+ This section focuses on investigating the potential interactions between Maleimide and + two key enzymes, Alginate Lyase and Alpha-Amylase, through molecular docking analysis. + Utilizing computational tools, we identified the active sites of the enzymes and + evaluated their compatibility with Maleimide binding. The results indicate that neither + enzyme is hindered by the presence of Maleimide, suggesting potential applicability for + future delivery systems. +
+ ++ We explore the potential binding of Maleimide with Alginate Lyase and Alpha-Amylase. By + leveraging molecular docking analysis and active site identification using Pymol, + CB-Dock, and literature review we draw conclusions on the compatibility of these enzymes + with a liposome, considering the implications for future applications in drug delivery + systems. +
+ +1. Protein Structure Acquisition
++ 3D structures of the described enzymes used were retrieved from the Protein Data + Bank (PDB). The specific PDB identifiers for the enzymes are as follows: +
+Alginate Lyase: PDB Identifier 1HV6 (Figure 1)
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+ Figure 1. 3D representation of Alginate Lyase in Pymol
+ +Alpha-Amylase: PDB Identifier 1MWO (Figure 2)
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+ Figure 2. 3D representation of Alpha-Amylase in Pymol.
+ +2. Molecular Docking Analysis
++ CB-Dock was used to predict the binding interactions between each enzyme and + Maleimide. The binding site of the enzymes allows us to understand whether it would + be possible to deliver these in the future using a liposome. +
++ 3. Active Site Identification and Literature Review +
++ We conducted a literature review to identify the active site of Alginate Lyase and + Alpha-Amylase. This information allowed us to interpret the docking results and + identify whether the activity of the enzymes is being compromised. +
+1. Interaction Between Alpha-Amylase and Maleimide
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+ + Figure 3. Interaction between Alpha Amylase and maleimide predicted by + CB-Dock. The structure represents the binding site of Alpha-Amylase. +
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+ + Figure 4. Vina Score of -4.6 is associated with the most favourable binding + site of Alpha-Amylase. +
+ ++ 2. Interaction Between Alginate Lyase and Maleimide +
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+ + Figure 5. Interaction between Alginate Lyase and maleimide predicted by + CB-Dock. The structure represents the binding site of Alginate Lyase. +
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+ + Figure 6. Vina Score of -4.3 is associated with the most favourable binding + site of Alginate Lyase. +
+ +1. Literature Review
+a. Alginate Lyase
+ ++ The active site of Alginate Lyase includes glutamine residues (Gln134, Gln138), + tyrosine residues (Tyr180, Tyr246, Tyr249) histidine residues (His192, His245), + tryptophan residue (Trp141), asparagine residue (Asn191), aspartic acid residue + (Asp314), and arginine residues (Arg88, Arg342, Arg306, Arg312) (Yoon, et. al, + 2001). +
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+ + Figure 7. The bound trisaccharide molecule on the active site of Alginate + Lyase. The Figure shows the bound trisaccharide molecule and the surrounding + amino acid residues and water molecules interacting with the trisaccharide. + The trisaccharide molecule is represented by means of an orange ball-and-stick + model. The side chains of Tyr and Trp, Asn and Gln, Asp, Arg, and His residues + are coloured yellow, green, red, cyan and purple, respectively (Yoon, et. al, + 2001). +
+ +b. Alpha-Amylase
+ ++ The active site of Alpha-Amylase includes tyrosine residue (Tyr199, Tyr62), + tryptophan residue (Trp224), lysine residue (Lys201), histidine residue (His288), + phenylalanine residue (Phe159), aspartic acid residue (Asp289, Asp198), arginine + residue (Arg196), and glutamic acid residue (Glu222). +
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+ + Figure 8. Active site residues of Alpha-Amylase. W stands for Trp, K stands + for Lys, Y stands for Tyr, E stands for Glu, F stands for Phe, D stands for + Asp, H stands for His, and R stands for Arg (Linden, et. al, 2003). +
+ +2. Maleimide and Alpha-Amylase Interaction
++ Based on the literature review we performed, Alpha-Amylase does not bind to + maleimide with its active site. The residues predicted by CB-Dock software do not + align with the documented active site residues. This means that the active site of + Alpha-Amylase would remain unobstructed and the enzyme’s function will not be + disrupted. +
+3. Maleimide and Alginate Lyase Interaction
++ Based on the literature review we performed, Alginate Lyase also does not bind to + maleimide with its active site. The residues predicted by CB-Dock software do not + align with the documented active site residues. +
++ Through a computational investigation, we have revealed that both Alginate Lyase and + Alpha-Amylase maintain their enzymatic functionalities without significant hindrance + from Maleimide. Our study underscores the potential feasibility of utilizing these + enzymes for drug delivery purposes, without compromising their essential catalytic + activities. +
+ ++ Linden, A., Mayans, O., Meyer-Klaucke, W., Antranikian, G., & Wilmanns, M. (2003). + Differential regulation of a hyperthermophilic α-amylase with a novel (ca,Zn) + two-metal center by zinc. Journal of Biological Chemistry, 278(11), 9875–9884. + https://doi.org/10.1074/jbc.m211339200 +
++ Yoon, H.-J., Hashimoto, W., Miyake, O., Murata, K., & Mikami, B. (2001). Crystal + structure of alginate lyase A1-III complexed with Trisaccharide product at 2.0 Å + Resolution. Journal of Molecular Biology, 307(1), 9–16. + https://doi.org/10.1006/jmbi.2000.4509 +
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