通过机器学习和基于结构的分子对接模拟来识别活性化合物作为新型二二酶-4抑制剂
Shahid Ali1,2, Sibhghatulla Shaikh1,2, Khurshid Ahmad1,2
1Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea.
Journal of biomolecular structure & dynamics
|December 15, 2023
概括
研究人员通过将机器学习和虚拟查结合起来,发现一种新的2型糖尿病 (T2DM) 潜在治疗方法,以寻找二二酶4 (DPP4) 抑制剂. 化合物Z-997显示稳定结合DPP4,表明治疗潜力.
科学领域:
- 生物化学 生物化学
- 计算化学计算化学
- 药理学 药理学是指药理学的学科.
背景情况:
- 二基化酶4 (DPP4) 是2型糖尿病 (T2DM) 的治疗点.
- 现有的DPP4抑制剂具有不良副作用,因此需要更安全的替代品.
- 需要新的治疗策略来有效管理T2DM.
研究的目的:
- 为了识别用于2型糖尿病 (T2DM) 治疗的新型二基化酶4 (DPP4) 抑制剂.
- 开发和验证用于预测DPP4抑制活性的机器学习 (ML) 模型.
- 通过结合ML和基于结构的虚拟选方法选天然化合物库并识别选择性DPP4抑制剂.
主要方法:
- 在DPP4 IC50数据集上训练了两个ML模型,即随机森林 (RF) 和多层感知器 (MLP).
- 使用ML模型选一个自然化合物库,然后进行基于结构的虚拟选.
- 评估了化合物 (Z-614,Z-997) 的结合亲和力,药物相似性和与DPP的相互作用4.
- 进行了分子动力学 (MD) 模拟,以评估DPP4化合物复合物的稳定性.
主要成果:
- ML模型 (RF,MLP) 在预测DPP4抑制方面表现出高准确度 (AUC 0.93,0.91).
- 从自然图书馆中选择了217种化合物进行进一步选.
- Z-614和Z-997对DPP4催化口袋表现出高的结合亲和力和特异性.
- MD模拟表明Z-997比Z-614结合得更稳定,结合的自由能量为-70.3kJ/mol.
结论:
- 结合ML和基于结构的虚拟查方法成功识别了强大的DPP4抑制剂.
- 作为T2DM治疗的稳定DPP4抑制剂,Z-997显示出显著的治疗潜力.
- 对Z-997进行进一步的研究是有必要的,以使其成为一种新的抗糖尿病药物.
相关概念视频
Dipeptidyl Peptidase 4 Inhibitors
190
Dipeptidyl peptidase 4 (DPP-4) is a serine protease widely distributed in the body. It's involved in the inactivation of GLP-1 and GIP hormones, which are crucial for insulin regulation. DPP-4 inhibitors, such as sitagliptin (Januvia), saxagliptin (Onglyza), linagliptin (Tradjenta), alogliptin (Nesina), and vildagliptin (Galvus), help increase the proportion of active GLP-1, enhancing insulin secretion. These inhibitors work by competitively binding to DPP-4. This binding causes a...
190
Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Drug Discovery: Overview
7.9K
Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
7.9K
Ligand Binding Sites
12.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.9K


