Gogoi Dhrubajyoti, Dutta Partha Pratim, Gogoi Bhaskarjyoti, Baruah Vishwa Jyoti, Paul Rasna, Sarmah Bhaswati, Baruah Anupaul, Kakoti Bibhuti Bhusan, Kalita Bulumoni, Dutta Prafulla, Yadav R N S
Programme of Biotechnology, Faculty of Science, Assam down town University, Guwahati, Assam, India.
Faculty of Pharmaceutical Science, Assam down town University, Guwahati, Assam, India.
Comput Biol Med. 2025 Sep;196(Pt C):110955. doi: 10.1016/j.compbiomed.2025.110955. Epub 2025 Aug 20.
The development of drug resistance in Plasmodium falciparum is predominantly associated with the mutations in Plasmodium falciparum dihydrofolate reductase (pfDHFR) enzyme, a crucial target for antifolate antimalarial medications such as pyrimethamine and cycloguanil. Specific nucleotide substitutions in the pfDHFR gene, occurring either singly or in various combinations, substantially reduce the effectiveness of antifolate treatments, thus intensifying the worldwide struggle against malaria.
The present investigation, pharmacophore modeling assisted virtual screening, and, in vitro investigations were conducted to address this resistance issue by identifying novel inhibitors targeting mutant pfDHFR. A ligand-oriented pharmacophore model (r = 0.94) was developed utilizing a dataset of 17 compounds exhibiting inhibitory activity spanning four orders of magnitude.
The most statistically robust hypothesis designated Hypo1, was subsequently employed as a three-dimensional query to conduct screening of cheminformatics repositories. The screening process incorporated drug-likeness parameters, ADME/Tox assessment, and pharmacophore mapping and validation techniques. Through molecular docking analyses and molecular dynamics (MD) simulations, we have identified 28 compounds that exhibited robust binding affinities to resistant variants of pfDHFR. The most promising candidates displayed in vitro antimalarial efficacy, indicating their potential to circumvent anti-folate drug resistance.
The top compound exhibited IC values of 30.822 μg/mL and 126.077 μg/mL against the 3D7 and Dd2 strains of P. falciparum, respectively, significantly outperforming other compounds (p < 0.05). This comprehensive approach underscores the critical role of integrating pharmacophore modeling with experimental methods to discover alternative antimalarial therapies.
恶性疟原虫耐药性的发展主要与恶性疟原虫二氢叶酸还原酶（pfDHFR）的突变有关，pfDHFR是乙胺嘧啶和环氯胍等抗叶酸抗疟药物的关键靶点。pfDHFR基因中的特定核苷酸取代，单独或多种组合出现，会大幅降低抗叶酸治疗的效果，从而加剧全球对抗疟疾的斗争。
本研究通过识别针对突变型pfDHFR的新型抑制剂来解决这一耐药问题，进行了药效团建模辅助虚拟筛选和体外研究。利用17种具有四个数量级抑制活性的化合物数据集开发了一个面向配体的药效团模型（r = 0.94）。
统计学上最可靠的假设Hypo1随后被用作三维查询，对化学信息学数据库进行筛选。筛选过程纳入了类药性质参数、ADME/Tox评估以及药效团映射和验证技术。通过分子对接分析和分子动力学（MD）模拟，我们鉴定出28种对pfDHFR耐药变体具有强大结合亲和力的化合物。最有前景的候选物显示出体外抗疟效果，表明它们有克服抗叶酸耐药性的潜力。
顶级化合物对恶性疟原虫的3D7和Dd2菌株的IC值分别为30.822μg/mL和126.077μg/mL，显著优于其他化合物（p < 0.05）。这种综合方法强调了将药效团建模与实验方法相结合以发现替代抗疟疗法的关键作用。
