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豆科植物降香黄檀(Dalbergia odorifera (Lour.) Stokes)中植物化合物的二肽基肽酶IV抑制作用:分子对接研究与ADME-Tox预测方法

Dipeptidyl peptidase IV inhibition of phytocompounds from (Lour.) Stokes: molecular docking study and ADME-Tox prediction approach.

作者信息

Supandi Supandi, Wulandari Mesy Savira, Samsul Erwin, Azminah Azminah, Purwoko Reza Yuridian, Herman Herman, Kuncoro Hadi, Ibrahim Arsyik, Silfi Ambarwati Neneng Siti, Rosmalena Rosmalena, Azizah Rizqi Nur, Paramita Swandari, Ahmad Islamudin

机构信息

Department of Pharmaceutical Analysis, Faculty of Pharmacy and Science, Universitas Muhammadiyah Prof. Dr. HAMKA, South Jakarta, Indonesia.

Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia.

出版信息

J Adv Pharm Technol Res. 2022 Jul-Sep;13(3):207-215. doi: 10.4103/japtr.japtr_376_22. Epub 2022 Jul 5.

Abstract

The present study examines the potential activity prediction based on free binding energy (ΔG) and interaction confirmation of phytocompounds from (Lour.) Stokes with macromolecule protein receptor of dipeptidyl peptidase IV (DPP-IV) using molecular docking studies and physicochemical and pharmacokinetic properties (ADME-Tox) prediction approaches. The active subsites of the DPP-IV receptor macromolecule protein Protein Data Bank (ID: 1 × 70) were docked using Autodock v4.2.6 (100 docking runs). A grid box of 52 × 28 × 26 Å points spaced by 0.37 Å was centered on the active site of x = 40.926 Å; y = 50.522 Å; z = 35.031 Å. For ADME-Tox prediction, Swiss ADME online-based application programs were used. The results show that 12 pythocompounds from have the potential as DPP-IV inhibitors based on ΔG value and interaction conformation. There are five pythocompounds with lower ΔG values and inhibition constants than the native ligand and seven pythocompounds with ΔG values and inhibition constants close to the native ligand. The 12 compounds form an interaction conformation at the active subsites of the DPP-IV receptor. At the same time, the results of the ADME-Tox prediction analysis showed that the 12 compounds had different physicochemical and pharmacokinetic properties.

摘要

本研究采用分子对接研究以及物理化学和药代动力学性质(ADME-Tox)预测方法,基于游离结合能(ΔG)以及来自假人参(Lour.) Stokes的植物化合物与二肽基肽酶IV(DPP-IV)大分子蛋白受体的相互作用构象,来检验潜在的活性预测。使用Autodock v4.2.6(进行100次对接运行)对DPP-IV受体大分子蛋白的蛋白质数据库(ID:1×70)的活性亚位点进行对接。一个由52×28×26 Å点组成、间距为0.37 Å的网格框以x = 40.926 Å;y = 50.522 Å;z = 35.031 Å的活性位点为中心。对于ADME-Tox预测,使用了基于瑞士ADME在线的应用程序。结果表明,基于ΔG值和相互作用构象,来自假人参的12种植物化合物具有作为DPP-IV抑制剂的潜力。有5种植物化合物的ΔG值和抑制常数低于天然配体,7种植物化合物的ΔG值和抑制常数与天然配体接近。这12种化合物在DPP-IV受体的活性亚位点形成相互作用构象。同时,ADME-Tox预测分析结果表明这12种化合物具有不同的物理化学和药代动力学性质。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c0b7/9355056/889633760718/JAPTR-13-207-g001.jpg

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