Antoniciello Federico, Roncarati Davide, Zannoni Annamaria, Chiti Elena, Scarlato Vincenzo, Chiappori Federica
Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy.
Istituto di Tecnologie Biomediche-Consiglio Nazionale Delle Ricerche (ITB-CNR), Segrate (Mi), Italy.
Front Mol Biosci. 2022 May 11;9:887564. doi: 10.3389/fmolb.2022.887564. eCollection 2022.
Antibiotic-resistant bacterial pathogens are a very challenging problem nowadays. is one of the most widespread and successful human pathogens since it colonizes half of the world population causing chronic and atrophic gastritis, peptic ulcer, mucosa-associated lymphoid tissue-lymphoma, and even gastric adenocarcinoma. Moreover, it displays resistance to numerous antibiotics. One of the pivotal transcription factors, HP1043, plays a fundamental role in regulating essential cellular processes. Like other bacterial transcription factors, HP1043 does not display a eukaryote homolog. These characteristics make HP1043 a promising candidate to develop novel antibacterial strategies. Drug repositioning is a relatively recent strategy employed in drug development; testing approved drugs on new targets considerably reduces the time and cost of this process. The combined computational and approach further reduces the number of compounds to be tested . Our aim was to identify a subset of known drugs able to prevent HP1043 binding to DNA promoters. This result was reached through evaluation by molecular docking the binding capacity of about 14,350 molecules on the HP1043 dimer in both conformations, bound and unbound to the DNA. Employing an ad hoc pipeline including MMGBSA molecular dynamics, a selection of seven drugs was obtained. These were tested by electrophoretic mobility shift assay to evaluate the HP1043-DNA interaction. Among these, three returned promising results showing an appreciable reduction of the DNA-binding activity of HP1043. Overall, we applied a computational methodology coupled with experimental validation of the results to screen a large number of known drugs on one of the essential transcription factors. This methodology allowed a rapid reduction of the number of drugs to be tested, and the drug repositioning approach considerably reduced the drug design costs. Identified drugs do not belong to the same pharmaceutical category and, by computational analysis, bound different cavities, but all display a reduction of HP1043 binding activity on the DNA.
抗生素耐药性细菌病原体是当今一个极具挑战性的问题。幽门螺杆菌是最广泛传播且最为成功的人类病原体之一，因为它定植于全球一半的人口中，会引发慢性萎缩性胃炎、消化性溃疡、黏膜相关淋巴组织淋巴瘤，甚至胃腺癌。此外，它对多种抗生素具有耐药性。关键转录因子之一HP1043在调节基本细胞过程中发挥着重要作用。与其他细菌转录因子一样，HP1043没有真核生物同源物。这些特性使HP1043成为开发新型抗菌策略的有前景的候选对象。药物重新定位是药物开发中一种相对较新的策略；在新靶点上测试已批准的药物可大幅减少这一过程的时间和成本。计算与实验相结合的方法进一步减少了待测试化合物的数量。我们的目标是识别出一组已知药物，它们能够阻止HP1043与DNA启动子结合。通过分子对接评估约14350种分子在HP1043二聚体处于结合和未结合DNA的两种构象下的结合能力，从而得出这一结果。采用包括MMGBSA分子动力学的专门流程，筛选出了七种药物。通过电泳迁移率变动分析对这些药物进行测试，以评估HP1043与DNA的相互作用。其中，三种药物给出了有前景的结果，显示HP1043的DNA结合活性明显降低。总体而言，我们应用了一种计算方法，并结合结果的实验验证，在一种关键转录因子上筛选了大量已知药物。这种方法能够迅速减少待测试药物的数量，并且药物重新定位方法大幅降低了药物设计成本。所识别出的药物不属于同一药物类别，通过计算分析，它们结合不同的腔，但都显示出HP1043对DNA的结合活性降低。
