Colorectal cancer (CRC) ranks third among all cancers in terms of prevalence. There is growing evidence that gut microbiota has a role in the development of colorectal cancer. Fusobacterium nucleatum is overrepresented in the gastrointestinal tract and tumor microenvironment of patients with CRC. This suggests the role of F. nucleatum as a potential risk factor in the development of CRC. Hence, we aimed to explore whole genomes of F. nucleatum strains related to CRC to predict potential therapeutic markers through a pan-genome integrated subtractive genomics approach. In the current study, we identified 538 proteins as essential for F. nucleatum survival, 209 non-homologous to a human host, and 12 as drug targets. Eventually, riboflavin synthase (RiS) was selected as a therapeutic target for further processing. Three different inhibitor libraries of lead-like natural products, i.e., cyanobactins (n = 237), streptomycins (n = 607), and marine bacterial secondary metabolites (n = 1226) were screened against it. After the structure-based study, three compounds, i.e., CMNPD3609 (−7.63) > Malyngamide V (−7.03) > ZINC06804365 (−7.01) were prioritized as potential inhibitors of F. nucleatum. Additionally, the stability and flexibility of these compounds bound to RiS were determined via a molecular dynamics simulation of 50 ns. Results revealed the stability of these compounds within the binding pocket, after 5 ns. ADMET profiling showed compounds as drug-like, non-permeable to the blood brain barrier, non-toxic, and HIA permeable. Pan-genomics mediated drug target identification and the virtual screening of inhibitors is the preliminary step towards inhibition of this pathogenic oncobacterium and we suggest mouse model experiments to validate our findings.

中文翻译：

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结直肠癌相关具核梭杆菌核黄素合酶的治疗靶标鉴定和抑制剂筛选。

就患病率而言，结直肠癌 (CRC) 在所有癌症中排名第三。越来越多的证据表明肠道微生物群在结直肠癌的发展中发挥作用。具核梭杆菌在 CRC 患者的胃肠道和肿瘤微环境中数量过多。这表明 F. nucleatum 作为 CRC 发展中的潜在风险因素的作用。因此，我们旨在探索与 CRC 相关的 F. nucleatum 菌株的全基因组，以通过泛基因组整合减法基因组学方法预测潜在的治疗标志物。在当前的研究中，我们确定了 538 种蛋白质对于 F. nucleatum 存活至关重要，209 种与人类宿主非同源，12 种作为药物靶标。最终，核黄素合酶 (RiS) 被选为进一步加工的治疗靶点。针对它筛选了三种不同的铅样天然产物抑制剂库，即蓝藻素 (n = 237)、链霉素 (n = 607) 和海洋细菌次级代谢产物 (n = 1226)。在基于结构的研究之后，三种化合物，即 CMNPD3609 (-7.63) > Malyngamide V (-7.03) > ZINC06804365 (-7.01) 被优先作为具核梭杆菌的潜在抑制剂。此外，这些与 RiS 结合的化合物的稳定性和灵活性是通过 50 ns 的分子动力学模拟确定的。结果揭示了 5 ns 后这些化合物在结合口袋内的稳定性。ADMET 分析表明化合物具有药物样性、不可渗透血脑屏障、无毒且可渗透 HIA。