A r t i c l e I n f o A b s t r a c t Keywords:ADTC3, E-cadherin domain EC1, Gromacs, dockingThe treatment of diseases that attack the brain is very difficult, because the delivery of drug molecules to the brain is often hindered by the molecules of blood-brain barrier (BBB). Thus, it was developed the new method using synthetic peptide which derived from the amino acids sequence of cadherin and ADTC3 predicted able to modulate the intercellular junction peptide. The intermolecular interaction between ADTC3 and Ecadherin is hypothesized as the driving force of modulation. In this research have been calculated the interaction energy between ADTC3 and E-cadherin. The method used in this research is molecular dynamics (MD) and molecular docking. The results show that cyclic peptide ADTC3 (Ac-CADTPC-NH2) simulated for 20 ns (20,000 ps) has considerable interaction with EC1 domain of E-cadherin which have the binding energies -31.55 kJ.mol -1 and inhibition constant Ki 2.96 μM at the 4487 conformation. This highly interaction energy was predicted as the driving force in modulating intercellular junctions. The binding site of E-cadherin reside on amino acid residues Asp1, Trp2, Val3, Ile4, Lys25, Met92 in the adhesion arm-acceptor pocket region. A b s t r a kKata kunci: ADTC3, E-cadherin domain EC1, Gromacs, docking 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 Ekadherin Asp1, Trp2, Val3, Ile4, Lys25, Met92 yang berada pada daerah adhesion armacceptor pocket.

Abstract. 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.

The treatment of diseases that attack the brain is very difficult, because the delivery of drug molecules to the brain is often hindered by the blood-brain barrier (BBB). So that the drug delivery is not right on the target cell. Thus, was developed a method in modulation of intercellular junctions using ADTC3 cadherin peptide, Where the cadherin peptide is derived from the cadherin sequence itself. The method used in this research is molecular dynamics (DM) and molecular docking. In this study have been evaluated some peptide conformation in modulating intercellular junction. The results show that cyclic peptide ADT-C3 (Ac-CADTPC-NH2) was conducted DM for 120 ns (120000 ps), which has considerable activity in modulating intercellular junctions with binding energies of -33.10 kJ.mol-1 and Ki of 1.58 μM at the 79187 ps conformation. The binding site on residues Asp1, Trp2, Ile4, Lys25, Ser26, Asn27, Met92 in the adhesion arm-acceptor pocket region.