Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2‐3)Gal: a study by in silico mutations and molecular dynamics simulations

Abstract

Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.

Identification of the binding roles of terminal and internal glycan epitopes using enzymatically synthesized N-glycans containing tandem epitopes

“…63 As expected, BA-01 and BA-21 , both with terminal Neu5Acα2–6Galβ1–4GlcNAc (s6LacNAc) epitope, presented strong binding, and the binding to BA-21 appeared higher than BA-01 . Although the internal s6LacNAc could not directly bind the swine virus (no binding to BA-23 , which only has internal s6LacNAc), its presence still resulted in the higher binding of BA-21 compared to BA-01 , clarifying that internal s6LacNAc facilitated the binding of terminal s6LacNAc.…”

Recent Developments and Applications of the MMPBSA Method

“…They also utilized a quantitative structure activity relationship (QSAR) model to improve the correlation to 0.88, combining affinities from MMPBSA, QM/MMGBSA, and Glide scoring (Slynko et al, 2014 ). There were other attractive targets including indoleamine 2,3-dioxygenase 1 (Zou et al, 2017 ), translationally controlled tumor protein (Kumar R. et al, 2017 ), estrogen receptor (Anbarasu and Jayanthi, 2017 ), MutT homolog 1 (Zhou et al, 2016 ), survivin (Sarvagalla et al, 2016 ), CD44 (Nguyen et al, 2016 ), calmodulin (Gonzalez-Andrade et al, 2016 ), androgen receptor (Liu H. L. et al, 2016 ), human topoisomerase I (Guruge et al, 2016 ), Mcl-1 (Zhao et al, 2015 ), vascular endothelial growth factor receptor-2 (Wu et al, 2015 ), tubulin (Liao et al, 2014a , b ; Santoshi and Naik, 2014 ; Suri and Naik, 2015 ; Suri et al, 2015 ), the Hsp70 protein family (Bhattacharjee et al, 2015 ; Schneider et al, 2016 ), the Hsp90 protein family (Arba et al, 2015 ), glucose 6-phosphate dehydrogenase (Obiol-Pardo et al, 2014 ; Zhao et al, 2014 ), lysozyme (Zhan et al, 2015 ), p53 (Verma S. et al, 2016 ), wheat germ agglutinin (Parasuraman et al, 2014 ), bromodomains (Muvva et al, 2014 ), matrix metalloproteinases (Zhou et al, 2014 ), protein arginine methyltransferases (Hong et al, 2014 ; Yan et al, 2014 ), human arsenic methyltransferase (Abro and Azam, 2016 ), Atox1 proteins (Wang X. L. et al, 2014 ), tyrosyl-DNA phosphodiesterase 2 (Kossmann et al, 2016 ), and urokinase-type plasminogen activator (Sa et al, 2014 ).…”

Lectins: an effective tool for screening of potential cancer biomarkers

“…Neu5Ac N-linked Nagata and Burger, 1972;Parasuraman et al, 2014 White button mushroom (Agaricus bisporus) lectin…”