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)
Article
Medicine, General & Internal
Minoh Ko, Jung Mi Oh, In-Wha Kim
Summary: This study used a computational method to integrate reported drug adverse event data, disease-specific gene expression profiles, and drug-induced gene expression profiles in order to predict drug candidates for psoriasis. The inverse signals calculated from the drug and adverse event data were used to identify reversal genes and candidate compounds. The correlations between the reverse gene expression scores and IC50 values were validated using data from ChEMBL.
FRONTIERS IN MEDICINE
(2023)
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)
Article
Mathematics, Applied
Ying Ying Keng, Kiam Heong Kwa, Kurunathan Ratnavelu
Summary: The study demonstrates the significance of central drugs in a drug network for drug repositioning, suggesting that top central drugs are more likely to repurpose their neighboring drugs as new treatment options. This research provides novel insights into complementing drug repositioning efforts and highlights the importance of network centrality measures in guiding systematic analysis.
APPLIED MATHEMATICS AND COMPUTATION
(2021)
Article
Biochemistry & Molecular Biology
Zheng Yao Low, Ashley Jia Wen Yip, Sunil K. Lal
Summary: Ivermectin, an FDA-approved drug traditionally used for parasitic infections, has shown antiviral potential in previous in vitro studies. With the recent COVID-19 pandemic, there is growing interest in repurposing Ivermectin to combat SARS-CoV-2. Multiple studies have demonstrated its effectiveness in inhibiting viral proteins and reducing cytokine storms, making it a strong candidate for clinical trials against COVID-19.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
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.
Article
Biochemistry & Molecular Biology
Pierre Mounkoro, Thomas Michel, Marie-Pierre Golinelli-Cohen, Stephanie Blandin, Elisabeth Davioud-Charvet, Brigitte Meunier
Summary: Malaria, caused by protozoan parasites, is a major public health issue in subtropical countries. Despite the availability of antimalarial treatments, resistance is spreading, urging the development of new antimalarial compounds. Plasmodione is a redox-active compound that impairs the redox balance of parasites leading to cell death, with its mode of action involving the generation of active metabolites that act as subversive substrates of flavoproteins initiating a redox cycling process.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Biochemical Research Methods
Yajie Meng, Changcheng Lu, Min Jin, Junlin Xu, Xiangxiang Zeng, Jialiang Yang
Summary: In this study, a novel neural collaborative filtering approach is proposed for drug repositioning, which utilizes deep-learning approaches based on a heterogeneous network. The approach takes advantage of localized information in different networks and models the complex drug-disease associations effectively. The effectiveness of the approach is verified through benchmarking comparisons and validated against clinical trials and authoritative databases.
BRIEFINGS IN BIOINFORMATICS
(2022)
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
Immunology
Xinyue Yin, Xinming Rang, Xiangxiang Hong, Yinglian Zhou, Chaohan Xu, Jin Fu
Summary: In this study, target genes and target pathways for drug repositioning in multiple sclerosis (MS) were identified based on transcriptomic changes in MS immune cells. The study found that targeting both the PI3K-Akt signaling pathway and Chemokine signaling pathway, or using tyrosine kinase inhibitors may be potential therapies for the treatment of MS.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Michael Brand, Lei Wang, Stefano Agnello, Silvia Gazzola, Flavio M. Gall, Luka Raguz, Marcel Kaiser, Remo S. Schmidt, Amelie Ritschl, Jennifer Jelk, Andrew Hemphill, Pascal Maser, Peter Butikofer, Michael Adams, Rainer Riedl
Summary: Researchers used Trypanosoma brucei as a model organism to study the potent antiprotozoal compound Leucinostatin A and its derivatives, showing that the main site of action is destabilization of the inner mitochondrial membrane. Resistance to the synthetic derivatives was not observed after long-term exposure and screening of thousands of mutants.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Seo-Mi-Gon Jeong, Tae-Jin Yoon
Summary: Skin color is determined by melanin synthesis and distribution, and issues in this process can result in pigmentation defects. Through research on substances or drugs associated with pigmentation control, certain medications have been identified as potential therapeutics for pigmentation disorders through drug repositioning.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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.
Review
Chemistry, Medicinal
Xiaona Lang, Jinlei Liu, Guangzhong Zhang, Xin Feng, Wenchao Dan
Summary: This paper conducted a bibliometric analysis of articles related to drug repositioning in recent years and analyzed the current research focus and trends. The findings show a significant improvement in the quality and quantity of articles published in recent years. Keywords in the literature include molecular docking, virtual screening, drug discovery, machine learning, and drug-target interaction.
DRUG DESIGN DEVELOPMENT AND THERAPY
(2023)
Review
Neurosciences
Alessandra Rufini, Florence Malisan, Ivano Condo, Roberto Testi
Summary: Friedreich ataxia is a rare neurodegenerative disorder caused by insufficient levels of the essential mitochondrial protein frataxin. It leads to reduced activity of mitochondrial enzymes, impaired mitochondrial metabolism, reduced ATP production and inefficient anti-oxidant response, resulting in the progressive loss of movement coordination and daily activity performance. Drug repositioning is a viable alternative for identifying a therapy for Friedreich ataxia.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Genetics & Heredity
Limin Shang, Yuehui Zhang, Yuchen Liu, Chaozhi Jin, Yanzhi Yuan, Chunyan Tian, Ming Ni, Xiaochen Bo, Li Zhang, Dong Li, Fuchu He, Jian Wang
Summary: In this study, a high-efficiency BiFC-seq method coupled with next-generation DNA sequencing was used for genome-wide interactome mapping. By applying this method to investigate the intraviral network of the Ebola virus and the interactome of the tumor protein p53, as well as screening potential interactors in a more complex background, satisfactory results were obtained.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Pharmacology & Pharmacy
Yang Han, Zhilong Jia, Jinlong Shi, Weidong Wang, Kunlun He
Summary: SARS-CoV-2 infection profoundly altered the lung microbiota of COVID-19 patients, with the presence of various pathogens, immunomodulatory probiotics, and Tobacco mosaic virus in the COVID-19 group indicating a complex and active lung microbiota disorder.
Article
Biochemical Research Methods
Dafei Xie, Song He, Lu Han, Lianlian Wu, Hai Huang, Huan Tao, Pingkun Zhou, Xunlong Shi, Hui Bai, Xiaochen Bo
Summary: Inhibition of host protein functions using established drugs shows promising antiviral effects with safety profiles and decreased resistance. This study integrates known virus-targeted host proteins (VTHPs) and drug targets to propose a comprehensive strategy for identifying potential antiviral targets and repositioned drugs. The results provide insights for the development of novel antiviral host proteins and drugs for combating viral infections.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
John D. Isaacs, Sarah Brockbank, Ayako Wakatsuki Pedersen, Catharien Hilkens, Amy Anderson, Philip Stocks, Dennis Lendrem, Jessica Tarn, Graham R. Smith, Ben Allen, John Casement, Julie Diboll, Rachel Harry, Faye A. H. Cooles, Andrew P. Cope, Gemma Simpson, Ruth Toward, Hayley Noble, Angela Parke, Wing Wu, Fiona Clarke, David Scott, Ian C. Scott, James Galloway, Heidi Lempp, Fowzia Ibrahim, Samana Schwank, Gemma Molyneux, Tomi Lazarov, Frederic Geissmann, Carl S. Goodyear, Iain B. McInnes, Iona Donnelly, Ashley Gilmour, Aysin Tulunay Virlan, Duncan Porter, Frederique Ponchel, Paul Emery, Jehan El-Jawhari, Rekha Parmar, Michael F. McDermott, Benjamin A. Fisher, Steve P. Young, Philip Jones, Karim Raza, Andrew Filer, Costantino Pitzalis, Michael R. Barnes, David S. Watson, Rafael Henkin, Georgina Thorborn, Liliane Fossati-Jimack, Stephen Kelly, Frances Humby, Michele Bombardieri, Sharmila Rana, Zhilong Jia, Katriona Goldmann, Myles Lewis, Sandra Ng, Adriano Barbosa-Silva, Evan Tzanis, Amaya Gallagher-Syed, Christopher R. John, Michael R. Ehrenstein, Gioia Altobelli, Sandra Martins, Dao Nguyen, Humayara Ali, Coziana Ciurtin, Maya Buch, Deborah Symmons, Jane Worthington, Ian N. Bruce, Jamie C. Sergeant, Suzanne M. M. Verstappen, Fiona Stirling, Adwoa Hughes-Morley, Brian Tom, Vernon Farewell, Yujie Zhong, Peter C. Taylor, Christopher D. Buckley, Sarah Keidel, Carolyn Cuff, Marc Levesque, Andrew Long, Zheng Liu, Samantha Lipsky, Bohdan Harvey, Michael Macoritto, Feng Hong, Sukru Kaymakcalan, Wayne Tsuji, Tony Sabin, Neil Ward, Susan Talbot, Desmond Padhji, Matthew Sleeman, Donna Finch, Athula Herath, Catharina Lindholm, Martin Jenkins, Meilien Ho, Sally Hollis, Chris Marshall, Gerry Parker, Matt Page, Hannah Edwards, Alexandru Cuza, Neil Gozzard, Ioannis Pandis, Anthony Rowe, Francisco Bonachela Capdevila, Matthew J. Loza, Mark Curran, Denny Verbeeck, Dan Baker, Christopher M. Mela, Ivana Vranic, Catherine T. Mela, Stephen Wright, Lucy Rowell, Emma Vernon, Nina Joseph, Neil Payne, Ravi Rao, Michael Binks, Alexandra Belson, Valerie Ludbrook, Kirsty Hicks, Hannah Tipney, Joanne Ellis, Samiul Hasan, Arnaud Didierlaurent, Wivine Burny, Andrea Haynes, Chris Larminie, Ray Harris, Daniela Dastros-Pitei, Claudio Carini, Blerina Kola, Scott Jelinsky, Martin Hodge, Mateusz Maciejewski, Daniel Ziemek, Peter Schulz-Knappe, Hans-Dieter Zucht, Petra Budde, Mark Coles, James A. Butler, Simon Read
Summary: This study conducted comprehensive clinical and molecular profiling of early, drug naive RA patients, establishing a high-quality sample biobank and performing multi-omic immune phenotyping. The data obtained is expected to provide important insights into the pathogenesis, progression, and therapeutic response of RA.
Article
Biology
Jing Yang, Zhilong Jia, Xinyu Song, Jinlong Shi, Xiaoreng Wang, Xiaojing Zhao, Kunlun He
Summary: A study was conducted on a longitudinal cohort of 53 individuals to analyze AMS symptom phenotypes, clinical indexes, and plasma proteomic profiles. It was found that RET played a significant role in the pathogenesis of AMS, and using machine learning, ADAM15, PHGDH, and TRAF2 were identified as protective, predictive, and diagnostic biomarkers for AMS with high accuracies.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lianlian Wu, Bowei Yan, Junshan Han, Ruijiang Li, Jian Xiao, Song He, Xiaochen Bo
Summary: TOXRIC is a comprehensive database that provides toxicological data, standardized attribute data, practical benchmarks, and informative visualization of molecular representations. It can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery, and the development of computational methods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Zhuo-Xing Shi, Zhi-Chao Chen, Jia-Yong Zhong, Kun-Hua Hu, Ying-Feng Zheng, Ying Chen, Shang-Qian Xie, Xiao-Chen Bo, Feng Luo, Chong Tang, Chuan-Le Xiao, Yi-Zhi Liu
Summary: Long-read single-cell RNA isoform sequencing can reveal the complex landscape of alternative RNA splicing in individual cells, but it has a low read throughput. The authors developed circular consensus sequencing methods to achieve high-throughput and high-accuracy single-cell RNA isoform sequencing.
NATURE COMMUNICATIONS
(2023)
Article
Pharmacology & Pharmacy
Liuyang Tian, Zhilong Jia, Yan Yan, Qian Jia, Wenjie Shi, Saijia Cui, Huining Chen, Yang Han, Xiaojing Zhao, Kunlun He
Summary: This study found that low-dose caffeine can alleviate high-altitude pulmonary edema (HAPE) by promoting PINK1/parkin-dependent mitophagy and mitochondrial fission to control mitochondrial quality. Therefore, caffeine could be a potential treatment for HAPE.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Medicine, General & Internal
Fabiola Eto, Miriam Samuel, Rafael Henkin, Meera Mahesh, Tahania Ahmad, Alisha Angdembe, R. Hamish McAllister-Williams, Paolo Missier, Nick J. Reynolds, Michael R. Barnes, Sally Hull, Sarah Finer, Rohini Mathur
Summary: The prevalence of early onset multimorbidity is increasing among young adults, especially in minority ethnic groups and socioeconomically deprived areas. This study used a data-driven approach to identify clusters of individuals with early onset multimorbidity in a diverse population, and examined the associations between these clusters and various health outcomes.
Article
Biology
Lu Han, Bin Song, Peilin Zhang, Zhi Zhong, Yongxiang Zhang, Xiaochen Bo, Hongyang Wang, Yong Zhang, Xiuliang Cui, Wenxia Zhou
Summary: Cellular transitions play a crucial role in translational medicine research. This study introduces a computational framework, PC3T, which enriches small molecules that induce desired cellular transitions. The framework was able to predict the reprogramming of fibroblasts into hepatic progenitor-like cells and provide a valuable resource for cell state transition research.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Longteng Wang, Yang Zheng, Yu Sun, Shulin Mao, Hao Li, Xiaochen Bo, Cheng Li, Hebing Chen
Summary: Early embryonic development relies on proper cell-cell communication, and this study developed a computational framework called TimeTalk to decipher the secrets of early embryo development. By analyzing time-course mouse scRNA-seq data, this study found that ligand-receptor pairs play a crucial role in cell fate decisions and morphogenesis during early embryo development.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Lianlian Wu, Jie Gao, Yixin Zhang, Binsheng Sui, Yuqi Wen, Qingqiang Wu, Kunhong Liu, Song He, Xiaochen Bo
Summary: Combination therapy is a promising approach for treating complex diseases, but the large search space of drug combinations poses challenges for experimental screening. In this study, we propose an improved deep forest-based method called ForSyn to predict synergistic drug combinations in different cancer cell lines. ForSyn effectively handles imbalanced and high-dimensional data in medium-/small-scale datasets, outperforming 12 state-of-the-art methods in terms of predictive performance. We also validate the predictive value of ForSyn with cell-based experiments and identify key genes that may play important roles in cancer.
CELL REPORTS METHODS
(2023)
Article
Biochemical Research Methods
Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu
Summary: COMMO is the first web server capable of identifying and analyzing consensus gene functionally related gene modules from different module detection methods. It offers a variety of module detection methods, data sources, and analysis functions, providing a user-friendly solution for precision medicine research.
Article
Physics, Multidisciplinary
Ze Zhan, Ying Fei, Chongxin Run, Zhiwen Zong, Liang Xiang, Wenyan Jin, Zhilong Jia, Peng Duan, Guoping Guo, Jianlan Wu, Yi Yin
Summary: A quantum eigensolver is developed using a multilayer cluster mean-field algorithm, which successfully predicts the ground states of quantum systems by partitioning them into separate clusters.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Dongjin Leng, Linyi Zheng, Yuqi Wen, Yunhao Zhang, Lianlian Wu, Jing Wang, Meihong Wang, Zhongnan Zhang, Song He, Xiaochen Bo
Summary: This study comprehensively evaluates 16 representative deep learning methods on simulated, single-cell, and cancer multi-omics datasets. The benchmarking results indicate that moGAT achieves the best classification performance, while efmmdVAE, efVAE, and IfmmdVAE show the most promising performance across all complementary contexts in clustering tasks.