Abstract
Platelet-activating factor receptors (PAF-r) is known as one of the receptors that affect asthma, while the Y-21480 ligand is reported as an effective, specific, and active PAF-r antagonist for asthma patients. Research in building structure-based virtual screening protocol (SBVS) for identification of PAF-r ligand inhibitors has been performed, the receptor crystal structure was obtained from the Protein Data Bank (PDB ID: 5zkp), while the ligand used as a leading compound is Y-24180, obtained from U.S. National Library of Medicine. Interactions between ligands and receptors are observed through molecular dynamics simulations using the YASARA program at intervals up to 20 nanoseconds, ligand-receptor binding stability occurs after a time interval of 2 nanoseconds, the lowest ligand-receptor binding energy occurs at a time interval of 1,401 picoseconds. Internal validation by re-docking 1,000 times the ligand to receptor resulted in a value of Root Mean Square Deviation (RMSD) of 0.6037 Å, confirmed that SBVS protocol was accurately able to reproduce the Y-24180 ligand pose on the 5zkp crystal structure, the protocol can be used as a new approach for investigation or design of compounds that have therapeutic potential as anti-asthma.
Highlights
Platelet-activating factor receptors (PAF-r) is known as one of the receptors that affect asthma, while the Y-21480 ligand is reported as an effective, specific, and active platelet-activating factor (PAF)-r antagonist for asthma patients
the receptor crystal structure was obtained from the Protein Data Bank
while the ligand used as a leading compound is Y-24180
Summary
Vol 11, No 1, March 2020 enzimatik dari biosintesis PAF bertanggung jawab pada peradangan akut dan kronis[20]. Pendekatan teoritis berbasis komputer atau uji in silico sangat penting untuk merancang, menemukan, dan optimisasi senyawa bioaktif dalam proses pengembangan obat[24], pendekatan ini membutuhkan waktu penelitian yang lebih sedikit dan biaya yang jauh lebih murah, penapisan data set molekul dari senyawa model dapat dijadikan proses yang efektif dalam mendesain obat[25]. Tujuan penelitian ini fokus pada simulasi in silico reseptor PAF dengan senyawa penuntun Y-24180 yang diketahui sebagai antagonis reseptor PAF[9], senyawa ini juga diketahui efektif menekan respons hiper-antigen yang diinduksi antigen pada hewan[26]. Hipotesis yang dibangun bahwa senyawa Y24180 dapat digunakan sebagai senyawa penuntun dalam pengembangan protokol penapisan virtual berbasis struktur (PVBS), dengan harapan protokol yang dihasilkan dari simulasi virtual ini dapat dipakai untuk melakukan pencarian senyawa obat baru untuk terapi asma, baik pada senyawa-senyawa sintesis, semi sintesis, ataupun pada senyawa bahan alam
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
