Molecular Docking of Interaction between E-Cadherin Protein and Conformational Structure of Cyclic Peptide ADTC3 (Ac-CADTPC-NH2) Simulated on 20 ns

DOI: https://doi.org/10.14710/jksa.20.1.30-36
License URL: http://creativecommons.org/licenses/by-sa/4.0/

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Article Info
Published: 01-04-2017
Section: Research Articles
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Pengobatan penyakit yang menyerang otak sangat sulit dilakukan karena penghantaran molekul obat menuju otak terhalang oleh molekul-molekul blood-brain barrier (BBB). Untuk mengatasinya telah dikembangkan metode baru dengan memodulasi junction antar sel menggunakan peptida. Salah satu peptida yang diperkirakan mampu memodulasi adalah ADTC3, yang diturunkan dari susunan asam amino kadherin. Modulasi terjadi diduga karena interaksi antara ADTC3 dengan E-kadherin. Pada penelitian ini telah dihitung energi interaksi antara ADTC3 dengan E-kadherin. Metode yang digunakan adalah dinamika molekul (DM) dan molecular docking. Hasil penelitian menunjukkan bahwa peptida siklik ADTC3 (Ac-CADTPC-NH2) hasil simulasi 20 ns (20.000 ns) berinteraksi kuat dengan domain EC1 E-kadherin dengan energy binding sebesar -31,55 kJ.mol-1 dan tetapan inhibisi Ki sebesar 2,96 µM pada konformasi ke-4487. Interaksi yang kuat ini diperkirakan sebagai daya penggerak memodulasi junction antar sel. Interaksi antara ADTC3 dengan E-kadherin terjadi pada situs residu E-kadherin Asp1, Trp2, Val3, Ile4, Lys25, Met92 yang berada pada daerah adhesion arm-acceptor pocket.

Keywords

ADTC3; E-cadherin domain EC1; Gromacs; docking

  1. Atiatul Manna 
    Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University Jl. Prof. Soedarto, SH., Tembalang, Semarang, Indonesia
  2. Marlyn Dian Laksitorini 
    Faculty of Pharmacy, Gadjah Mada University, Indonesia
  3. Dwi Hudiyanti  Orcid Scopus Sinta
    Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University Jl. Prof. Soedarto, SH., Tembalang, Semarang, Indonesia
  4. Parsaoran Siahaan  Scopus Sinta
    Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University Jl. Prof. Soedarto, SH., Tembalang, Semarang, Indonesia
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