Akhter Mymoona
Drug Design and Medicinal Chemistry Lab, Faculty of Pharmacy, Jamia Hamdard, New Delhi, India.
Int J Mycobacteriol. 2016 Dec;5 Suppl 1:S96. doi: 10.1016/j.ijmyco.2016.09.026. Epub 2016 Nov 9.
OBJECTIVES/BACKGROUND: Dihydrofolate reductase (DHFR) is one of the validated drug targets in Mycobacterium tuberculosis (Mtb) infection. DHFR inhibitors have been used to treat various life-threatening diseases such as cancer, malaria, and several bacterial infections. However, all clinically effective DHFR inhibitors are non-selective, and inhibit both human and pathogenic DHFRs more or less to a similar extent. The crystal structure of various DHFRs complexed with nicotinamide adenine dinucleotide phosphate and different inhibitors is available in the protein data bank. The crystal structures are validated and have been used for new drug designing. M. tuberculosis DHFRs and human (h) DHFRs show 26% structure similarity, but their active sites are not identical and this characteristic forms the basis of this study. Because most of the reported inhibitors of M. tuberculosis DHFR are pteridine based and nonselective in nature, that is, they inhibit both microbial and host DHFRs, this study aimed to design and develop selective nonpteridine M. tuberculosis DHFR inhibitors.
In the ternary complex of methotrexate with M. tuberculosis DHFR, whose structure is also available in the protein data bank, the side of the aminopterin ring is accessible to the solvent; additionally, a glycerol "A" molecule is found in a depression nearby. This glycerol molecule interacts with the side chains of Trp22, Asp27, and Gln28, which form a pocket in M. tuberculosis DHFR; by contrast, glycerol is absent in h-DHFR. In the h-DHFRs (complexed with folate or N-(4-carboxy-{-[(2, 4-diamino pteridine-6-yl methyl)-amino]-benzoyl amino} -butyl) pthalamic acid (COP)), the site is well packed with three hydrophobic residue side chains, Leu22, Pro26, and Phe31, which correspond to Leu20, Arg23, and Gln28, respectively, found in M. tuberculosis DHFR. Therefore, compounds with side chain, which could mimic the binding mode of glycerol to protein, may bind to M. tuberculosis DHFR selectively. Such a derivative should be sterically and chemically hindered from forming a complex with h-DHFR. This assumption forms the basis of this study and this understanding has been used for designing selective inhibitors of M. tuberculosis DHFR.
A number of novel nonpteridine-based molecules have been identified after the virtual screening of three databases (MDPI, NCI and inhouse databases). The best molecules identified after screening the three databases have been synthesized and tested for antitubercular activity. The results are promising and require further work in this direction.
Structure based drug design can be used as an effective tool for the design of new cheiocal entity. Number of novel agents have been identified as antitubercular agents whose mechanism of action needs to be ascertained.
目的/背景：二氢叶酸还原酶（DHFR）是结核分枝杆菌（Mtb）感染中已得到验证的药物靶点之一。DHFR抑制剂已被用于治疗各种危及生命的疾病，如癌症、疟疾和几种细菌感染。然而，所有临床有效的DHFR抑制剂都是非选择性的，或多或少会以相似的程度抑制人类和致病性DHFR。蛋白质数据库中提供了与烟酰胺腺嘌呤二核苷酸磷酸和不同抑制剂复合的各种DHFR的晶体结构。这些晶体结构经过验证，并已用于新药设计。结核分枝杆菌DHFR和人类（h）DHFR显示出26%的结构相似性，但它们的活性位点并不相同，这一特性构成了本研究的基础。由于大多数已报道的结核分枝杆菌DHFR抑制剂都是基于蝶啶的，且本质上是非选择性的，即它们同时抑制微生物和宿主DHFR，因此本研究旨在设计和开发选择性非蝶啶类结核分枝杆菌DHFR抑制剂。
在甲氨蝶呤与结核分枝杆菌DHFR的三元复合物中（其结构在蛋白质数据库中也可获得），氨基蝶呤环的一侧可被溶剂接触；此外，在附近的一个凹陷处发现了一个甘油“A”分子。该甘油分子与Trp22、Asp27和Gln28的侧链相互作用，这些侧链在结核分枝杆菌DHFR中形成一个口袋；相比之下，h-DHFR中不存在甘油。在h-DHFR（与叶酸或N-（4-羧基-{[（2,4-二氨基蝶啶-6-基甲基）-氨基]-苯甲酰氨基}-丁基）邻苯二甲酸（COP）复合）中，该位点被三个疏水残基侧链Leu22、Pro26和Phe31紧密填充，它们分别对应于结核分枝杆菌DHFR中发现的Leu20、Arg23和Gln28。因此，具有可模拟甘油与蛋白质结合模式的侧链的化合物可能会选择性地与结核分枝杆菌DHFR结合。这种衍生物在空间和化学上应受到阻碍，无法与h-DHFR形成复合物。这一假设构成了本研究的基础，并且这一认识已被用于设计结核分枝杆菌DHFR的选择性抑制剂。
在对三个数据库（MDPI、NCI和内部数据库）进行虚拟筛选后，鉴定出了许多新型的非蝶啶类分子。在对这三个数据库进行筛选后鉴定出的最佳分子已被合成并测试其抗结核活性。结果很有前景，需要在这个方向上进一步开展工作。
基于结构的药物设计可作为设计新化学实体的有效工具。已鉴定出多种新型抗结核药物，但它们的作用机制有待确定。
