ATP-Binding Site of Bacterial Enzymes as a Target for Antibacterial Drug Design
ATP-Binding Site of Bacterial Enzymes as a Target for Antibacterial Drug Design
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DOI：
10.1021/jm101121s
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发表时间：
2011-02-24
影响因子：
7.3
通讯作者：
Zega, Anamarija
中科院分区：
文献类型：
--
作者：
Skedelj, Veronika;Tomasic, Tihomir;Zega, Anamarija
细菌对抗菌药物产生耐药性的显著能力是继续寻找新的抗菌靶点和开发新型抗菌药物的原因。尽管细菌对公众健康构成威胁，但目前只有五家大型制药公司，即阿斯特拉-利康、葛兰素史克、默克、诺华和辉瑞，有积极的抗菌药物发现项目。发现抗菌药物的痛苦现实是，开发出一种可以被批准用于临床的抗菌药物的成功概率很低。在过去的40年里，只有两种新的结构类型的抗菌药物，达托霉素和利奈唑胺，被引入临床，在他们发现后，使用经验筛选方法。自20世纪90年代末以来，细菌基因组学的兴起使新的目标得以确定，有望使合成抗菌剂的研究重新焕发活力。然而，基于靶标的高通量筛选（HTS）方法可能是抗菌药物化学多样性的重要来源，并在其他治疗领域取得了丰硕成果，但取得的成功有限。低HTS命中率可能有多种原因。在抗菌药物发现领域，HTS靶点被定义为化学上易于处理的低微摩尔靶点抑制剂，对同一靶点的人类版本具有至少10倍的选择性，而先导是具有抗菌活性的靶点，并有证据表明抗菌活性的机制是通过抑制筛选的靶点来实现的。对已知抗菌药物化学性质的分析表明，它们占据了一个独特的性质空间，与其他治疗领域的药物不同，它们通常不具备口服生物利用度所需的物理化学性质，尽管公司的化合物收集严重倾向于具有口服生物利用度的化合物。3,7,8因此，应用广泛的药物发现项目的能力是有限的，这些项目通常针对人类靶标家族（如激酶）筛选化合物类别。然而，考虑到目前受感染宿主的靶点相关性和抗菌药物到达靶点的能力的不确定性，结合全细胞筛选试验，为其他治疗领域开发的化合物文库可能与为抗菌筛选开发的化合物文库一样有可能获得成功。最近，Miller和辉瑞公司的同事通过在全细胞抗菌试验中筛选外部化合物文库，展示了重新利用它们的实用性。他们发现一系列吡啶嘧啶（图7），最初来源于针对真核蛋白激酶的程序，也对革兰氏阴性细菌的一个子集有活性。通过遗传和生化手段，发现这些化合物靶向细菌酶生物素羧化酶（BC）的atp结合位点。这些结果和我们将在本文中描述的其他例子证明了寻找具有良好选择性的atp竞争性抗菌药物的可行性，并表明细菌酶的atp结合位点可以成为抗菌药物设计的有希望的靶点。细菌基因组编码数百种atp结合蛋白。其中包括经过充分验证的靶标，如DNA回转酶和许多新的或未开发的酶。然而，在抗菌药物发现领域，设计针对细菌酶的atp结合位点的抑制剂一直是一个禁忌话题。为了显示体内活性，ATP竞争抑制剂必须首先能够与细菌体内的ATP浓度竞争。
The remarkable ability of bacteria to develop resistance to antibacterial agents is the reason for the continued need to search for new antibacterial targets and develop novel antimicrobial agents. 1, 2 Despite bacterial threats to public health, at present, only five major pharmaceutical companies, Astra-Zeneca, GSK, a Merck, Novartis, and Pfizer, have active antibacterial drug discovery programs. 1, 3 The painful reality of antibacterial drug discovery is the low probability of success in developing an antibacterial drug that can be approved for clinical use. 4 Over the past 40 years only two new structural types of antibacterial drugs, daptomycin and linezolid, have been introduced to the clinic, following their discovery using empirical screening methods. 5 Since the late 1990s, the rise of bacterial genomics, by which new targets have been identified, promised to rejuvenate the search for synthetic antibacterial agents. However, the targetbased high-throughput screening (HTS) approach that could be an important generator of chemical diversity of antibacterials and has been fruitful in other therapeutic areas has had limited success. 6 There may be a combination of reasons for the low HTS hit rates. In the field of antibacterial drug discovery a HTS hit is defined as a chemically tractable, low-micromolar inhibitor of the target with at least 10-fold selectivity against the human version of the same target, while a lead is a hit with antibacterial activity, together with evidence that the mechanism of antibacterial activity is achieved via inhibition of the target screened. 6 Analysis of the chemical properties of known antibacterial drugs shows that they occupy a unique property space that is different from that of drugs in other therapeutic areas and that they do not generally possess the physicochemical properties required for oral bioavailability although corporate compound collections are heavily biased toward compounds that do. 3, 7, 8 The ability therefore to apply the extensive drug discovery project with compound classes commonly screened against human target families, such as kinases, is limited. 6 However, given the current level of uncertainty about target relevance in an infected host and about the ability of an antibacterial drug to get to its target, compound libraries developed for other therapeutic areas, in combination with whole-cell screening assays, may be just as likely to harbor hits as compound libraries developed for antibacterial screening. Recently, Miller and co-workers from Pfizer showed the utility of repurposing external compound libraries by screening them in a whole-cell antibacterial assay. They found that a series of pyridopyrimidines (Figure 7), originally derived from a program targeting eukaryotic protein kinases, were also active against a subset of Gram-negative bacteria. By use of genetic and biochemical tools, it was shown that these compounds target the ATP-binding site of the bacterial enzyme biotin carboxylase (BC). These results and other examples that we will describe in this paper demonstrate the feasibility of finding ATP-competitive antibacterials with good selectivity profiles and indicate that the ATP-binding site of bacterial enzymes can be a promising target for antibacterial drug design. 9Bacterial genomes encode hundreds of ATP-binding proteins. These include well-validated targets like DNA gyrase and a host of new or underexplored enzymes. However, in the field of antibacterial drug discovery, the design of inhibitors targeting the ATP-binding site of bacterial enzymes has been a taboo theme for a long time. To show in vivo activity, ATP-competitive inhibitors must first be able to compete with the ATP concentration in the bacterial …