Bahramimehr Faranak, Guthart Axel, Kurz Stefanie, Hai Yuanping, Dawood Mona, Yücer Rümeysa, Shahhamzehei Nasim, Weiskirchen Ralf, Roth Wilfried, Stremmel Wolfgang, Bringmann Gerhard, Efferth Thomas
Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
Department of Molecular Biology, Faculty of Medical Laboratory Science, Al-Neelain University, Khartoum 11121, Sudan.
Molecules. 2025 Apr 24;30(9):1897. doi: 10.3390/molecules30091897.
Crohn's disease is an inflammatory bowel disease (IBD) that currently lacks satisfactory treatment options. Therefore, new targets for new drugs are urgently needed to combat this disease. In the present study, we investigated the transcriptomics-based mRNA expression of intestinal biopsies from patients with Crohn's disease. We compared the mRNA expression profiles of the ileum and colon of patients with those of healthy individuals. A total of 72 genes in the ileum and 33 genes in the colon were differentially regulated. Among these, six genes were overexpressed in both tissues, including , , , , , and . We further focused on /oncostatin M. To confirm the responsiveness of intestinal tissues from patients with Crohn's disease to oncostatin M inhibition, we examined the expression of the oncostatin M using immunohistochemistry in patient biopsies as well as in kindlin-1 and kindlin-2 knockout mice, which exhibit an inflammatory bowel disease (IBD) phenotype, and found strong oncostatin M expression in all samples examined. Next, we conducted a drug-repurposing study using the supercomputer MOGON and bioinformatic methods. A total of 13 candidate compounds out of 1577 FDA-approved drugs were identified by PyRx-based virtual drug screening and AutoDock-based molecular docking. Their lowest binding energies (LBEs) ranged from -10.46 (±0.08) to -8.77 (±0.08) kcal/mol, and their predicted inhibition constants (pK) ranged from 21.62 (±2.97) to 373.78 (±36.78) nM. Ecamsule has an interesting stereostructure with two C-symmetric enantiomers (1,4-1',4' and 1,4-1',4') ( and ) and one diastereomer (1,4-1',4') (). These three stereoisomers showed strong, albeit differing, binding affinities in molecular docking. As examined by nuclear magnetic resonance and polarimetry, the 1,4-1',4' isomer was the stereoisomer present in our commercially available preparations used for microscale thermophoresis. Ecamsule () was chosen for in vitro validation using recombinant oncostatin M and microscale thermophoresis. Considerable dissociation constants were obtained for ecamsule after three repetitions with a K value of 11.36 ± 2.83 µM. Subsequently, we evaluated, by qRT-PCR, the efficacy of ecamsule () as a potential drug that could prevent oncostatin M activation by inhibiting downstream inflammatory marker genes (, , and ). In conclusion, we have identified oncostatin M as a promising new drug target for Crohn's disease through transcriptomics and ecamsule as a potential new drug candidate for Crohn's disease through a drug-repurposing approach both in silico and in vitro.
克罗恩病是一种炎症性肠病（IBD），目前缺乏令人满意的治疗方案。因此，迫切需要新的药物靶点来对抗这种疾病。在本研究中，我们调查了克罗恩病患者肠道活检组织基于转录组学的mRNA表达情况。我们将患者回肠和结肠的mRNA表达谱与健康个体的进行了比较。回。回肠中有72个基因、结肠中有33个基因的表达存在差异调节。其中，有6个基因在两种组织中均过度表达，包括 、 、 、 、 和 。我们进一步聚焦于 /抑瘤素M。为了证实克罗恩病患者的肠道组织对抑瘤素M抑制的反应性，我们在患者活检组织以及表现出炎症性肠病（IBD）表型的kindlin-1和kindlin-2基因敲除小鼠中，使用免疫组织化学检测了抑瘤素M的表达，发现在所有检测样本中均有强烈的抑瘤素M表达。接下来，我们使用超级计算机MOGON和生物信息学方法进行了药物再利用研究。通过基于PyRx的虚拟药物筛选和基于AutoDock的分子对接，在1577种FDA批准的药物中总共鉴定出13种候选化合物。它们的最低结合能（LBEs）范围为-10.46（±0.08）至-8.77（±0.08）kcal/mol，预测抑制常数（pK）范围为21.62（±2.97）至373.78（±36.78）nM。依卡倍特钠具有有趣的立体结构，有两种C对称对映体（1,4-1',4'和1,4-1',4'）（ 和 ）以及一种非对映异构体（1,4-1',4'）（ ）。这三种立体异构体在分子对接中显示出强烈的（尽管有所不同）结合亲和力。通过核磁共振和旋光测定法检测，1,4-1',4'异构体是我们用于微量热泳的市售制剂中存在的立体异构体。选择依卡倍特钠（ ）使用重组抑瘤素M和微量热泳进行体外验证。经过三次重复实验，依卡倍特钠获得了相当可观的解离常数，K值为11.36±2.83µM。随后，我们通过qRT-PCR评估了依卡倍特钠（ ）作为一种潜在药物通过抑制下游炎症标记基因（ 、 和 ）来预防抑瘤素M激活的功效。总之，我们通过转录组学确定抑瘤素M是克罗恩病一个有前景的新药物靶点，并且通过计算机模拟和体外的药物再利用方法确定依卡倍特钠是克罗恩病一种潜在的新候选药物。
