Computational drug repurposing by exploiting large-scale gene expression data: Strategy, methods and applications

He, Hao; Duo, Hongrui; Hao, Youjin; Zhang, Xiaoxi; Zhou, Xinyi; Zeng, Yujie; Li, Yinghong; Li, Bo

doi:10.1016/j.compbiomed.2023.106671

Cited by 17 publications

(15 citation statements)

References 147 publications

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“… 87 There is in silico drug repurposing in MS by using scRNA-Seq Data. 88 The current publication indicates fair knowledge of cell metabolism’s effect on disease initiation, progression and eradication.…”

Section: Resultsmentioning

confidence: 99%

Uncovering novel therapeutic targets in glucose, nucleotides and lipids metabolism during cancer and neurological diseases

Jovičić

2024

Int J Immunopathol Pharmacol

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Background Cell metabolism functions without a stop in normal and pathological cells. Different metabolic changes occur in the disease. Cell metabolism influences biochemical and metabolic processes, signaling pathways, and gene regulation. Knowledge regarding disease metabolism is limited. Objective The review examines the cell metabolism of glucose, nucleotides, and lipids during homeostatic and pathological conditions of neurotoxicity, neuroimmunological disease, Parkinson’s disease, thymoma in myasthenia gravis, and colorectal cancer. Methods Data collection includes electronic databases, the National Center for Biotechnology Information, and Google Scholar, with several inclusion criteria: cell metabolism, glucose metabolism, nucleotide metabolism, and lipid metabolism in health and disease patients suffering from neurotoxicity, neuroinflammation, Parkinson’s disease, thymoma in myasthenia gravis. The initial number of collected and analyzed papers is 250. The final analysis included 150 studies out of 94 selected papers. After the selection process, 62.67% remains useful. Results and Conclusion A literature search shows that signaling molecules are involved in metabolic changes in cells. Differences between cancer and neuroimmunological diseases are present in the result section. Our finding enables insight into novel therapeutic targets and the development of scientific approaches for cancer and neurological disease onset, outcome, progression, and treatment, highlighting the importance of metabolic dysregulation. Current understanding, emerging research technologies and potential therapeutic interventions in metabolic programming is disucussed and highlighted.

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Section: Resultsmentioning

confidence: 99%

Uncovering novel therapeutic targets in glucose, nucleotides and lipids metabolism during cancer and neurological diseases

Jovičić

2024

Int J Immunopathol Pharmacol

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“…Transcriptome-based drug repositioning has emerged as a promising strategy for identifying novel uses for existing drugs in cancer treatment. By analyzing gene expression profiles from cancer samples, researchers can identify drugs that have the potential to target specific pathways or molecular signatures associated with cancer [105,106]. One example is imatinib, a tyrosine kinase inhibitor initially developed to treat chronic myeloid leukemia (CML).…”

Section: Transcriptome-based Drug Repurposing Using Gastrointestinal ...mentioning

confidence: 99%

“…ML, AI, and DL are applied in various stages of drug discovery and development, including drug repurposing for cancer treatment (Figure 5). Exploring PubMed abstracts with natural language processing (NLP) is a method utilized to uncover evidence of non-cancer drugs' potential anticancer effects [105,106]. For instance, Zeng et al developed RetriLite, a framework employing NLP and domain-specific knowledge to sift through papers and extract pertinent information [117].…”

Section: Machine Learning (Ml) Artificial Intelligence (Ai) and Deep ...mentioning

confidence: 99%

Revitalizing Cancer Treatment: Exploring the Role of Drug Repurposing

Malla,

Viswanathan,

Makena

et al. 2024

Cancers

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Cancer persists as a global challenge necessitating continual innovation in treatment strategies. Despite significant advancements in comprehending the disease, cancer remains a leading cause of mortality worldwide, exerting substantial economic burdens on healthcare systems and societies. The emergence of drug resistance further complicates therapeutic efficacy, underscoring the urgent need for alternative approaches. Drug repurposing, characterized by the utilization of existing drugs for novel clinical applications, emerges as a promising avenue for addressing these challenges. Repurposed drugs, comprising FDA-approved (in other disease indications), generic, off-patent, and failed medications, offer distinct advantages including established safety profiles, cost-effectiveness, and expedited development timelines compared to novel drug discovery processes. Various methodologies, such as knowledge-based analyses, drug-centric strategies, and computational approaches, play pivotal roles in identifying potential candidates for repurposing. However, despite the promise of repurposed drugs, drug repositioning confronts formidable obstacles. Patenting issues, financial constraints associated with conducting extensive clinical trials, and the necessity for combination therapies to overcome the limitations of monotherapy pose significant challenges. This review provides an in-depth exploration of drug repurposing, covering a diverse array of approaches including experimental, re-engineering protein, nanotechnology, and computational methods. Each of these avenues presents distinct opportunities and obstacles in the pursuit of identifying novel clinical uses for established drugs. By examining the multifaceted landscape of drug repurposing, this review aims to offer comprehensive insights into its potential to transform cancer therapeutics.

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“…In view of the many problems confronted by de novo drug discovery, finding new indications for existing drugs has become an attractive new strategy 106 , 107 . Drug repurposing is a strategy to identify new uses for drugs that have been approved or are being studied 108 , 109 , 110 , 111 . Compared with the traditional discovery of new drugs, drug repurposing has the following advantages: simpler research and development process, shorter research and development cycle, low cost, low toxicity, clear mechanism of action, clear side effects and less adverse reactions 112 , 113 .…”

Section: Drug Repurposing Strategiesmentioning

confidence: 99%