Department of Medicinal Chemistry, College of Pharmacy, Institute for Therapeutics Discovery and Development, and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55414-2959, USA.
J Chem Inf Model. 2009 Dec;49(12):2726-34. doi: 10.1021/ci900186w.
Anthrax is an infectious disease caused by Bacillus anthracis, a Gram-positive, rod-shaped, anaerobic bacterium. The lethal factor (LF) enzyme is secreted by B. anthracis as part of a tripartite exotoxin and is chiefly responsible for anthrax-related cytotoxicity. As LF can remain in the system long after antibiotics have eradicated B. anthracis from the body, the preferred therapeutic modality would be the administration of antibiotics together with an effective LF inhibitor. Although LF has garnered a great deal of attention as an attractive target for rational drug design, relatively few published inhibitors have demonstrated activity in cell-based assays and, to date, no LF inhibitor is available as a therapeutic or preventive agent. Here we present a novel in silico high-throughput virtual screening protocol that successfully identified 5 non-hydroxamic acid small molecules as new, preliminary LF inhibitor scaffolds with low micromolar inhibition against that target, resulting in a 12.8% experimental hit rate. This protocol screened approximately 35 million nonredundant compounds for potential activity against LF and comprised topomeric searching, docking and scoring, and drug-like filtering. Among these 5 hit compounds, none of which has previously been identified as a LF inhibitor, three exhibited experimental IC(50) values less than 100 microM. These three preliminary hits may potentially serve as scaffolds for lead optimization as well as templates for probe compounds to be used in mechanistic studies. Notably, our docking simulations predicted that these novel hits are likely to engage in critical ligand-receptor interactions with nearby residues in at least two of the three (S1', S1-S2, and S2') subsites in the LF substrate binding area. Further experimental characterization of these compounds is in process. We found that micromolar-level LF inhibition can be attained by compounds with non-hydroxamate zinc-binding groups that exhibit monodentate zinc chelation as long as key hydrophobic interactions with at least two LF subsites are retained.
炭疽是一种由炭疽芽孢杆菌引起的传染病，炭疽芽孢杆菌是一种革兰氏阳性、杆状、厌氧细菌。致死因子 (LF) 酶是炭疽芽孢杆菌作为三部分外毒素的一部分分泌的，主要负责与炭疽相关的细胞毒性。由于 LF 在抗生素从体内根除炭疽芽孢杆菌后很长时间仍会留在体内，因此首选的治疗方式是同时使用抗生素和有效的 LF 抑制剂。尽管 LF 作为合理药物设计的有吸引力的靶标已经引起了广泛关注，但相对较少的已发表抑制剂在基于细胞的测定中表现出活性，迄今为止，尚无 LF 抑制剂可用作治疗或预防剂。在这里，我们提出了一种新的计算高通量虚拟筛选方案，该方案成功地鉴定了 5 种非羟肟酸小分子作为新的、初步的 LF 抑制剂支架，对该靶标具有低微摩尔抑制作用，实验命中率为 12.8%。该方案筛选了大约 3500 万个非冗余化合物，以确定它们对 LF 的潜在活性，其中包括拓扑搜索、对接和评分以及类药性过滤。在这 5 种命中化合物中，没有一种以前被鉴定为 LF 抑制剂，其中 3 种表现出的实验 IC50 值小于 100μM。这 3 个初步命中可能有潜力作为优化先导化合物的骨架，以及用于机制研究的探针化合物的模板。值得注意的是，我们的对接模拟预测，这些新型命中化合物可能与 LF 底物结合区域中至少两个（S1'、S1-S2 和 S2'）亚位点中的附近残基发生关键的配体-受体相互作用。这些化合物的进一步实验表征正在进行中。我们发现，只要保留与至少两个 LF 亚位点的关键疏水相互作用，具有非羟肟酸锌结合基团的化合物就可以达到微摩尔级别的 LF 抑制。
