Nyambo Kudakwashe, Soko Vivette, Tapfuma Kudzanai Ian, Motaung Bongani, Adu-Amankwaah Francis, Julius Lauren, Klein Ashwil, Keyster Marshall, Baatjies Lucinda, Smith Liezel, Govender Krishna Kuben, Ngxande Mkhuseli, Loxton Andre G, Mavumengwana Vuyo
DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.
South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.
Sci Rep. 2025 Feb 28;15(1):7109. doi: 10.1038/s41598-025-91096-8.
Computational approaches complement traditional in-vitro or in-vivo assays, significantly accelerating the drug discovery process by increasing the probability of identifying promising lead compounds. In this study, the apoptotic compounds were assessed for antimycobacterial activity and immunomodulatory potential in infected THP-1 macrophage cells. The antimycobacterial activity of the apoptotic compounds was evaluated using the minimum inhibitory concentration (MIC) assay. The immunomodulatory potential of the apoptotic compounds was determined on mycobacterial-infected THP-1 and non-infected THP-1 macrophage cells. The potential binding dynamics of the compounds against InhA were predicted using molecular docking, molecular dynamics, and MM-GBSA binding free energies. The in-vitro MIC assay showed that cepharanthine (CEP) had the highest antimycobacterial activity against Mycobacterium smegmatis mc155 and Mycobacterium tuberculosis H37Rv, with MICs of 3.1 and 1.5 µg/mL, respectively, followed by CP-31398 dihydrochloride hydrate (DIH) (MICs = 6.2 and 3.1 µg/mL, respectively), marinopyrrole A (MAR) (MICs = 25 and 12.5 µg/mL, respectively), and nutlin-3a (NUT) (MICs = 50 and 25 µg/mL, respectively). MICs for the rest of the drugs were > 200 µg/mL against both M. smegmatis mc155 and M. tuberculosis H37Rv. Furthermore, the growth of M. smegmatis mc155 in infected THP-1 macrophage cells treated with DIH, CEP, carboxyatractyloside potassium salt (CAR), and NUT was inhibited by the mentioned drugs. Cytokine profiling showed that DIH optimally regulated the secretion of IL-1β and TNF-α which potentially enhanced the clearance of the intracellular pathogen. Molecular dynamics simulations showed that NUT, MAR, 17-(allylamino)-17-demethoxygeldanamycin (17-AAG), and BV02 strongly bind to InhA. However, 17-AAG and BV02 did not show significant activity in-vitro. This study highlights the importance of probing already existing chemical scaffolds as a starting point for discovery of therapeutic agents against M. tuberculosis H37Rv using both pathogen and host directed approaches. The integration of molecular dynamics simulations provides valuable insights into potential scaffold modifications to enhance the affinity.
计算方法补充了传统的体外或体内试验，通过提高识别有前景的先导化合物的概率，显著加速了药物发现过程。在本研究中，评估了凋亡化合物在感染的THP-1巨噬细胞中的抗分枝杆菌活性和免疫调节潜力。使用最低抑菌浓度（MIC）试验评估凋亡化合物的抗分枝杆菌活性。在感染分枝杆菌的THP-1和未感染的THP-1巨噬细胞上测定凋亡化合物的免疫调节潜力。使用分子对接、分子动力学和MM-GBSA结合自由能预测化合物与InhA的潜在结合动力学。体外MIC试验表明，千金藤素（CEP）对耻垢分枝杆菌mc155和结核分枝杆菌H37Rv具有最高的抗分枝杆菌活性，MIC分别为3.1和1.5 μg/mL，其次是盐酸CP-31398水合物（DIH）（MIC分别为6.2和3.1 μg/mL）、海茴香吡咯A（MAR）（MIC分别为25和12.5 μg/mL）和Nutlin-3a（NUT）（MIC分别为50和25 μg/mL）。其余药物对耻垢分枝杆菌mc155和结核分枝杆菌H37Rv的MIC均>200 μg/mL。此外，DIH、CEP、羧基苍术苷钾盐（CAR）和NUT处理的感染THP-1巨噬细胞中耻垢分枝杆菌mc155的生长受到上述药物的抑制。细胞因子分析表明，DIH能最佳调节IL-1β和TNF-α的分泌，这可能增强细胞内病原体的清除。分子动力学模拟表明，NUT、MAR、17-（烯丙基氨基）-17-去甲氧基格尔德霉素（17-AAG）和BV02与InhA强烈结合。然而，17-AAG和BV02在体外未显示出显著活性。本研究强调了探索现有化学支架作为使用病原体和宿主导向方法发现抗结核分枝杆菌H37Rv治疗药物起点的重要性。分子动力学模拟的整合为增强亲和力的潜在支架修饰提供了有价值的见解。
