Sharma Aman, Rani Rinkle
Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.
J Bioinform Comput Biol. 2018 Oct;16(5):1850017. doi: 10.1142/S0219720018500178. Epub 2018 Jun 28.
Combination drug therapy is considered a better treatment option for various diseases, such as cancer, HIV, hypertension, and infections as compared to targeted drug therapies. Combination or synergism helps to overcome drug resistance, reduction in drug toxicity and dosage. Considering the complexity and heterogeneity among cancer types, drug combination provides promising treatment strategy. Increase in drug combination data raises a challenge for developing a computational approach that can effectively predict drugs synergism. There is a need to model the combination drug screening data to predict new synergistic drug combinations for successful cancer treatment. In such a scenario, machine learning approaches can be used to alleviate the process of drugs synergy prediction. Experimental data from a single-agent or multi-agent drug screens provides feature data for model training. On the contrary, identification of effective drug combination using clinical trials is a time consuming and resource intensive task. This paper attempts to address the aforementioned challenges by developing a computational approach to effectively predict drug synergy. Single-drug efficacy is used for predicting drug synergism. Our approach obviates the need to understand the underlying drug mechanism to predict drug combination synergy. For this purpose, nine machine learning algorithms are trained. It is observed that the Random forest models, in comparison to other models, have shown significant performance. The -fold cross-validation is performed to evaluate the robustness of the best predictive model. The proposed approach is applied to mutant-BRAF melanoma and further validated using melanoma cell-lines from AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge dataset.
与靶向药物治疗相比,联合药物疗法被认为是治疗各种疾病(如癌症、艾滋病、高血压和感染)的更好选择。联合用药或协同作用有助于克服耐药性、降低药物毒性和剂量。考虑到癌症类型之间的复杂性和异质性,药物联合提供了有前景的治疗策略。联合用药数据的增加对开发一种能够有效预测药物协同作用的计算方法提出了挑战。需要对联合药物筛选数据进行建模,以预测新的协同药物组合,从而成功治疗癌症。在这种情况下,可以使用机器学习方法来简化药物协同作用预测过程。来自单药或多药筛选的实验数据为模型训练提供特征数据。相反,通过临床试验确定有效的药物组合是一项耗时且资源密集的任务。本文试图通过开发一种有效预测药物协同作用的计算方法来应对上述挑战。利用单药疗效来预测药物协同作用。我们的方法无需了解潜在的药物作用机制即可预测药物组合的协同作用。为此,训练了九种机器学习算法。观察到,与其他模型相比,随机森林模型表现出显著的性能。进行 -折交叉验证以评估最佳预测模型的稳健性。所提出的方法应用于突变型BRAF黑色素瘤,并使用来自阿斯利康-桑格药物联合预测DREAM挑战数据集的黑色素瘤细胞系进行进一步验证。