Discovery and Structure-Based Optimization of 2‑Ureidothiophene-3-carboxylic Acids as Dual Bacterial RNA Polymerase and Viral Reverse Transcriptase Inhibitors

We are concerned with the development of novel anti-infectives with dual antibacterial and antiretroviral activities for MRSA/HIV-1 co-infection. To achieve this goal, we exploited for the first time the mechanistic function similarity between the bacterial RNA polymerase (RNAP) “switch region” and the viral non-nucleoside reverse transcriptase inhibitor (NNRTI) binding site. Starting from our previously discovered RNAP inhibitors, we managed to develop potent RT inhibitors effective against several resistant HIV-1 strains with maintained or enhanced RNAP inhibitory properties following a structure-based design approach. A quantitative structure–activity relationship (QSAR) analysis revealed distinct molecular features necessary for RT inhibition. Furthermore, mode of action (MoA) studies revealed that these compounds inhibit RT noncompetitively, through a new mechanism via closing of the RT clamp. In addition, the novel RNAP/RT inhibitors are characterized by a potent antibacterial activity against S. aureus and in cellulo antiretroviral activity against NNRTI-resistant strains. In HeLa and HEK 293 cells, the compounds showed only marginal cytotoxicity.本研究致力于开发针对耐甲氧西林金黄色葡萄球菌（Methicillin-resistant Staphylococcus aureus, MRSA）/人类免疫缺陷病毒1型（Human Immunodeficiency Virus Type 1, HIV-1）共感染的兼具抗菌与抗逆转录病毒双重活性的新型抗感染药物。为实现该研究目标，我们首次利用了细菌RNA聚合酶（RNA polymerase, RNAP）“开关区域”与病毒非核苷类逆转录酶抑制剂（non-nucleoside reverse transcriptase inhibitor, NNRTI）结合位点之间的机制功能相似性。基于本团队此前发现的RNAP抑制剂，通过基于结构的设计策略，我们成功开发出强效逆转录酶（reverse transcriptase, RT）抑制剂，该抑制剂对多种耐药HIV-1毒株有效，且保留或增强了RNAP抑制活性。定量构效关系（quantitative structure–activity relationship, QSAR）分析揭示了RT抑制所需的独特分子特征。进一步的作用模式（mode of action, MoA）研究表明，此类化合物通过一种全新的机制——闭合RT钳状结构——以非竞争性方式抑制RT活性。此外，这类新型RNAP/RT抑制剂对金黄色葡萄球菌（Staphylococcus aureus, S. aureus）展现出强效抗菌活性，且对耐NNRTI毒株具有细胞水平的抗逆转录病毒活性。在海拉（HeLa）细胞与人类胚胎肾293（HEK 293）细胞中，此类化合物仅表现出微弱的细胞毒性。