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Deciphering the Molecular Basis of Mutated Binding Site Bromodomain-Ligand Complexes: Insights from Molecular Dynamics Simulations and Decoded Interaction Fingerprint Analysis Riandono, Fransiscus Deddy
Jurnal Ilmu Farmasi dan Farmasi Klinik Vol 20, No 2 (2023)
Publisher : Universitas Wahid Hasyim Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31942/jiffk.v20i2.8760

Abstract

This study aims to predict structural stability changes and to identify the molecular determinants of ligand-bromodomain complex interactions that undergo mutations in the ligand binding site (LBS) using computational chemistry methods. The stability changes of the complexes were investigated using Molecular Dynamics (MD) simulations during a 25 ns production run. The identification of molecular interaction determinants was performed by decoding the interaction fingerprint, utilizing the output of trajectory data of the MD simulations, which were converted into a series of pdb files along the time step. The system preparations were done using CHARMM-GUI. The MD simulations were carried out using the GROMACS program. Protein-ligand interaction fingerprints (PLIF) were identified using the PyPLIF-HIPPOS program. This study successfully predicted the stability of both wild-type and mutated ligand-bromodomain complex structures, where the W81A mutation led to a decrease in complex stability. The key residues and non-hydrophobic interaction types responsible for the stabilities were identified as TRP81 aromatic edge-to-face, TYR139 aromatic edge-to-face, and TYR139 aromatic face-to-face.
Identifikasi Determinan Molekul Interaksi STK630921 pada Interleukin-17A Riandono, Fransiscus Deddy; Istyastono, Enade Perdana
JSFK (Jurnal Sains Farmasi & Klinis) Vol 9 No 1 (2022): J Sains Farm Klin 9(1), April 2022
Publisher : Fakultas Farmasi Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jsfk.9.1.57-63.2022

Abstract

Interleukin-17A (IL-17A) merupakan sitokin pro-inflamasi yang terlibat dalam patogenesis beberapa penyakit, antara lain psoriasis, rheumatoid arthritis, kanker, diabetes dan penyakit ginjal stadium akhir. Peningkatan kadar serum IL-17A memberikan petunjuk adanya keterkaitan antara IL-17A pada kejadian nefropati diabetik. Keterkaitan ini juga diperjelas dengan temuan bahwa penghambatan aktivitas IL-17A dapat menurunkan albuminuria, cedera ginjal dan menunda perkembangan nefropati diabetik. Peranan IL-17A ini menjadikannya sebagai pilihan target potensial terapi nefropati diabetik yang sejauh ini bertumpu pada pengendalian optimal sistem renin angiotensin. Penelitian ini bertujuan mengidentifikasi determinan molekul interaksi STK630921 pada IL-17A. Penelitian dilakukan dengan penambatan molekul STK630921 pada protein IL-17A, dilanjutkan dengan simulasi dinamika molekul selama 15 ns. Identifikasi determinan molekul dilakukan menggunakan bantuan perangkat lunak PyPLIF-HIPPOS terhadap hasil simulasi dinamika molekul. Penelitian ini berhasil mengidentifikasikan asam-asam amino yang berperan penting yaitu His29, Trp67, Asn27, Lys114 dan Glu95 dengan interaksi aromatik dan interaksi hidrogen sebagai jenis interaksi yang berperan pada aktivitas STK630921 pada struktur protein 4HR9.