Obakachi Vincent A, Govender Krishna K, Govender Penny P
Department of Chemical Sciences, Doornfontein Campus, University of Johannesburg, P.O. Box 17011, Johannesburg, 2028, South Africa.
Mol Divers. 2025 Jul 10. doi: 10.1007/s11030-025-11263-x.
Breast cancer, a major global health challenge, is driven by aberrant receptor tyrosine kinase (RTK) signaling via epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor (VEGFR). This study employs a "Dynamic Scapping" workflow, integrating molecular docking, 500 ns molecular dynamics (MD) simulations, and MM/GBSA binding free energy calculations to identify natural products with potential for dual binding to EGFR (PDB: 1M17) and VEGFR (PDB: 3VHE). From ~ 20,000 natural products, virtual screening shortlisted 13 EGFR and 12 VEGFR hits, with Digitonin, Cyclamin, Vicenin-2, Glucosylorientin, and Nicotiflorin selected for EGFR, and Quercetagetin, Silychristin, Quercetin, Scutellarein, and Isorhamnetin for VEGFR, alongside references (Erlotinib, Pyrrolopyrimidine). MD simulations, conducted as single trajectories per system, revealed stable complexes (RMSD: 1.73-2.92 Å), with Digitonin, Cyclamin, and Silychristin showing binding energies (ΔG: - 84.29, - 81.47, - 63.33 kcal/mol) compared to references (Erlotinib: - 43.32 kcal/mol and Pyrrolopyrimidine: - 61.63 kcal/mol). Dynamic analyses (DCCM, PCA) indicated restricted motions, while per-residue decomposition highlighted interactions with Met769 (EGFR) and Cys919 (VEGFR). The MM/GBSA calculations excluded the entropy term, potentially affecting absolute binding energies but supporting relative ranking. These computational findings suggest Digitonin, Cyclamin, and Silychristin as candidates with the potential for dual binding to EGFR and VEGFR, addressing the need for accessible treatments globally and in regions like South Africa with high incidence rates. Experimental validation is essential to confirm their functional dual modulation and inhibitory potency for breast cancer therapy.
乳腺癌是一项重大的全球健康挑战,由表皮生长因子受体(EGFR)和血管内皮生长因子受体(VEGFR)介导的异常受体酪氨酸激酶(RTK)信号传导驱动。本研究采用“动态筛选”工作流程,整合分子对接、500纳秒分子动力学(MD)模拟和MM/GBSA结合自由能计算,以鉴定具有同时结合EGFR(PDB:1M17)和VEGFR(PDB:3VHE)潜力的天然产物。从约20000种天然产物中,虚拟筛选出13种EGFR命中物和12种VEGFR命中物,其中洋地黄皂苷、仙客来素、异荭草苷、葡萄糖基荭草素和芦丁被选用于EGFR,槲皮万寿菊素、水飞蓟宾、槲皮素、黄芩素和异鼠李素被选用于VEGFR,同时还有对照物(厄洛替尼、吡咯并嘧啶)。每个系统以单轨迹进行MD模拟,结果显示形成了稳定的复合物(RMSD:1.73 - 2.92 Å),与对照物(厄洛替尼:-43.32 kcal/mol和吡咯并嘧啶:-61.63 kcal/mol)相比,洋地黄皂苷、仙客来素和水飞蓟宾显示出结合能(ΔG:-84.29、-81.47、-63.33 kcal/mol)。动态分析(DCCM, PCA)表明运动受限,而逐个残基分解突出了与Met769(EGFR)和Cys919(VEGFR)的相互作用。MM/GBSA计算排除了熵项,这可能会影响绝对结合能,但支持相对排名。这些计算结果表明,洋地黄皂苷、仙客来素和水飞蓟宾有可能同时结合EGFR和VEGFR,满足全球以及南非等高发病率地区对可及治疗方法的需求。实验验证对于确认它们对乳腺癌治疗的功能双重调节和抑制效力至关重要。