Data_Sheet_8_Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction.xlsx

The opportunistic pathogen Klebsiella pneumoniae is a causative agent of several hospital-acquired infections. It has become resistant to a wide range of currently available antibiotics, leading to high mortality rates among patients; this has further led to a demand for novel therapeutic intervention to treat such infections. Using a series of in silico analyses, the present study aims to explore novel drug/vaccine candidates from the hypothetical proteins of K. pneumoniae. A total of 540 proteins were found to be hypothetical in this organism. Analysis of these 540 hypothetical proteins revealed 30 pathogen-specific proteins essential for pathogen survival. A motifs/domain family analysis, similarity search against known proteins, gene ontology, and protein–protein interaction analysis of the shortlisted 30 proteins led to functional assignment for 17 proteins. They were mainly cataloged as enzymes, lipoproteins, stress-induced proteins, transporters, and other proteins (viz., two-component proteins, skeletal proteins and toxins). Among the annotated proteins, 16 proteins, located in the cytoplasm, periplasm, and inner membrane, were considered as potential drug targets, and one extracellular protein was considered as a vaccine candidate. A druggability analysis indicated that the identified 17 drug/vaccine candidates were “novel”. Furthermore, a host–pathogen interaction analysis of these identified target candidates revealed a betaine/carnitine/choline transporters (BCCT) family protein showing interactions with five host proteins. Structure prediction and validation were carried out for this protein, which could aid in structure-based inhibitor design.

机会致病菌肺炎克雷伯菌（Klebsiella pneumoniae）是多种医院获得性感染的致病菌。该菌已对多种现有抗生素产生耐药性，导致患者死亡率居高不下，这进一步催生了针对此类感染的新型治疗干预手段的需求。本研究通过一系列计算机模拟分析（in silico analyses），旨在从肺炎克雷伯菌的假设蛋白（hypothetical proteins）中挖掘新型药物/疫苗候选靶点。本研究在该菌中共鉴定出540个假设蛋白，对这540个假设蛋白的分析筛选出30个病原菌特异性且对病原菌存活至关重要的蛋白。对筛选出的30个蛋白进行基序/结构域家族分析、已知蛋白相似性搜索、基因本体（gene ontology, GO）注释以及蛋白质相互作用（protein–protein interaction）分析后，为其中17个蛋白完成了功能注释。这些蛋白主要可分为酶类、脂蛋白、应激诱导蛋白、转运蛋白以及其他类蛋白（即双组分蛋白、骨架蛋白与毒素蛋白）。在完成注释的蛋白中，16个定位于细胞质、周质与内膜的蛋白被认定为潜在药物靶点，另有1个胞外蛋白被选为疫苗候选靶点。成药性分析（druggability analysis）结果显示，本次鉴定出的17个药物/疫苗候选靶点均为"新型靶点"。此外，对上述筛选出的候选靶点进行宿主-病原菌相互作用（host–pathogen interaction）分析后，发现1个甜菜碱/肉碱/胆碱转运体（betaine/carnitine/choline transporters, BCCT）家族蛋白可与5个宿主蛋白产生相互作用。研究人员对该蛋白完成了结构预测与验证，该结果可为基于结构的抑制剂开发提供助力。