Pradeepkiran Jangampalli Adi, Sainath Sri Bhashyam, Kumar Konidala Kranthi, Bhaskar Matcha
Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, India.
CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, Porto, Portugal ; Department of Biotechnology, Vikrama Simhapuri University, Nellore, Andhra Pradesh, India.
Drug Des Devel Ther. 2015 Mar 19;9:1691-706. doi: 10.2147/DDDT.S76948. eCollection 2015.
Brucella melitensis 16M is a Gram-negative coccobacillus that infects both animals and humans. It causes a disease known as brucellosis, which is characterized by acute febrile illness in humans and causes abortions in livestock. To prevent and control brucellosis, identification of putative drug targets is crucial. The present study aimed to identify drug targets in B. melitensis 16M by using a subtractive genomic approach. We used available database repositories (Database of Essential Genes, Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server, and Kyoto Encyclopedia of Genes and Genomes) to identify putative genes that are nonhomologous to humans and essential for pathogen B. melitensis 16M. The results revealed that among 3 Mb genome size of pathogen, 53 putative characterized and 13 uncharacterized hypothetical genes were identified; further, from Basic Local Alignment Search Tool protein analysis, one hypothetical protein showed a close resemblance (50%) to Silicibacter pomeroyi DUF1285 family protein (2RE3). A further homology model of the target was constructed using MODELLER 9.12 and optimized through variable target function method by molecular dynamics optimization with simulating annealing. The stereochemical quality of the restrained model was evaluated by PROCHECK, VERIFY-3D, ERRAT, and WHATIF servers. Furthermore, structure-based virtual screening was carried out against the predicted active site of the respective protein using the glycerol structural analogs from the PubChem database. We identified five best inhibitors with strong affinities, stable interactions, and also with reliable drug-like properties. Hence, these leads might be used as the most effective inhibitors of modeled protein. The outcome of the present work of virtual screening of putative gene targets might facilitate design of potential drugs for better treatment against brucellosis.
羊种布鲁氏菌16M是一种革兰氏阴性球杆菌，可感染动物和人类。它会引发一种名为布鲁氏菌病的疾病，其特征是人类出现急性发热病症，并导致家畜流产。为预防和控制布鲁氏菌病，确定潜在的药物靶点至关重要。本研究旨在通过消减基因组方法确定羊种布鲁氏菌16M中的药物靶点。我们利用现有的数据库资源（必需基因数据库、京都基因与基因组百科全书自动注释服务器以及京都基因与基因组百科全书）来确定与人类无同源性且对病原体羊种布鲁氏菌16M必不可少的潜在基因。结果显示，在病原体3 Mb的基因组大小中，确定了53个推定的已表征基因和13个未表征的假设基因；此外，通过基本局部比对搜索工具蛋白质分析，一种假设蛋白质与波氏硅杆菌DUF1285家族蛋白质（2RE3）显示出密切相似性（50%）。使用MODELLER 9.12构建了该靶点的进一步同源模型，并通过可变目标函数方法，结合模拟退火进行分子动力学优化。通过PROCHECK、VERIFY - 3D、ERRAT和WHATIF服务器评估受限模型的立体化学质量。此外，使用来自PubChem数据库的甘油结构类似物，针对相应蛋白质的预测活性位点进行了基于结构的虚拟筛选。我们确定了五种具有强亲和力、稳定相互作用且具有可靠类药性质的最佳抑制剂。因此，这些先导化合物可能用作模拟蛋白质的最有效抑制剂。对推定基因靶点进行虚拟筛选的当前工作成果可能有助于设计出更有效的药物来更好地治疗布鲁氏菌病。
