Probing the Interaction between Cyclic ADTC1 Ac-CADTPPVC-NH2) Peptide with EC1-EC2 domain of E-cadherin using Molecular Docking Approach

12th Joint Conference on Chemistry

Siahaan, P.^1 ; Wuning, S.^1 ; Manna, A.^1 ; Prasasty, V.D.^2 ; Hudiyanti, D.^1

Departement of Chemistry, Faculty of Science and Mathematics, Diponegoro University, Indonesia^1

Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Indonesia^2

关键词: Amino acid alanines;    Best position;    E-cadherins;    Interaction properties;    Intermolecular interactions;    Microscopic and macroscopic properties;    Molecular docking;    Paracellular;   

Others  :  https://iopscience.iop.org/article/10.1088/1757-899X/349/1/012050/pdf
DOI  :  10.1088/1757-899X/349/1/012050

来源: IOP

【 摘 要 】

Deeply understanding that intermolecular interaction between molecules on the paracellular pathway has given insight to its microscopic and macroscopic properties. In the paracellular pathway, synthetic cyclic ADTC1 (Ac-CADTPPVC-NH2) peptide has been studied to modulate EC1-EC2 domain, computationally using molecular docking method. The aim of this research is to probe the effect of amino acid alanine (A) of ADTC1 on its interaction properties. The study carried out in two steps: 1. the optimization using GROMACS v4.6.5 program and; 2. Determination of the interaction properties using AutoDock 4.2 program. The interaction was done for A-J box, and the best position of the binding site and binding energy on the OC and CC ADTC1 peptides against the EC1-EC2 domain of E-cadherin was selected. The result showed that the CC of the F box ADTC1 has the best interaction with binding energy of - 26.36 kJ/mol and its energy was lower than ADTC5 without alanine amino acid. ADTC1 interacted with EC1 of EC1-EC2 on Asp1, Trp2, Val3, Ile4, Ile24, Lys25, Ser26, Asn27, and Met92 residues.