Rodríguez-Fonseca Rolando Alberto, Sixto-López Yudibeth, Fragoso-Vázquez M Jonathan, Flores-Mejía Raul, Cabrera-Pérez Laura Cristina, Vázquez-Moctezuma Ismael, Rosales-Hernández Martha Cecilia, Bello Martiniano, Martínez-Archundia M, Trujillo-Ferrara Jose Guadalupe, Becerra-Martínez Elvia, Correa-Basurto Jose
Laboratorio de Modelado Molecular, Diseno de farmacos y Bioinformatica, Escuela Superior de Medicina, Instituto Politecnico Nacional, Mexico, Plan de San Luis y Salvador Diaz Miron S/N, Col. Casco de Santo Tomas, Distrito Federal 11340. Mexico.
Departamento de Quimica Organica, Escuela Nacional de Ciencias, Biologicas, Instituto Politecnico Nacional, Prolongacion de Carpio y Plan de Ayala, Col. Casco de Santo Thomas, Mexico City 11340. Mexico.
Anticancer Agents Med Chem. 2017;17(10):1441-1454. doi: 10.2174/1871520617666170103092851.
The epigenetic regulation of genes in cancer could be targeted by inhibiting Histone deacetylase 6 (HDAC6), an enzyme involved in several types of cancer such as lymphoma, leukemia, ovarian cancer, etc.
Through in silico methods, a set of Phenyl butyric acid derivatives with possible HDAC6 inhibitory activity were designed, rendering monophenylamides and biphenylamides using tubacin (HDAC6 selective inhibitor) as reference.
The target compounds were submitted to theoretical ADMET analyses and their binding properties on different HDAC6 conformers were evaluated through docking calculations.
These in silico studies allowed us to identify a compound named B-R2B. In order to have more information about the B-R2B binding recognition properties on HDAC6, the B-R2B-HDAC6 complex was submitted through 100 ns-long Molecular Dynamics (MD) simulation coupled to MMGBSA approach, revealing that B-R2B is located at the entrance of HDAC6 active pocket, blocking the passage of the substrate without reaching the HDAC6 binding site. Based on these results, B-R2B was synthesized, characterized and biologically tested. The HDAC6 fluorometric drug discovery kit Fluor-de-Lys (ENZO Life Sciences Inc.) was used to determine the HDAC6 human inhibitory activity (IC50 value) of B-R2B compound. In addition, B-R2B show IC50 values on cancer cell lines (HeLa; IC50 = 72.6 µM), acute myeloid leukemia (THP-1; IC50 = 16.5 µM), human mast leukemia (HMC; IC50 = 79.29 µM) and chronic myelogenous leukemia (Kasumi; IC50 = 101 µM).
These results show that B-R2B is a HDAC6 inhibitor, specifically a non-competitive type in a similar way that tubacin does, according to MD simulations.
癌症中基因的表观遗传调控可通过抑制组蛋白去乙酰化酶6（HDAC6）来实现，HDAC6是一种参与多种癌症（如淋巴瘤、白血病、卵巢癌等）的酶。
通过计算机模拟方法，设计了一组可能具有HDAC6抑制活性的苯基丁酸衍生物，以tubacin（HDAC6选择性抑制剂）为参考合成了单苯基酰胺和联苯基酰胺。
对目标化合物进行理论ADMET分析，并通过对接计算评估其在不同HDAC6构象体上的结合特性。
这些计算机模拟研究使我们鉴定出一种名为B-R2B的化合物。为了获得更多关于B-R2B与HDAC6结合识别特性的信息，通过与MMGBSA方法相结合的100纳秒长分子动力学（MD）模拟提交了B-R2B-HDAC6复合物，结果表明B-R2B位于HDAC6活性口袋的入口处，在未到达HDAC6结合位点的情况下阻断了底物的通道。基于这些结果，合成、表征并对B-R2B进行了生物学测试。使用HDAC6荧光药物发现试剂盒Fluor-de-Lys（ENZO生命科学公司）测定B-R2B化合物对人HDAC6的抑制活性（IC50值）。此外，B-R2B在癌细胞系（HeLa；IC50 = 72.6 μM）、急性髓性白血病（THP-1；IC50 = 16.5 μM）、人肥大细胞白血病（HMC；IC50 = 79.29 μM）和慢性粒细胞白血病（Kasumi；IC50 = 101 μM）中也显示出IC50值。
这些结果表明，根据分子动力学模拟，B-R2B是一种HDAC6抑制剂，具体为非竞争性类型，与tubacin类似。
