摘要
力达霉素是我国从土壤中筛选出的一个新的烯二炔类抗肿瘤抗生素,以力达霉素(LDP-AE)为基础,制备的重组融合蛋白(LDP-D3、Fv-LDP、Fv-LDP-D3)及其抗体偶联药物(LDP-D3-AE、Fv-LDP-AE、Fv-LDP-D3-AE)具有良好的抗肿瘤活性,但其相关蛋白结构尚未解析,所合成的抗体偶联药物结构是否稳定也尚未验证。基于以上研究背景,采用AlphaFold3对Fv-LDP、LDP-D3、Fv-LDP-D3重组融合蛋白的三级折叠结构进行预测,将LDP及3种重组融合蛋白分别与AE对接得到LDP-AE、LDP-D3-AE、Fv-LDP-AE和Fv-LDP-D3-AE 4种复合物,通过动力学模拟及结合自由能计算分析了4种复合物结构的稳定性,其中Fv是抗EGFR单链可变区片段,D3是人血清白蛋白(HSA)的结构域Ⅲ,LDP是力达霉素(LDM)的辅基蛋白,AE是LDM的活性烯二炔发色团。分子对接结果显示4种蛋白质均能与AE形成稳定结构,且均结合在LDP片段部分。采用多种方法对动力学模拟结果进行深入分析探讨,不同的分析方法之间可以相互印证,结果表明LDP、LDP-D3、Fv-LDP和Fv-LDP-D3均能与AE形成结构稳定的复合物,其中范德华力在这4个复合物形成的过程中起着重要作用,氢键作用也有相当一部分的贡献。
Lidamycin is a novel enediyne-class antitumor antibiotic isolated from soil samples in China.The recombinant fusion proteins(LDP-D3,Fv-LDP,Fv-LDP-D3)and their antibody-conjugated drugs(LDP-D3-AE,Fv-LDP-AE,Fv-LDP-D3-AE),constructed based on lidamycin(LDP-AE),have demonstrated potent anti-tumor activity.However,the structural information of these protein remain unsolved,and the stability of the synthesized antibody-drug conjugates has yet to be confirmed.To address this gap,AlphaFold3 was utilized to predict the tertiary folding structures of the recombinant fusion proteins Fv-LDP,LDP-D3,and Fv-LDP-D3.These proteins were then docked with AE,yielding four complexes:LDP-AE,LDP-D3-AE,Fv-LDP-AE,and Fv-LDP-D3-AE.The structural stability of these four complexes was analyzed through molecular dynamics simulations and binding free energy calculations.Specifically,Fv represented the single-chain variable fragment(scFv)of anti-EGFR,D3 was domainⅢof human serum albumin(HSA),LDP was the ligand-binding protein of lidamycin(LDM),and AE refered to the active enediyne chromophore of LDM.Molecular docking results revealed that all four proteins form stable structures with AE,with binding occurring specifically within the LDP fragment regions.Multiple analytical methods were applied to further analyze the molecular dynamics simulation results,and the results corroborated each other.The results demonstrate that LDP,LDP-D3,Fv-LDP,and Fv-LDP-D3 can all form structurally stable complexes with AE with Van der Waals forces playing a crucial role in complexes formation and hydrogen bonding providing additional stability.
作者
刘梦婷
郭一涵
孟姿
刘思雨
韩田超
赵文伯
LIU Meng-ting;GUO Yi-han;MENG Zi;LIU Si-yu;HAN Tian-chao;ZHAO Wen-bo(School of Chemistry and Chemical Engineering,Zhengzhou Normal University,Zhengzhou 450000,China)
出处
《化学试剂》
2025年第8期16-22,共7页
Chemical Reagents
基金
2024年国家级大学生创新创业训练计划项目(202412949005)
郑州师范学院大学生创新训练计划项目(DCY2023003)。
关键词
蛋白质结构预测
分子对接
分子动力学模拟
抗体偶联药物
力达霉素
Protein structure prediction
molecular docking
molecular dynamics simulation
antibody-conjugated drugs
lidamycin
