability for prediction of the relative compound activities. Furthermore, all inhibitors were docked into the active site of the PfAM1 and pAPN receptors, the hydrogen-bond interactions between the compound 33 with Glu497, Glu463 and Arg489 of the PfAM1, and the compound 4 with Ala348, Glu384 and Phe467 of the receptor pAPN are able to help to stabilize the conformation. The above results would provide helpful clues to predicting the binding activity of novel inhibitors and the foundation for understanding the interaction mechanism between the inhibitors and the receptors.

Graphical abstract

Keywords

Aminopeptidase CoMFA CoMSIA 2D-QSAR Molecular docking 

Notes

Compliance with ethical standards

Conflict of interest

We wish to confirm that there are no known conflicts of interest associated with this publication.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11030_2019_9921_MOESM1_ESM.doc (4.9 mb)
Supplementary material 1 (DOC 5062 kb)

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.School of Life ScienceLinyi UniversityLinyiChina
  2. 2.State Key Laboratory of Functions and Applications of Medicinal Plants, College of Basic MedicalGuizhou Medical UniversityGuiyangChina

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