Article
Biochemical Research Methods
A. K. M. Azad, Mojdeh Dinarvand, Alireza Nematollahi, Joshua Swift, Louise Lutze-Mann, Fatemeh Vafaee
Summary: Drug similarity studies aim to explore similar therapeutic actions among drugs, utilizing various sources of evidence to derive a multi-modal drug-drug similarity network. The resulting database, DrugSimDB, provides an exhaustive platform for identifying validated repositioning candidates and in-silico drug development applications.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Hai-Cheng Yi, Zhu-Hong You, Lei Wang, Xiao-Rui Su, Xi Zhou, Tong-Hai Jiang
Summary: This study developed a deep gated recurrent units model to predict potential drug-disease interactions using comprehensive similarity measures and Gaussian interaction profile kernel, successfully predicting new potential indications for drugs and evaluating the model on two benchmark datasets.
BMC BIOINFORMATICS
(2021)
Review
Oncology
Binsheng He, Fangxing Hou, Changjing Ren, Pingping Bing, Xiangzuo Xiao
Summary: Drug repositioning, the practice of using existing drugs for new disease indications, has become popular due to the high cost and failure rate of developing new drugs. With the aid of high-throughput sequencing techniques, efficient methods have been proposed and applied in drug repositioning and personalized tumor treatment. Computational methods for drug repositioning can be divided into four categories, with future directions focusing on more sensitive methods for individualized tumor treatment.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemical Research Methods
Hailin Chen, Zuping Zhang, Jingpu Zhang
Summary: This research utilized integrated drug features to improve the accuracy of drug repositioning and proposed a fusion method. The results showed that the integration of similarity measurements had the best performance in predicting drug-disease associations.
BMC BIOINFORMATICS
(2021)
Review
Oncology
Fangting You, Caiyi Zhang, Xiaoxiao Liu, Daofei Ji, Tong Zhang, Rutong Yu, Shangfeng Gao
Summary: Psychotropic drugs, in addition to their use in mental disorders, have potential for cancer therapy, particularly for glioma. They can inhibit malignant progression of glioma by targeting signaling pathways or increasing sensitivity of glioma cells to conventional treatments. Repurposing established psychotropic drugs as anticancer agents provides new options for glioma treatment.
Review
Biochemistry & Molecular Biology
Yoonbee Kim, Yi-Sue Jung, Jong-Hoon Park, Seon-Jun Kim, Young-Rae Cho
Summary: Drug repositioning, utilizing heterogeneous networks, is an effective approach to identify new therapeutic indications for approved drugs. This review summarizes network-based methods, including graph mining, matrix factorization, and deep learning, for predicting drug-disease associations. A comparison of predictive performances was conducted, revealing that methods in the graph mining and matrix factorization categories performed well overall.
Article
Biochemistry & Molecular Biology
A. S. Ben Geoffrey, Rafal Madaj, Pavan Preetham Valluri
Summary: This study uses deep learning algorithms to predict biological network data and generate scientifically useful predictions. By training on compound-drug target interaction network data, a classification and prediction model is built for PubChem compounds. Additionally, a deep learning-based optimization protocol is employed to optimize compounds for drug likeness. The tool also includes automated In Silico modeling to uncover interaction profiles between compounds and predicted drug targets.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Alessandro Orro, Matteo Uggeri, Marco Rusnati, Chiara Urbinati, Nicoletta Pedemonte, Emanuela Pesce, Marco Moscatelli, Rita Padoan, Elena Cichero, Paola Fossa, Pasqualina D'Ursi
Summary: Computational drug repositioning is gaining attention for its ability to quickly screen potential drugs and reduce development costs and time. Cystic fibrosis, caused by a deletion in the CFTR protein, is still a fatal disease with treatments available but in need of newer drugs with stronger therapeutic benefits and fewer side effects.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biology
Muhammad I. Ismail, Hanan M. Ragab, Adnan A. Bekhit, Tamer M. Ibrahim
Summary: By utilizing molecular dynamics simulation, ensemble docking approach, and X-ray structures, this study focused on drug repositioning for PLpro in the context of the COVID-19 pandemic. The results identified potential consensus binders and highlighted the stability and binding of selected drugs against PLpro through further MD simulations. This approach could aid in identifying drugs for repurposing to target crucial proteins in the rapidly evolving COVID-19 pandemic.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Pharmacology & Pharmacy
Utid Suriya, Panupong Mahalapbutr, Thanyada Rungrotmongkol
Summary: In this study, lomitapide and nilotinib were identified as potential novel inhibitors of p38α MAPK. Molecular dynamics simulations and free energy calculations revealed comparable binding affinity of these screened drugs with a known inhibitor. Noncovalent contacts and hydrogen bond formation were found to be important for binding recognition. Hydrophobic residues were identified as key influential amino acids, while charged residues like E71 and D168 were considered crucial due to strong hydrogen bond formation with the drugs.
Article
Biochemical Research Methods
Kuo Yang, Yuxia Yang, Shuyue Fan, Jianan Xia, Qiguang Zheng, Xin Dong, Jun Liu, Qiong Liu, Lei Lei, Yingying Zhang, Bing Li, Zhuye Gao, Runshun Zhang, Baoyan Liu, Zhong Wang, Xuezhong Zhou
Summary: Drug repositioning is an important method in drug development that identifies new indications of approved drugs through analysis of clinical and experimental data. This study proposes a drug repositioning framework called DRONet, which combines network embedding and ranking learning to utilize the effectiveness comparative relationships among drugs. Experimental results show that DRONet achieves higher prediction accuracy than existing methods and demonstrates potential for guiding clinical drug development.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Lemessa Etana Bultum, Gemechu Bekele Tolossa, Gwangmin Kim, Ohhyeon Kwon, Doheon Lee
Summary: In silico profiling and network analysis revealed the therapeutic activities of phytochemicals from Ethiopian indigenous aloes. These phytochemicals were found to have multiple targets involved in various diseases, including cancer and diseases of immune system, metabolism, and neurological system. The main pathways associated with these targets were metabolism of steroid hormone biosynthesis, lipid and atherosclerosis, chemical carcinogenesis, and pathways in cancer.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Sha Zhu, Qifeng Bai, Lanqing Li, Tingyang Xu
Summary: Drug repositioning plays a significant role in drug development and machine learning methods can accelerate this process. This article focuses on the repurposing potential of type 2 diabetes mellitus drugs for various diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Pharmacology & Pharmacy
Guojun Sun, Dashun Dong, Zuojun Dong, Qian Zhang, Hui Fang, Chaojun Wang, Shaoya Zhang, Shuaijun Wu, Yichen Dong, Yuehua Wan
Summary: Drug repurposing has become an effective approach to drug discovery. This study provides a bibliometric analysis of drug repurposing publications from 2010 to 2020. The findings show that the United States leads in this area of research, followed by China, the United Kingdom, and India. The Chinese Academy of Science published the most research studies, and NIH ranked first on the h-index. COVID-19/SARS-CoV-2/coronavirus is the most popular topic for current drug repurposing research.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Chemistry, Analytical
Saurabh B. Ganorkar, Yvan Vander Heyden
Summary: Pharmaceutical drug analysis can enrich drug discovery by suggesting new leads through computational predictions, expanding the application scope of drug analysis, and aiding in the identification of potential drug candidates.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)