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Picard M, Scott-Boyer MP, Bodein A, Leclercq M, Prunier J, Périn O, Droit A. Target repositioning using multi-layer networks and machine learning: The case of prostate cancer. Comput Struct Biotechnol J 2024; 24:464-475. [PMID: 38983753 PMCID: PMC11231507 DOI: 10.1016/j.csbj.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
The discovery of novel therapeutic targets, defined as proteins which drugs can interact with to induce therapeutic benefits, typically represent the first and most important step of drug discovery. One solution for target discovery is target repositioning, a strategy which relies on the repurposing of known targets for new diseases, leading to new treatments, less side effects and potential drug synergies. Biological networks have emerged as powerful tools for integrating heterogeneous data and facilitating the prediction of biological or therapeutic properties. Consequently, they are widely employed to predict new therapeutic targets by characterizing potential candidates, often based on their interactions within a Protein-Protein Interaction (PPI) network, and their proximity to genes associated with the disease. However, over-reliance on PPI networks and the assumption that potential targets are necessarily near known genes can introduce biases that may limit the effectiveness of these methods. This study addresses these limitations in two ways. First, by exploiting a multi-layer network which incorporates additional information such as gene regulation, metabolite interactions, metabolic pathways, and several disease signatures such as Differentially Expressed Genes, mutated genes, Copy Number Alteration, and structural variants. Second, by extracting relevant features from the network using several approaches including proximity to disease-associated genes, but also unbiased approaches such as propagation-based methods, topological metrics, and module detection algorithms. Using prostate cancer as a case study, the best features were identified and utilized to train machine learning algorithms to predict 5 novel promising therapeutic targets for prostate cancer: IGF2R, C5AR, RAB7, SETD2 and NPBWR1.
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Affiliation(s)
- Milan Picard
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Julien Prunier
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Transformation and Innovation Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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Singh S, Kaur N, Gehlot A. Application of artificial intelligence in drug design: A review. Comput Biol Med 2024; 179:108810. [PMID: 38991316 DOI: 10.1016/j.compbiomed.2024.108810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/31/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024]
Abstract
Artificial intelligence (AI) is a field of computer science that involves acquiring information, developing rule bases, and mimicking human behaviour. The fundamental concept behind AI is to create intelligent computer systems that can operate with minimal human intervention or without any intervention at all. These rule-based systems are developed using various machine learning and deep learning models, enabling them to solve complex problems. AI is integrated with these models to learn, understand, and analyse provided data. The rapid advancement of Artificial Intelligence (AI) is reshaping numerous industries, with the pharmaceutical sector experiencing a notable transformation. AI is increasingly being employed to automate, optimize, and personalize various facets of the pharmaceutical industry, particularly in pharmacological research. Traditional drug development methods areknown for being time-consuming, expensive, and less efficient, often taking around a decade and costing billions of dollars. The integration of artificial intelligence (AI) techniques addresses these challenges by enabling the examination of compounds with desired properties from a vast pool of input drugs. Furthermore, it plays a crucial role in drug screening by predicting toxicity, bioactivity, ADME properties (absorption, distribution, metabolism, and excretion), physicochemical properties, and more. AI enhances the drug design process by improving the efficiency and accuracy of predicting drug behaviour, interactions, and properties. These approaches further significantly improve the precision of drug discovery processes and decrease clinical trial costs leading to the development of more effective drugs.
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Affiliation(s)
- Simrandeep Singh
- Department of Electronics & Communication Engineering, UCRD, Chandigarh University, Gharuan, Punjab, India.
| | - Navjot Kaur
- Department of Pharmacognosy, Amar Shaheed Baba Ajit Singh Jujhar Singh Memorial College of Pharmacy, Bela, Ropar, India
| | - Anita Gehlot
- Uttaranchal Institute of technology, Uttaranchal University, Dehradun, India
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Ma C, Gurkan-Cavusoglu E. A comprehensive review of computational cell cycle models in guiding cancer treatment strategies. NPJ Syst Biol Appl 2024; 10:71. [PMID: 38969664 PMCID: PMC11226463 DOI: 10.1038/s41540-024-00397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
This article reviews the current knowledge and recent advancements in computational modeling of the cell cycle. It offers a comparative analysis of various modeling paradigms, highlighting their unique strengths, limitations, and applications. Specifically, the article compares deterministic and stochastic models, single-cell versus population models, and mechanistic versus abstract models. This detailed analysis helps determine the most suitable modeling framework for various research needs. Additionally, the discussion extends to the utilization of these computational models to illuminate cell cycle dynamics, with a particular focus on cell cycle viability, crosstalk with signaling pathways, tumor microenvironment, DNA replication, and repair mechanisms, underscoring their critical roles in tumor progression and the optimization of cancer therapies. By applying these models to crucial aspects of cancer therapy planning for better outcomes, including drug efficacy quantification, drug discovery, drug resistance analysis, and dose optimization, the review highlights the significant potential of computational insights in enhancing the precision and effectiveness of cancer treatments. This emphasis on the intricate relationship between computational modeling and therapeutic strategy development underscores the pivotal role of advanced modeling techniques in navigating the complexities of cell cycle dynamics and their implications for cancer therapy.
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Affiliation(s)
- Chenhui Ma
- Department of Electrical, Computer and Systems Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Evren Gurkan-Cavusoglu
- Department of Electrical, Computer and Systems Engineering, Case Western Reserve University, Cleveland, OH, USA
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Zhang W, Huang RS. Computer-aided drug discovery strategies for novel therapeutics for prostate cancer leveraging next-generating sequencing data. Expert Opin Drug Discov 2024; 19:841-853. [PMID: 38860709 DOI: 10.1080/17460441.2024.2365370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
INTRODUCTION Prostate cancer (PC) is the most common malignancy and accounts for a significant proportion of cancer deaths among men. Although initial therapy success can often be observed in patients diagnosed with localized PC, many patients eventually develop disease recurrence and metastasis. Without effective treatments, patients with aggressive PC display very poor survival. To curb the current high mortality rate, many investigations have been carried out to identify efficacious therapeutics. Compared to de novo drug designs, computational methods have been widely employed to offer actionable drug predictions in a fast and cost-efficient way. Particularly, powered by an increasing availability of next-generation sequencing molecular profiles from PC patients, computer-aided approaches can be tailored to screen for candidate drugs. AREAS COVERED Herein, the authors review the recent advances in computational methods for drug discovery utilizing molecular profiles from PC patients. Given the uniqueness in PC therapeutic needs, they discuss in detail the drug discovery goals of these studies, highlighting their translational values for clinically impactful drug nomination. EXPERT OPINION Evolving molecular profiling techniques may enable new perspectives for computer-aided approaches to offer drug candidates for different tumor microenvironments. With ongoing efforts to incorporate new compounds into large-scale high-throughput screens, the authors envision continued expansion of drug candidate pools.
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Affiliation(s)
- Weijie Zhang
- Department of Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - R Stephanie Huang
- Department of Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
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5
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Paudel KR, Singh M, De Rubis G, Kumbhar P, Mehndiratta S, Kokkinis S, El-Sherkawi T, Gupta G, Singh SK, Malik MZ, Mohammed Y, Oliver BG, Disouza J, Patravale V, Hansbro PM, Dua K. Computational and biological approaches in repurposing ribavirin for lung cancer treatment: Unveiling antitumorigenic strategies. Life Sci 2024; 352:122859. [PMID: 38925223 DOI: 10.1016/j.lfs.2024.122859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/11/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024]
Abstract
Lung cancer is among leading causes of death worldwide. The five-year survival rate of this disease is extremely low (17.8 %), mainly due to difficult early diagnosis and to the limited efficacy of currently available chemotherapeutics. This underlines the necessity to develop innovative therapies for lung cancer. In this context, drug repurposing represents a viable approach, as it reduces the turnaround time of drug development removing costs associated to safety testing of new molecular entities. Ribavirin, an antiviral molecule used to treat hepatitis C virus infections, is particularly promising as repurposed drug for cancer treatment, having shown therapeutic activity against glioblastoma, acute myeloid leukemia, and nasopharyngeal carcinoma. In the present study, we thoroughly investigated the in vitro anticancer activity of ribavirin against A549 human lung adenocarcinoma cells. From a functional standpoint, ribavirin significantly inhibits cancer hallmarks such as cell proliferation, migration, and colony formation. Mechanistically, ribavirin downregulates the expression of numerous proteins and genes regulating cell migration, proliferation, apoptosis, and cancer angiogenesis. The anticancer potential of ribavirin was further investigated in silico through gene ontology pathway enrichment and protein-protein interaction networks, identifying five putative molecular interactors of ribavirin (Erb-B2 Receptor Tyrosine Kinase 4 (Erb-B4); KRAS; Intercellular Adhesion Molecule 1 (ICAM-1); amphiregulin (AREG); and neuregulin-1 (NRG1)). These interactions were characterized via molecular docking and molecular dynamic simulations. The results of this study highlight the potential of ribavirin as a repurposed chemotherapy against lung cancer, warranting further studies to ascertain the in vivo anticancer activity of this molecule.
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Affiliation(s)
- Keshav Raj Paudel
- Centre of Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia
| | - Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida, Uttar Pradesh, India; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Gabriele De Rubis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Popat Kumbhar
- Department of Pharmaceutics, Tatyasaheb Kore College of Pharmacy, Warananagar, Tal: Panhala, Dist: Kolhapur, Maharashtra 416113, India
| | - Samir Mehndiratta
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Sofia Kokkinis
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tammam El-Sherkawi
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Sachin Kumar Singh
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi GT Road, Phagwara 144411, Punjab, India
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait city 15462, Kuwait
| | - Yousuf Mohammed
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Brian G Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia; School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - John Disouza
- Department of Pharmaceutics, Tatyasaheb Kore College of Pharmacy, Warananagar, Tal: Panhala, Dist: Kolhapur, Maharashtra 416113, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Philip Michael Hansbro
- Centre of Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia.
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia.
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Abu-Zahra T, Grimm SE, Scholte M, Raymakers AJN, Kesselheim AS, Joore M. How health technology assessment can help to address challenges in drug repurposing: a conceptual framework. Drug Discov Today 2024; 29:104008. [PMID: 38692506 DOI: 10.1016/j.drudis.2024.104008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
Drug repurposing faces various challenges that can impede its success. We developed a framework outlining key challenges in drug repurposing to explore when and how health technology assessment (HTA) methods can address them. We identified 20 drug-repurposing challenges across the categories of data access, research and development, collaboration, business case, regulatory and legal challenges. Early incorporation of HTA methods, including literature review, empirical research, stakeholder consultation, health economic evaluation and uncertainty assessment, can help to address these challenges. HTA methods canassess the value proposition of repurposed drugs, inform further research and ultimately help to bring cost-effective repurposed drugs to patients.
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Affiliation(s)
- Teebah Abu-Zahra
- Department of Clinical Epidemiology & Medical Technology Assessment (KEMTA), Maastricht University Medical Centre, Maastricht, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, the Netherlands.
| | - Sabine E Grimm
- Department of Clinical Epidemiology & Medical Technology Assessment (KEMTA), Maastricht University Medical Centre, Maastricht, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, the Netherlands
| | - Mirre Scholte
- Department of Clinical Epidemiology & Medical Technology Assessment (KEMTA), Maastricht University Medical Centre, Maastricht, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, the Netherlands
| | - Adam J N Raymakers
- Program on Regulation, Therapeutics, and Law, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron S Kesselheim
- Program on Regulation, Therapeutics, and Law, Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Manuela Joore
- Department of Clinical Epidemiology & Medical Technology Assessment (KEMTA), Maastricht University Medical Centre, Maastricht, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, the Netherlands
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7
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Xu M, Li W, He J, Wang Y, Lv J, He W, Chen L, Zhi H. DDCM: A Computational Strategy for Drug Repositioning Based on Support-Vector Regression Algorithm. Int J Mol Sci 2024; 25:5267. [PMID: 38791306 PMCID: PMC11121335 DOI: 10.3390/ijms25105267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Computational drug-repositioning technology is an effective tool for speeding up drug development. As biological data resources continue to grow, it becomes more important to find effective methods to identify potential therapeutic drugs for diseases. The effective use of valuable data has become a more rational and efficient approach to drug repositioning. The disease-drug correlation method (DDCM) proposed in this study is a novel approach that integrates data from multiple sources and different levels to predict potential treatments for diseases, utilizing support-vector regression (SVR). The DDCM approach resulted in potential therapeutic drugs for neoplasms and cardiovascular diseases by constructing a correlation hybrid matrix containing the respective similarities of drugs and diseases, implementing the SVR algorithm to predict the correlation scores, and undergoing a randomized perturbation and stepwise screening pipeline. Some potential therapeutic drugs were predicted by this approach. The potential therapeutic ability of these drugs has been well-validated in terms of the literature, function, drug target, and survival-essential genes. The method's feasibility was confirmed by comparing the predicted results with the classical method and conducting a co-drug analysis of the sub-branch. Our method challenges the conventional approach to studying disease-drug correlations and presents a fresh perspective for understanding the pathogenesis of diseases.
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Affiliation(s)
- Manyi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
| | - Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
| | - Jiaheng He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
| | - Yahui Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
| | - Junjie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
| | - Weiming He
- Institute of Opto-Electronics, Harbin Institute of Technology, Harbin 150000, China;
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150000, China; (M.X.); (W.L.); (J.H.); (Y.W.); (J.L.)
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Israr J, Alam S, Kumar A. Approaches of pre-clinical and clinical trials of repurposed drug. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:259-275. [PMID: 38789183 DOI: 10.1016/bs.pmbts.2024.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Medications that are currently on the market and have proven therapeutic usage can have new therapeutic indications discovered through a process called drug repurposing, which is also called drug repositioning. This approach presents a viable method for drug developers and pharmaceutical companies to discern novel targets for FDA-approved medications. Drug repurposing presents several advantages, including reduced time consumption, lower costs, and diminished risk of failure. Sildenafil, commonly known as Viagra, serves as a notable illustration of a repurposed pharmaceutical agent, initially developed and introduced to the market as an antianginal medication. However, in the current context, its application has been redirected towards serving as a pharmaceutical intervention for the treatment of erectile dysfunction. Comparably, a multitude of pharmaceutical agents exist that have demonstrated efficacy in repurposing for therapeutic management of various clinical conditions. Focusing on the historical use of repurposed pharmaceuticals and their present state of application in disease therapies, this chapter seeks to offer a thorough review of drug repurposing methodologies. Furthermore, the rules and regulations that control the repurposing of drugs will be covered in detail in this chapter.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh, India; Department of Biotechnology Era University, Lucknow, Uttar Pradesh, India
| | - Shabroz Alam
- Department of Biotechnology Era University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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Afzaal H, Waseem T, Saeed A, Noori FA, Obaidullah, Babar MM. Regulatory considerations and intellectual property rights of repurposed drugs. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:357-375. [PMID: 38789186 DOI: 10.1016/bs.pmbts.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Drug repurposing has emerged as a promising approach in the drug discovery and development process as it offers safe and effective therapeutic options in a time effective manner. Though the issues related to pre-clinical and clinical aspects of drug development process are greatly addressed during drug repurposing yet regulatory perspectives gain even more However, like traditional drug development the repurposed drugs face multiple challenges. Such challenges range from the patenting rights, novelty of repurposing, data and market exclusivity to affordability and equitable access to the patient population. In order to optimize the market access of repurposed drugs, regulatory organizations throughout the world have developed accelerated approval procedures. The regulatory bodies have recognized the importance of repurposing approaches and repurposed drugs. Regulatory bodies can encourage the development of repurposed drugs by providing incentives to pharmaceutical companies and more accessible and affordable repurposed agents for the general population. This chapter summarizes the regulatory and ethical considerations pertaining to the repurposed drugs and highlights a few cases of intellectual property rights for repurposed drugs that have helped improve patient's access to safe, efficacious and cost-effective therapeutic options.
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Affiliation(s)
- Hasan Afzaal
- Drug Regulatory Authority of Pakistan, Islamabad, Pakistan
| | - Tanya Waseem
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Adil Saeed
- Drug Regulatory Authority of Pakistan, Islamabad, Pakistan; Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Fahad Ali Noori
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Obaidullah
- Drug Regulatory Authority of Pakistan, Islamabad, Pakistan
| | - Mustafeez Mujtaba Babar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.
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Rani N, Kaushik A, Kardam S, Kag S, Raj VS, Ambasta RK, Kumar P. Reimagining old drugs with new tricks: Mechanisms, strategies and notable success stories in drug repurposing for neurological diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:23-70. [PMID: 38789181 DOI: 10.1016/bs.pmbts.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Recent evolution in drug repurposing has brought new anticipation, especially in the conflict against neurodegenerative diseases (NDDs). The traditional approach to developing novel drugs for these complex disorders is laborious, time-consuming, and often abortive. However, drug reprofiling which is the implementation of illuminating novel therapeutic applications of existing approved drugs, has shown potential as a promising strategy to accelerate the hunt for therapeutics. The advancement of computational approaches and artificial intelligence has expedited drug repurposing. These progressive technologies have enabled scientists to analyse extensive datasets and predict potential drug-disease interactions. By prospecting into the existing pharmacological knowledge, scientists can recognise potential therapeutic candidates for reprofiling, saving precious time and resources. Preclinical models have also played a pivotal role in this field, confirming the effectiveness and mechanisms of action of repurposed drugs. Several studies have occurred in recent years, including the discovery of available drugs that demonstrate significant protective effects in NDDs, relieve debilitating symptoms, or slow down the progression of the disease. These findings highlight the potential of repurposed drugs to change the landscape of NDD treatment. Here, we present an overview of recent developments and major advances in drug repurposing intending to provide an in-depth analysis of traditional drug discovery and the strategies, approaches and technologies that have contributed to drug repositioning. In addition, this chapter attempts to highlight successful case studies of drug repositioning in various therapeutic areas related to NDDs and explore the clinical trials, challenges and limitations faced by researchers in the field. Finally, the importance of drug repositioning in drug discovery and development and its potential to address discontented medical needs is also highlighted.
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Affiliation(s)
- Neetu Rani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shefali Kardam
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Sonika Kag
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - V Samuel Raj
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India.
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Almoyad MAA, Alsayari A, Wahab S, Chandra S. Hematopoietic cell kinase as a nexus for drug repurposing: implications for cancer and HIV therapy. J Biomol Struct Dyn 2024:1-11. [PMID: 38529911 DOI: 10.1080/07391102.2024.2331092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/10/2024] [Indexed: 03/27/2024]
Abstract
Hematopoietic cell kinase (HCK) has emerged as a potential target for therapeutic intervention in cancer and HIV infection because of its critical role in critical signaling pathways. Repurposing FDA-approved drugs offers an efficient strategy to identify new treatment options. Here, we address the need for novel therapies in cancer and HIV by investigating the potential of repurposed drugs against HCK. Our goal was to identify promising drug candidates with high binding affinities and specific interactions within the HCK binding pocket. We employed an integrated computational approach combining molecular docking and extensive molecular dynamics (MD) simulations. Initially, we analyzed the binding affinities and interaction patterns of a library of FDA-approved drugs sourced from DrugBank. After careful analysis, we focused on two compounds, Nilotinib and Radotinib, which exhibit exceptional binding affinities and specificity to the HCK binding pocket, including the active site. Additionally, we assessed the pharmacological properties of Nilotinib and Radotinib, making them attractive candidates for further drug development. Extensive all-atom MD simulations spanning 200 nanoseconds (ns) elucidated the conformational dynamics and stability of the HCK-Nilotinib and HCK-Radotinib complexes. These simulations demonstrate the robustness of these complexes over extended timescales. Our findings highlighted the potential of Nilotinib and Radotinib as promising candidates against HCK that offer valuable insights into their binding mechanisms. This computational approach provides a comprehensive understanding of drug interactions with HCK and sets the stage for future experimental validation and drug development endeavors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Khamis Mushyt, Saudi Arabia
| | - Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Saudi Arabia
| | - Subhash Chandra
- Department of Botany, Soban Singh Jeena University, Almora, India
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12
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Alrouji M, Yasmin S, Alhumaydhi FA, Sharaf SE, Shahwan M, Shamsi A. Unlocking therapeutic potential: computational insights into TREM2 protein targeting with FDA-approved drugs for neurodegeneration. J Biomol Struct Dyn 2024:1-11. [PMID: 38373093 DOI: 10.1080/07391102.2024.2317987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024]
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD) pose a significant global health challenge that requires the exploration of innovative therapeutic strategies. Triggering receptor expressed on myeloid cells-2 (TREM2) is one of the critical proteins involved in immune regulation and neuroinflammation. It has emerged as a promising therapeutic target to develop treatments for neurodegenerative disorders like AD. Here, we employed a comprehensive virtual screening approach to identify potential small molecule inhibitors among FDA-approved drugs for TREM2. The docking study reveals significant binding affinity, ranging from -7.8 kcal/mol to -8.5 kcal/mol, for the elucidated hits against TREM2, accompanied by several crucial interactions. Among the repurposed drugs identified in the initial screening, Carpipramine, Clocapramine, and Pimozide stood out due to their notable binding potential and favorable drug profiling. Further, we conducted molecular dynamics (MD) simulations on the selected molecules that probed their structural dynamics and stability within the TREM2 binding pocket. The structural parameters and hydrogen bond dynamics remained remarkably stable throughout the simulated trajectories. Furthermore, we performed principal component analysis (PCA) and constructed free energy landscapes (FELs) to gain deeper insights into ligand binding and conformational flexibility of TREM2. The findings revealed that the elucidated molecules, Carpipramine, Clocapramine, and Pimozide, exhibited an exceptional fit within the binding pocket of TREM2 with remarkable stability and interaction patterns throughout the 500 ns simulation window. Interestingly, these molecules possessed a spectrum of anti-neurodegenerative properties and favorable drug profiles, which suggest their potential as promising drug candidates for repurposing in the treatment of AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Sabina Yasmin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Sharaf E Sharaf
- Pharmaceutical Sciences Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Moyad Shahwan
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
- Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, United Arab Emirates
| | - Anas Shamsi
- Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, United Arab Emirates
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13
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Kaur J, Rana P, Matta T, Sodhi RK, Pathania K, Pawar SV, Kuhad A, Kondepudi KK, Kaur T, Dhingra N, Sah SP. Protective effect of olopatadine hydrochloride against LPS-induced acute lung injury: via targeting NF-κB signaling pathway. Inflammopharmacology 2024; 32:603-627. [PMID: 37847473 DOI: 10.1007/s10787-023-01353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/21/2023] [Indexed: 10/18/2023]
Abstract
BACKGROUND Morbidity and mortality rates associated with acute lung injury/acute respiratory distress syndrome (ALI/ARDS) are high (30-40%). Nuclear factor-kappa B (NF-κB) is a transcription factor, associated with transcription of numerous cytokines leading to cytokine storm, and thereby, plays a major role in ALI/ARDS and in advanced COVID-19 syndrome. METHODS Considering the role of NF-κB in ALI, cost-effective in silico approaches were utilized in the study to identify potential NF-κB inhibitor based on the docking and pharmacokinetic results. The identified compound was then pharmacologically validated in lipopolysaccharide (LPS) rodent model of acute lung injury. LPS induces ALI by altering alveolar membrane permeability, recruiting activated neutrophils and macrophages to the lungs, and compromising the alveolar membrane integrity and ultimately impairs the gaseous exchange. Furthermore, LPS exposure is associated with exaggerated production of various proinflammatory cytokines in lungs. RESULTS Based on in silico studies Olopatadine Hydrochloride (Olo), an FDA-approved drug was found as a potential NF-κB inhibitor which has been reported for the first time, and considered further for the pharmacological validation. Intraperitoneal LPS administration resulted in ALI/ARDS by fulfilling 3 out of the 4 criteria described by ATS committee (2011) published workshop report. However, treatment with Olo attenuated LPS-induced elevation of proinflammatory markers (IL-6 and NF-κB), oxidative stress, neutrophil infiltration, edema, and damage in lungs. Histopathological studies also revealed that Olo treatment significantly ameliorated LPS-induced lung injury, thus conferring improvement in survival. Especially, the effects produced by Olo medium dose (1 mg/kg) were comparable to dexamethasone standard. CONCLUSION In nutshell, inhibition of NF-κB pathway by Olo resulted in protection and reduced mortality in LPS- induced ALI and thus has potential to be used clinically to arrest disease progression in ALI/ARDS, since the drug is already in the market. However, the findings warrant further extensive studies, and also future studies can be planned to elucidate its role in COVID-19-associated ARDS or cytokine storm.
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Affiliation(s)
- Jaspreet Kaur
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
| | - Priyanka Rana
- Pharmaceutical Chemistry Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
| | - Tushar Matta
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
- Food and Nutrition Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupinder Kaur Sodhi
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
| | - Khushboo Pathania
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
| | - Sandip V Pawar
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
| | - Anurag Kuhad
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India
| | - Kanthi Kiran Kondepudi
- Food and Nutrition Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tanzeer Kaur
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
| | - Neelima Dhingra
- Pharmaceutical Chemistry Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India.
| | - Sangeeta Pilkhwal Sah
- Pharmacology Division, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, 160014, India.
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14
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Furkan M, Khan MS, Shahwan M, Hassan N, Yadav DK, Anwar S, Khan RH, Shamsi A. Identifying repurposed drugs as potential inhibitors of Apolipoprotein E: A bioinformatics approach to target complex diseases associated with lipid metabolism and neurodegeneration. Int J Biol Macromol 2024; 259:129167. [PMID: 38176507 DOI: 10.1016/j.ijbiomac.2023.129167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Apolipoprotein E (ApoE), a pivotal contributor to lipid metabolism and neurodegenerative disorders, emerges as an attractive target for therapeutic intervention. Within this study, we deployed an integrated in-silico strategy, harnessing structure-based virtual screening, to identify potential compounds from DrugBank database. Employing molecular docking, we unveil initial hits by evaluating their binding efficiency with ApoE. This first tier of screening narrows our focus to compounds that exhibit a strong propensity to bind with ApoE. Further, a detailed interaction analysis was carried out to explore the binding patterns of the selected hits towards the ApoE binding site. The selected compounds were then evaluated for the biological properties in PASS analysis, which showed anti-neurodegenerative properties. Building upon this foundation, we delve deeper, employing all-atom molecular dynamics (MD) simulations extending over an extensive 500 ns. In particular, Ergotamine and Dihydroergocristine emerge as noteworthy candidates, binding to ApoE in a competitive mode. This intriguing binding behavior positions these compounds as potential candidates warranting further analysis in the pursuit of novel therapeutics targeting complex diseases associated with lipid metabolism and neurodegeneration. This approach holds the promise of catalyzing advancements in therapeutic intervention for complex disorders, thereby reporting a meaningful pace towards improved healthcare outcomes.
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Affiliation(s)
- Mohammad Furkan
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Saudi Arabia.
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, P.O. Box 346, United Arab Emirates.
| | - Nageeb Hassan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates; Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, P.O. Box 346, United Arab Emirates.
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, Republic of Korea.
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates.
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15
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Hamid A, Mäser P, Mahmoud AB. Drug Repurposing in the Chemotherapy of Infectious Diseases. Molecules 2024; 29:635. [PMID: 38338378 PMCID: PMC10856722 DOI: 10.3390/molecules29030635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Repurposing is a universal mechanism for innovation, from the evolution of feathers to the invention of Velcro tape. Repurposing is particularly attractive for drug development, given that it costs more than a billion dollars and takes longer than ten years to make a new drug from scratch. The COVID-19 pandemic has triggered a large number of drug repurposing activities. At the same time, it has highlighted potential pitfalls, in particular when concessions are made to the target product profile. Here, we discuss the pros and cons of drug repurposing for infectious diseases and analyze different ways of repurposing. We distinguish between opportunistic and rational approaches, i.e., just saving time and money by screening compounds that are already approved versus repurposing based on a particular target that is common to different pathogens. The latter can be further distinguished into divergent and convergent: points of attack that are divergent share common ancestry (e.g., prokaryotic targets in the apicoplast of malaria parasites), whereas those that are convergent arise from a shared lifestyle (e.g., the susceptibility of bacteria, parasites, and tumor cells to antifolates due to their high rate of DNA synthesis). We illustrate how such different scenarios can be capitalized on by using examples of drugs that have been repurposed to, from, or within the field of anti-infective chemotherapy.
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Affiliation(s)
- Amal Hamid
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
| | - Pascal Mäser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, 4123 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Abdelhalim Babiker Mahmoud
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
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16
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Shamsi A, Khan MS, Altwaijry N, Hassan N, Shahwan M, Yadav DK. Targeting PDE4A for therapeutic potential: exploiting drug repurposing approach through virtual screening and molecular dynamics. J Biomol Struct Dyn 2024:1-13. [PMID: 38287492 DOI: 10.1080/07391102.2024.2308764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
cAMP-specific 3',5'-cyclic phosphodiesterase 4 A (PDE4A) holds a pivotal role in modulating intracellular levels of cyclic adenosine monophosphate (cAMP). Targeting PDE4A with novel therapeutic agents shows promise in addressing neurological disorders (e.g. Alzheimer's and Parkinson's diseases), mood disorders (depression, anxiety), inflammatory conditions (asthma, chronic obstructive pulmonary disease), and even cancer. In this study, we present a comprehensive approach that integrates virtual screening and molecular dynamics (MD) simulations to identify potential inhibitors of PDE4A from the existing pool of FDA-approved drugs. The initial compound selection was conducted focusing on binding affinity scores, which led to the identification of several high-affinity compounds with potential PDE4A binding properties. From the refined selection process, two promising compounds, Fluspirilene and Dihydroergocristine, emerged as strong candidates, displaying substantial affinity and specificity for the PDE4A binding site. Interaction analysis provided robust evidence of their binding capabilities. To gain deeper insights into the dynamic behavior of Fluspirilene and Dihydroergocristine in complex with PDE4A, we conducted 300 ns MD simulations, principal components analysis (PCA), and free energy landscape (FEL) analysis. These analyses revealed that Fluspirilene and Dihydroergocristine binding stabilized the PDE4A structure and induced minimal conformational changes, highlighting their potential as potent binders. In conclusion, our study systematically explores repurposing existing FDA-approved drugs as PDE4A inhibitors through a comprehensive virtual screening pipeline. The identified compounds, Fluspirilene and Dihydroergocristine, exhibit a strong affinity for PDE4A, displaying characteristics that support their suitability for further development as potential therapeutic agents for conditions associated with PDE4A dysfunction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nojood Altwaijry
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nageeb Hassan
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Dharmendra Kumar Yadav
- Department of Pharmacy, Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Incheon, Republic of Korea
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17
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Duranti E, Cordani N, Villa C. Edaravone: A Novel Possible Drug for Cancer Treatment? Int J Mol Sci 2024; 25:1633. [PMID: 38338912 PMCID: PMC10855093 DOI: 10.3390/ijms25031633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Despite significant advancements in understanding the causes and progression of tumors, cancer remains one of the leading causes of death worldwide. In light of advances in cancer therapy, there has been a growing interest in drug repurposing, which involves exploring new uses for medications that are already approved for clinical use. One such medication is edaravone, which is currently used to manage patients with cerebral infarction and amyotrophic lateral sclerosis. Due to its antioxidant and anti-inflammatory properties, edaravone has also been investigated for its potential activities in treating cancer, notably as an anti-proliferative and cytoprotective drug against side effects induced by traditional cancer therapies. This comprehensive review aims to provide updates on the various applications of edaravone in cancer therapy. It explores its potential as a standalone antitumor drug, either used alone or in combination with other medications, as well as its role as an adjuvant to mitigate the side effects of conventional anticancer treatments.
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Affiliation(s)
| | | | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (E.D.); (N.C.)
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18
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Sinha P, Yadav AK. Repurposing integrase inhibitors against human T-lymphotropic virus type-1: a computational approach. J Biomol Struct Dyn 2024:1-12. [PMID: 38234060 DOI: 10.1080/07391102.2024.2304681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Adult T-cell Lymphoma (ATL) is caused by the delta retrovirus family member known as Human T-cell Leukaemia Type I (HTLV-1). Due to the unavailability of any cure, the study gained motivation to identify some repurposed drugs against the virus. A quick and accurate method of screening licensed medications for finding a treatment for HTLV-1 is by cheminformatics drug repurposing in order to analyze a dataset of FDA approved integrase antivirals against HTLV-1 infection. To determine how the antiviral medications interacted with the important residues in the HTLV-1 integrase active regions, molecular docking modeling was used. The steady behavior of the ligands inside the active region was then confirmed by molecular dynamics for the probable receptor-drug complexes. Cabotegravir, Raltegravir and Elvitegravir had the best docking scores with the target, indicating that they can tightly bind to the HTLV-1 integrase. Moreover, MD simulation revealed that the Cabotegravir-HTLV-1, Raltegravir-HTLV-1 and Elvitegravir-HTLV-1 interactions were stable. It is obvious that more testing of these medicines in both clinical trials and experimental tests is necessary to demonstrate their efficacy against HTLV-1 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prashasti Sinha
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Anil Kumar Yadav
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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19
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Xiang S, Lawrence PJ, Peng B, Chiang C, Kim D, Shen L, Ning X. Modeling Path Importance for Effective Alzheimer's Disease Drug Repurposing. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024; 29:306-321. [PMID: 38160288 PMCID: PMC11056095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Recently, drug repurposing has emerged as an effective and resource-efficient paradigm for AD drug discovery. Among various methods for drug repurposing, network-based methods have shown promising results as they are capable of leveraging complex networks that integrate multiple interaction types, such as protein-protein interactions, to more effectively identify candidate drugs. However, existing approaches typically assume paths of the same length in the network have equal importance in identifying the therapeutic effect of drugs. Other domains have found that same length paths do not necessarily have the same importance. Thus, relying on this assumption may be deleterious to drug repurposing attempts. In this work, we propose MPI (Modeling Path Importance), a novel network-based method for AD drug repurposing. MPI is unique in that it prioritizes important paths via learned node embeddings, which can effectively capture a network's rich structural information. Thus, leveraging learned embeddings allows MPI to effectively differentiate the importance among paths. We evaluate MPI against a commonly used baseline method that identifies anti-AD drug candidates primarily based on the shortest paths between drugs and AD in the network. We observe that among the top-50 ranked drugs, MPI prioritizes 20.0% more drugs with anti-AD evidence compared to the baseline. Finally, Cox proportional-hazard models produced from insurance claims data aid us in identifying the use of etodolac, nicotine, and BBB-crossing ACE-INHs as having a reduced risk of AD, suggesting such drugs may be viable candidates for repurposing and should be explored further in future studies.
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Affiliation(s)
- Shunian Xiang
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick J. Lawrence
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Bo Peng
- Computer Science and Engineering Department, The Ohio State University, Columbus, OH 43210, USA
| | - ChienWei Chiang
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Li Shen
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Xia Ning
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
- Computer Science and Engineering Department, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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20
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Gao Z, Ding P, Xu R. IUPHAR review - Data-driven computational drug repurposing approaches for opioid use disorder. Pharmacol Res 2024; 199:106960. [PMID: 37832859 DOI: 10.1016/j.phrs.2023.106960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Opioid Use Disorder (OUD) is a chronic and relapsing condition characterized by the misuse of opioid drugs, causing significant morbidity and mortality in the United States. Existing medications for OUD are limited, and there is an immediate need to discover treatments with enhanced safety and efficacy. Drug repurposing aims to find new indications for existing medications, offering a time-saving and cost-efficient alternative strategy to traditional drug discovery. Computational approaches have been developed to further facilitate the drug repurposing process. In this paper, we reviewed state-of-the-art data-driven computational drug repurposing approaches for OUD and discussed their advantages and potential challenges. We also highlighted promising repurposed candidate drugs for OUD that were identified by computational drug repurposing techniques and reviewed studies supporting their potential mechanisms of action in treating OUD.
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Affiliation(s)
- Zhenxiang Gao
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Pingjian Ding
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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21
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Li D, Xiao Z, Sun H, Jiang X, Zhao W, Shen X. Prediction of Drug-Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:120-128. [PMID: 38051617 DOI: 10.1109/tcbb.2023.3339189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Computational drug repositioning can identify potential associations between drugs and diseases. This technology has been shown to be effective in accelerating drug development and reducing experimental costs. Although there has been plenty of research for this task, existing methods are deficient in utilizing complex relationships among biological entities, which may not be conducive to subsequent simulation of drug treatment processes. In this article, we propose a heterogeneous graph embedding method called HMLKGAT to infer novel potential drugs for diseases. More specifically, we first construct a heterogeneous information network by combining drug-disease, drug-protein and disease-protein biological networks. Then, a multi-layer graph attention model is utilized to capture the complex associations in the network to derive representations for drugs and diseases. Finally, to maintain the relationship of nodes in different feature spaces, we propose a multi-kernel learning method to transform and combine the representations. Experimental results demonstrate that HMLKGAT outperforms six state-of-the-art methods in drug-related disease prediction, and case studies of five classical drugs further demonstrate the effectiveness of HMLKGAT.
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22
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Alrouji M, Alhumaydhi FA, Alsayari A, Sharaf SE, Shafi S, Anwar S, Shahwan M, Atiya A, Shamsi A. Targeting Sirtuin 1 for therapeutic potential: Drug repurposing approach integrating docking and molecular dynamics simulations. PLoS One 2023; 18:e0293185. [PMID: 38117829 PMCID: PMC10732437 DOI: 10.1371/journal.pone.0293185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/08/2023] [Indexed: 12/22/2023] Open
Abstract
Identifying novel therapeutic agents is a fundamental challenge in contemporary drug development, especially in the context of complex diseases like cancer, neurodegenerative disorders, and metabolic syndromes. Here, we present a comprehensive computational study to identify potential inhibitors of SIRT1 (Sirtuin 1), a critical protein involved in various cellular processes and disease pathways. Leveraging the concept of drug repurposing, we employed a multifaceted approach that integrates molecular docking and molecular dynamics (MD) simulations to predict the binding affinities and dynamic behavior of a diverse set of FDA-approved drugs from DrugBank against the SIRT1. Initially, compounds were shortlisted based on their binding affinities and interaction analyses to identify safe and promising binding partners for SIRT1. Among these candidates, Doxercalciferol and Timiperone emerged as potential candidates, displaying notable affinity, efficiency, and specificity towards the binding pocket of SIRT1. Extensive evaluation revealed that these identified compounds boast a range of favorable biological properties and prefer binding to the active site of SIRT1. To delve deeper into the interactions, all-atom MD simulations were conducted for 500 nanoseconds (ns). These simulations assessed the conformational dynamics, stability, and interaction mechanism of the SIRT1-Doxercalciferol and SIRT1-Timiperone complexes. The MD simulations illustrated that the SIRT1-Doxercalciferol and SIRT1-Timiperone complexes maintain stability over a 500 ns trajectory. These insightful outcomes propose that Doxercalciferol and Timiperone hold promise as viable scaffolds for developing potential SIRT1 inhibitors, with implications for tackling complex diseases such as cancer, neurodegenerative disorders, and metabolic syndromes.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
- Complementary and Alternative Medicine Unit, King Khalid University (KKU), Abha, Saudi Arabia
| | - Sharaf E. Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University Makkah, Makkah, Saudi Arabia
| | - Sheeba Shafi
- Department of Nursing, College of Applied Medical Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
| | - Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
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23
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Pinzi L, Rastelli G. Trends and Applications in Computationally Driven Drug Repurposing. Int J Mol Sci 2023; 24:16511. [PMID: 38003701 PMCID: PMC10671888 DOI: 10.3390/ijms242216511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Drug repurposing is a widely used approach originally developed to aid in the identification of new uses of already existing drugs outside the scope of the original medical indication [...].
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Affiliation(s)
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy;
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Bourdakou MM, Fernández-Ginés R, Cuadrado A, Spyrou GM. Drug repurposing on Alzheimer's disease through modulation of NRF2 neighborhood. Redox Biol 2023; 67:102881. [PMID: 37696195 PMCID: PMC10500459 DOI: 10.1016/j.redox.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Alzheimer's disease (AD) is an age-dependent neurodegenerative disorder and the most common cause of cognitive decline. The alarming epidemiological features of Alzheimer's disease, combined with the high failure rate of candidate drugs tested in the preclinical phase, impose more intense investigations for new curative treatments. NRF2 (Nuclear factor-erythroid factor 2-related factor 2) plays a critical role in the inflammatory response and in the cellular redox homeostasis and provides cytoprotection in several diseases including those in the neurodegeneration spectrum. These roles suggest that NRF2 and its directly associated proteins may be novel attractive therapeutic targets in the fight against AD. In this study, through a systemics perspective, we propose an in silico drug repurposing approach for AD, based on the NRF2 interactome and regulome, with the aim of highlighting possible repurposed drugs for AD. Using publicly available information based on differential expressions of the NRF2-neighborhood in AD and through a computational drug repurposing pipeline, we derived to a short list of candidate repurposed drugs and small molecules that affect the expression levels of the majority of NRF2-partners. The relevance of these findings was assessed in a four-step computational meta-analysis including i) structural similarity comparisons with currently ongoing NRF2-related drugs in clinical trials ii) evaluation based on the NRF2-diseasome iii) comparison of relevance between targeted pathways of shortlisted drugs and NRF2-related drugs in clinical trials and iv) further comparison with existing knowledge on AD and NRF2-related drugs in clinical trials based on their known modes of action. Overall, our analysis yielded in 5 candidate repurposed drugs for AD. In cell culture, these 5 candidates activated a luciferase reporter for NRF2 activity and in hippocampus derived TH22 cells they increased NRF2 protein levels and the NRF2 transcriptional signatures as determined by increased expression of its downstream target heme oxygenase 1. We expect that our proposed candidate repurposed drugs will be useful for further research and clinical translation for AD.
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Affiliation(s)
- Marilena M Bourdakou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Raquel Fernández-Ginés
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
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Xiang S, Lawrence PJ, Peng B, Chiang C, Kim D, Shen L, Ning X. Modeling Path Importance for Effective Alzheimer's Disease Drug Repurposing. ARXIV 2023:arXiv:2310.15211v2. [PMID: 37961739 PMCID: PMC10635281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Recently, drug repurposing has emerged as an effective and resource-efficient paradigm for AD drug discovery. Among various methods for drug repurposing, network-based methods have shown promising results as they are capable of leveraging complex networks that integrate multiple interaction types, such as protein-protein interactions, to more effectively identify candidate drugs. However, existing approaches typically assume paths of the same length in the network have equal importance in identifying the therapeutic effect of drugs. Other domains have found that same length paths do not necessarily have the same importance. Thus, relying on this assumption may be deleterious to drug repurposing attempts. In this work, we propose MPI (Modeling Path Importance), a novel network-based method for AD drug repurposing. MPI is unique in that it prioritizes important paths via learned node embeddings, which can effectively capture a network's rich structural information. Thus, leveraging learned embeddings allows MPI to effectively differentiate the importance among paths. We evaluate MPI against a commonly used baseline method that identifies anti-AD drug candidates primarily based on the shortest paths between drugs and AD in the network. We observe that among the top-50 ranked drugs, MPI prioritizes 20.0% more drugs with anti-AD evidence compared to the baseline. Finally, Cox proportional-hazard models produced from insurance claims data aid us in identifying the use of etodolac, nicotine, and BBB-crossing ACE-INHs as having a reduced risk of AD, suggesting such drugs may be viable candidates for repurposing and should be explored further in future studies.
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Affiliation(s)
- Shunian Xiang
- Biomedical Informatics Department, The Ohio State University,
Columbus, OH 43210, USA
| | - Patrick J. Lawrence
- Biomedical Informatics Department, The Ohio State University,
Columbus, OH 43210, USA
| | - Bo Peng
- Computer Science and Engineering Department, The Ohio State
University, Columbus, OH 43210, USA
| | - ChienWei Chiang
- Biomedical Informatics Department, The Ohio State University,
Columbus, OH 43210, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology, and Informatics,
University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Li Shen
- Department of Biostatistics, Epidemiology, and Informatics,
University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Xia Ning
- Biomedical Informatics Department, The Ohio State University,
Columbus, OH 43210, USA
- Computer Science and Engineering Department, The Ohio State
University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State
University, Columbus, OH 43210, USA
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Rao M, McDuffie E, Sachs C. Artificial Intelligence/Machine Learning-Driven Small Molecule Repurposing via Off-Target Prediction and Transcriptomics. TOXICS 2023; 11:875. [PMID: 37888725 PMCID: PMC10611213 DOI: 10.3390/toxics11100875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]
Abstract
The process of discovering small molecule drugs involves screening numerous compounds and optimizing the most promising ones, both in vitro and in vivo. However, approximately 90% of these optimized candidates fail during trials due to unexpected toxicity or insufficient efficacy. Current concepts with respect to drug-protein interactions suggest that each small molecule interacts with an average of 6-11 targets. This implies that approved drugs and even discontinued compounds could be repurposed by leveraging their interactions with unintended targets. Therefore, we developed a computational repurposing framework for small molecules, which combines artificial intelligence/machine learning (AI/ML)-based and chemical similarity-based target prediction methods with cross-species transcriptomics information. This repurposing methodology incorporates eight distinct target prediction methods, including three machine learning methods. By using multiple orthogonal methods for a "dataset" composed of 2766 FDA-approved drugs targeting multiple therapeutic target classes, we identified 27,371 off-target interactions involving 2013 protein targets (i.e., an average of around 10 interactions per drug). Relative to the drugs in the dataset, we identified 150,620 structurally similar compounds. The highest number of predicted interactions were for drugs targeting G protein-coupled receptors (GPCRs), enzymes, and kinases with 10,648, 4081, and 3678 interactions, respectively. Notably, 17,283 (63%) of the off-target interactions have been confirmed in vitro. Approximately 4000 interactions had an IC50 of <100 nM for 1105 FDA-approved drugs and 1661 interactions had an IC50 of <10 nM for 696 FDA-approved drugs. Together, the confirmation of numerous predicted interactions and the exploration of tissue-specific expression patterns in human and animal tissues offer insights into potential drug repurposing for new therapeutic applications.
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Affiliation(s)
- Mohan Rao
- Neurocrine Biosciences, Inc., Nonclinical Toxicology, San Diego, CA 92130, USA; (E.M.); (C.S.)
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Ghafoor N, Yildiz A. Targeting MDM2-p53 Axis through Drug Repurposing for Cancer Therapy: A Multidisciplinary Approach. ACS OMEGA 2023; 8:34583-34596. [PMID: 37779953 PMCID: PMC10536845 DOI: 10.1021/acsomega.3c03471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Cancer remains a major cause of morbidity and mortality worldwide, and while current therapies, such as chemotherapy, immunotherapy, and cell therapy, have been effective in many patients, the development of novel therapeutic options remains an urgent priority. Mouse double minute 2 (MDM2) is a key regulator of the tumor suppressor protein p53, which plays a critical role in regulating cellular growth, apoptosis, and DNA repair. Consequently, MDM2 has been the subject of extensive research aimed at developing novel cancer therapies. In this study, we employed a machine learning-based approach to establish a quantitative structure-activity relationship model capable of predicting the potential in vitro efficacy of small molecules as MDM2 inhibitors. Our model was used to screen 5883 FDA-approved drugs, resulting in the identification of promising hits that were subsequently evaluated using molecular docking and molecular dynamics simulations. Two antihistamine drugs, cetirizine (CZ) and rupatadine (RP), exhibited particularly favorable results in the initial in silico analyses. To further assess their potential use as the activators of the p53 pathway, we investigated the antiproliferative capability of the abovementioned drugs on human glioblastoma and neuroblastoma cell lines. Both the compounds exhibited significant antiproliferative effects on the abovementioned cell lines in a dose-dependent manner. The half-maximal inhibitory concentration (IC50) of CZ was found to be 697.87 and 941.37 μM on U87 and SH-SY5Y cell lines, respectively, while the IC50 of RP was found to be 524.28 and 617.07 μM on the same cell lines, respectively. Further investigation by quantitative reverse transcriptase polymerase chain reaction analysis revealed that the CZ-treated cell lines upregulate the expression of the p53-regulated genes involved in cell cycle arrest, apoptosis, and DNA damage response compared to their respective vehicle controls. These findings suggest that CZ activates the p53 pathway by inhibiting MDM2. Our results provide compelling preclinical evidence supporting the potential use of CZ as a modulator of the MDM2-p53 axis and its plausible repurposing for cancer treatment.
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Affiliation(s)
- Naeem
Abdul Ghafoor
- Department
of Molecular Biology and Genetics, Graduate School of Natural and
Applied Sciences, Mugla Sitki Kocman University, 48000 Mugla, Turkey
| | - Aysegul Yildiz
- Department
of Molecular Biology and Genetics, Graduate School of Natural and
Applied Sciences, Mugla Sitki Kocman University, 48000 Mugla, Turkey
- Department
of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, 48000 Mugla, Turkey
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Das A, Pathak S, Premkumar M, Sarpparajan CV, Balaji ER, Duttaroy AK, Banerjee A. A brief overview of SARS-CoV-2 infection and its management strategies: a recent update. Mol Cell Biochem 2023:10.1007/s11010-023-04848-3. [PMID: 37742314 DOI: 10.1007/s11010-023-04848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023]
Abstract
The COVID-19 pandemic has become a global health crisis, inflicting substantial morbidity and mortality worldwide. A diverse range of symptoms, including fever, cough, dyspnea, and fatigue, characterizes COVID-19. A cytokine surge can exacerbate the disease's severity. This phenomenon involves an increased immune response, marked by the excessive release of inflammatory cytokines like IL-6, IL-8, TNF-α, and IFNγ, leading to tissue damage and organ dysfunction. Efforts to reduce the cytokine surge and its associated complications have garnered significant attention. Standardized management protocols have incorporated treatment strategies, with corticosteroids, chloroquine, and intravenous immunoglobulin taking the forefront. The recent therapeutic intervention has also assisted in novel strategies like repurposing existing medications and the utilization of in vitro drug screening methods to choose effective molecules against viral infections. Beyond acute management, the significance of comprehensive post-COVID-19 management strategies, like remedial measures including nutritional guidance, multidisciplinary care, and follow-up, has become increasingly evident. As the understanding of COVID-19 pathogenesis deepens, it is becoming increasingly evident that a tailored approach to therapy is imperative. This review focuses on effective treatment measures aimed at mitigating COVID-19 severity and highlights the significance of comprehensive COVID-19 management strategies that show promise in the battle against COVID-19.
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Affiliation(s)
- Alakesh Das
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Madhavi Premkumar
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Chitra Veena Sarpparajan
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Esther Raichel Balaji
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India
| | - Asim K Duttaroy
- Department of Nutrition, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, Tamil Nadu, 603103, India.
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Mohi-Ud-Din R, Chawla A, Sharma P, Mir PA, Potoo FH, Reiner Ž, Reiner I, Ateşşahin DA, Sharifi-Rad J, Mir RH, Calina D. Repurposing approved non-oncology drugs for cancer therapy: a comprehensive review of mechanisms, efficacy, and clinical prospects. Eur J Med Res 2023; 28:345. [PMID: 37710280 PMCID: PMC10500791 DOI: 10.1186/s40001-023-01275-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023] Open
Abstract
Cancer poses a significant global health challenge, with predictions of increasing prevalence in the coming years due to limited prevention, late diagnosis, and inadequate success with current therapies. In addition, the high cost of new anti-cancer drugs creates barriers in meeting the medical needs of cancer patients, especially in developing countries. The lengthy and costly process of developing novel drugs further hinders drug discovery and clinical implementation. Therefore, there has been a growing interest in repurposing approved drugs for other diseases to address the urgent need for effective cancer treatments. The aim of this comprehensive review is to provide an overview of the potential of approved non-oncology drugs as therapeutic options for cancer treatment. These drugs come from various chemotherapeutic classes, including antimalarials, antibiotics, antivirals, anti-inflammatory drugs, and antifungals, and have demonstrated significant antiproliferative, pro-apoptotic, immunomodulatory, and antimetastatic properties. A systematic review of the literature was conducted to identify relevant studies on the repurposing of approved non-oncology drugs for cancer therapy. Various electronic databases, such as PubMed, Scopus, and Google Scholar, were searched using appropriate keywords. Studies focusing on the therapeutic potential, mechanisms of action, efficacy, and clinical prospects of repurposed drugs in cancer treatment were included in the analysis. The review highlights the promising outcomes of repurposing approved non-oncology drugs for cancer therapy. Drugs belonging to different therapeutic classes have demonstrated notable antitumor effects, including inhibiting cell proliferation, promoting apoptosis, modulating the immune response, and suppressing metastasis. These findings suggest the potential of these repurposed drugs as effective therapeutic approaches in cancer treatment. Repurposing approved non-oncology drugs provides a promising strategy for addressing the urgent need for effective and accessible cancer treatments. The diverse classes of repurposed drugs, with their demonstrated antiproliferative, pro-apoptotic, immunomodulatory, and antimetastatic properties, offer new avenues for cancer therapy. Further research and clinical trials are warranted to explore the full potential of these repurposed drugs and optimize their use in treating various cancer types. Repurposing approved drugs can significantly expedite the process of identifying effective treatments and improve patient outcomes in a cost-effective manner.
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Affiliation(s)
- Roohi Mohi-Ud-Din
- Department of General Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, Jammu and Kashmir, 190001, India
| | - Apporva Chawla
- Khalsa College of Pharmacy, G.T. Road, Amritsar, Punjab, 143001, India
| | - Pooja Sharma
- Khalsa College of Pharmacy, G.T. Road, Amritsar, Punjab, 143001, India
| | - Prince Ahad Mir
- Khalsa College of Pharmacy, G.T. Road, Amritsar, Punjab, 143001, India
| | - Faheem Hyder Potoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 1982, 31441, Dammam, Saudi Arabia
| | - Željko Reiner
- Department of Internal Medicine, School of Medicine, University Hospital Center Zagreb, Zagreb, Croatia
| | - Ivan Reiner
- Department of Nursing Sciences, Catholic University of Croatia, Ilica 242, 10000, Zagreb, Croatia
| | - Dilek Arslan Ateşşahin
- Baskil Vocational School, Department of Plant and Animal Production, Fırat University, 23100, Elazıg, Turkey
| | | | - Reyaz Hassan Mir
- Pharmaceutical Chemistry Division, Department of Pharmaceutical Sciences, University of Kashmir, Hazratbal, Srinagar, Kashmir, 190006, India.
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
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Annamalai A, Karuppaiya V, Ezhumalai D, Cheruparambath P, Balakrishnan K, Venkatesan A. Nano-based techniques: A revolutionary approach to prevent covid-19 and enhancing human awareness. J Drug Deliv Sci Technol 2023; 86:104567. [PMID: 37313114 PMCID: PMC10183109 DOI: 10.1016/j.jddst.2023.104567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
In every century of history, there are many new diseases emerged, which are not even cured by many developed countries. Today, despite of scientific development, new deadly pandemic diseases are caused by microorganisms. Hygiene is considered to be one of the best methods of avoiding such communicable diseases, especially viral diseases. Illness caused by SARS-CoV-2 was termed COVID-19 by the WHO, the acronym derived from "coronavirus disease 2019. The globe is living in the worst epidemic era, with the highest infection and mortality rate owing to COVID-19 reaching 6.89% (data up to March 2023). In recent years, nano biotechnology has become a promising and visible field of nanotechnology. Interestingly, nanotechnology is being used to cure many ailments and it has revolutionized many aspects of our lives. Several COVID-19 diagnostic approaches based on nanomaterial have been developed. The various metal NPs, it is highly anticipated that could be viable and economical alternatives for treating drug resistant in many deadly pandemic diseases in near future. This review focuses on an overview of nanotechnology's increasing involvement in the diagnosis, prevention, and therapy of COVID-19, also this review provides readers with an awareness and knowledge of importance of hygiene.
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Affiliation(s)
- Asaikkutti Annamalai
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
| | - Vimala Karuppaiya
- Cancer Nanomedicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Dhineshkumar Ezhumalai
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | | | - Kaviarasu Balakrishnan
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | - Arul Venkatesan
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
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31
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Li F, Nian Y, Sun Z, Tao C. Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions. Yearb Med Inform 2023; 32:215-224. [PMID: 38147863 PMCID: PMC10751115 DOI: 10.1055/s-0043-1768735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
OBJECTIVES Graph representation learning (GRL) has emerged as a pivotal field that has contributed significantly to breakthroughs in various fields, including biomedicine. The objective of this survey is to review the latest advancements in GRL methods and their applications in the biomedical field. We also highlight key challenges currently faced by GRL and outline potential directions for future research. METHODS We conducted a comprehensive search of multiple databases, including PubMed, Web of Science, IEEE Xplore, and Google Scholar, to collect relevant publications from the past two years (2021-2022). The studies selected for review were based on their relevance to the topic and the publication quality. RESULTS A total of 78 articles were included in our analysis. We identified three main categories of GRL methods and summarized their methodological foundations and notable models. In terms of GRL applications, we focused on two main topics: drug and disease. We analyzed the study frameworks and achievements of the prominent research. Based on the current state-of-the-art, we discussed the challenges and future directions. CONCLUSIONS GRL methods applied in the biomedical field demonstrated several key characteristics, including the utilization of attention mechanisms to prioritize relevant features, a growing emphasis on model interpretability, and the combination of various techniques to improve model performance. There are also challenges needed to be addressed, including mitigating model bias, accommodating the heterogeneity of large-scale knowledge graphs, and improving the availability of high-quality graph data. To fully leverage the potential of GRL, future efforts should prioritize these areas of research.
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Affiliation(s)
- Fang Li
- McWilliams School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yi Nian
- McWilliams School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zenan Sun
- McWilliams School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Cui Tao
- McWilliams School of Biomedical Informatics, the University of Texas Health Science Center at Houston, Houston, TX, USA
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Bang D, Lim S, Lee S, Kim S. Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers. Nat Commun 2023; 14:3570. [PMID: 37322032 PMCID: PMC10272215 DOI: 10.1038/s41467-023-39301-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Computational drug repurposing aims to identify new indications for existing drugs by utilizing high-throughput data, often in the form of biomedical knowledge graphs. However, learning on biomedical knowledge graphs can be challenging due to the dominance of genes and a small number of drug and disease entities, resulting in less effective representations. To overcome this challenge, we propose a "semantic multi-layer guilt-by-association" approach that leverages the principle of guilt-by-association - "similar genes share similar functions", at the drug-gene-disease level. Using this approach, our model DREAMwalk: Drug Repurposing through Exploring Associations using Multi-layer random walk uses our semantic information-guided random walk to generate drug and disease-populated node sequences, allowing for effective mapping of both drugs and diseases in a unified embedding space. Compared to state-of-the-art link prediction models, our approach improves drug-disease association prediction accuracy by up to 16.8%. Moreover, exploration of the embedding space reveals a well-aligned harmony between biological and semantic contexts. We demonstrate the effectiveness of our approach through repurposing case studies for breast carcinoma and Alzheimer's disease, highlighting the potential of multi-layer guilt-by-association perspective for drug repurposing on biomedical knowledge graphs.
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Affiliation(s)
- Dongmin Bang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- AIGENDRUG Co., Ltd., Seoul, 08826, Republic of Korea
| | - Sangsoo Lim
- School of Artificial Intelligence Convergence, Dongguk University, Seoul, 04620, Republic of Korea
| | - Sangseon Lee
- Institute of Computer Technology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- AIGENDRUG Co., Ltd., Seoul, 08826, Republic of Korea.
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea.
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Zong N, Chowdhury S, Zhou S, Rajaganapathy S, yu Y, Wang L, Dai Q, Bielinski SJ, Chen Y, Cerhan JR. Artificial Intelligence-based Efficacy Prediction of Phase 3 Clinical Trial for Repurposing Heart Failure Therapies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.25.23290531. [PMID: 37398384 PMCID: PMC10312819 DOI: 10.1101/2023.05.25.23290531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Introduction Drug repurposing involves finding new therapeutic uses for already approved drugs, which can save costs as their pharmacokinetics and pharmacodynamics are already known. Predicting efficacy based on clinical endpoints is valuable for designing phase 3 trials and making Go/No-Go decisions, given the potential for confounding effects in phase 2. Objectives This study aims to predict the efficacy of the repurposed Heart Failure (HF) drugs for the Phase 3 Clinical Trial. Methods Our study presents a comprehensive framework for predicting drug efficacy in phase 3 trials, which combines drug-target prediction using biomedical knowledgebases with statistical analysis of real-world data. We developed a novel drug-target prediction model that uses low-dimensional representations of drug chemical structures and gene sequences, and biomedical knowledgebase. Furthermore, we conducted statistical analyses of electronic health records to assess the effectiveness of repurposed drugs in relation to clinical measurements (e.g., NT-proBNP). Results We identified 24 repurposed drugs (9 with a positive effect and 15 with a non-positive) for heart failure from 266 phase 3 clinical trials. We used 25 genes related to heart failure for drug-target prediction, as well as electronic health records (EHR) from the Mayo Clinic for screening, which contained over 58,000 heart failure patients treated with various drugs and categorized by heart failure subtypes. Our proposed drug-target predictive model performed exceptionally well in all seven tests in the BETA benchmark compared to the six cutting-edge baseline methods (i.e., best performed in 266 out of 404 tasks). For the overall prediction of the 24 drugs, our model achieved an AUCROC of 82.59% and PRAUC (average precision) of 73.39%. Conclusion The study demonstrated exceptional results in predicting the efficacy of repurposed drugs for phase 3 clinical trials, highlighting the potential of this method to facilitate computational drug repurposing.
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Affiliation(s)
- Nansu Zong
- Department of Artificial Intelligence and Informatics Research, Mayo Clinic, Rochester, MN, USA
| | - Shaika Chowdhury
- Department of Artificial Intelligence and Informatics Research, Mayo Clinic, Rochester, MN, USA
| | - Shibo Zhou
- Department of Artificial Intelligence and Informatics Research, Mayo Clinic, Rochester, MN, USA
| | - Sivaraman Rajaganapathy
- Department of Artificial Intelligence and Informatics Research, Mayo Clinic, Rochester, MN, USA
| | - Yue yu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Qiying Dai
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Yongbin Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R. Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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Duay SS, Yap RCY, Gaitano AL, Santos JAA, Macalino SJY. Roles of Virtual Screening and Molecular Dynamics Simulations in Discovering and Understanding Antimalarial Drugs. Int J Mol Sci 2023; 24:ijms24119289. [PMID: 37298256 DOI: 10.3390/ijms24119289] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Malaria continues to be a global health threat, with approximately 247 million cases worldwide. Despite therapeutic interventions being available, patient compliance is a problem due to the length of treatment. Moreover, drug-resistant strains have emerged over the years, necessitating urgent identification of novel and more potent treatments. Given that traditional drug discovery often requires a great deal of time and resources, most drug discovery efforts now use computational methods. In silico techniques such as quantitative structure-activity relationship (QSAR), docking, and molecular dynamics (MD) can be used to study protein-ligand interactions and determine the potency and safety profile of a set of candidate compounds to help prioritize those tested using assays and animal models. This paper provides an overview of antimalarial drug discovery and the application of computational methods in identifying candidate inhibitors and elucidating their potential mechanisms of action. We conclude with the continued challenges and future perspectives in the field of antimalarial drug discovery.
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Affiliation(s)
- Searle S Duay
- Department of Chemistry, De La Salle University, Manila 0922, Philippines
| | - Rianne Casey Y Yap
- Department of Chemistry, De La Salle University, Manila 0922, Philippines
| | - Arturo L Gaitano
- Chemistry Department, Adamson University, Manila 1000, Philippines
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Gao Z, Gorenflo M, Kaelber DC, Monnier VM, Xu R. Drug repurposing for reducing the risk of cataract extraction in patients with diabetes mellitus: integration of artificial intelligence-based drug prediction and clinical corroboration. Front Pharmacol 2023; 14:1181711. [PMID: 37274099 PMCID: PMC10232753 DOI: 10.3389/fphar.2023.1181711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023] Open
Abstract
Diabetes mellitus (DM) increases the incidence of age-related cataracts. Currently, no medication is approved or known to delay clinical cataract progression. Using a novel approach based on AI, we searched for drugs with potential cataract surgery-suppressing effects. We developed a drug discovery strategy that combines AI-based potential candidate prediction among 2650 Food and Drug Administration (FDA)-approved drugs with clinical corroboration leveraging multicenter electronic health records (EHRs) of approximately 800,000 cataract patients from the TriNetX platform. Among the top-10 AI-predicted repurposed candidate drugs, we identified three DM diagnostic ICD code groups, such as cataract patients with type 1 diabetes mellitus (T1DM), type 2 diabetes mellitus (T2DM), or hyperglycemia, and conducted retrospective cohort analyses to evaluate the efficacy of these candidate drugs in reducing the risk of cataract extraction. Aspirin, melatonin, and ibuprofen were associated with a reduced 5-, 10-, and 20-year cataract extraction risk in all types of diabetes. Acetylcysteine was associated with a reduced 5-, 10-, and 20-year cataract extraction risk in T2DM and hyperglycemia but not in T1DM patient groups. The suppressive effects of aspirin, acetylcysteine, and ibuprofen waned over time, while those of melatonin became stronger in both genders. Thus, the four repositioned drugs have the potential to delay cataract progression in both genders. All four drugs share the ability to directly or indirectly inhibit cyclooxygenase-2 (COX-2), an enzyme that is increased by multiple cataractogenic stimuli.
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Affiliation(s)
- Zhenxiang Gao
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Maria Gorenflo
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - David C. Kaelber
- The Center for Clinical Informatics Research and Education, The Metro Health System, Cleveland, OH, United States
| | - Vincent M. Monnier
- Department of Pathology and Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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Zhang W, Lee AM, Jena S, Huang Y, Ho Y, Tietz KT, Miller CR, Su MC, Mentzer J, Ling AL, Li Y, Dehm SM, Huang RS. Computational drug discovery for castration-resistant prostate cancers through in vitro drug response modeling. Proc Natl Acad Sci U S A 2023; 120:e2218522120. [PMID: 37068243 PMCID: PMC10151558 DOI: 10.1073/pnas.2218522120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Prostate cancer (PC) is the most frequently diagnosed malignancy and a leading cause of cancer deaths in US men. Many PC cases metastasize and develop resistance to systemic hormonal therapy, a stage known as castration-resistant prostate cancer (CRPC). Therefore, there is an urgent need to develop effective therapeutic strategies for CRPC. Traditional drug discovery pipelines require significant time and capital input, which highlights a need for novel methods to evaluate the repositioning potential of existing drugs. Here, we present a computational framework to predict drug sensitivities of clinical CRPC tumors to various existing compounds and identify treatment options with high potential for clinical impact. We applied this method to a CRPC patient cohort and nominated drugs to combat resistance to hormonal therapies including abiraterone and enzalutamide. The utility of this method was demonstrated by nomination of multiple drugs that are currently undergoing clinical trials for CRPC. Additionally, this method identified the tetracycline derivative COL-3, for which we validated higher efficacy in an isogenic cell line model of enzalutamide-resistant vs. enzalutamide-sensitive CRPC. In enzalutamide-resistant CRPC cells, COL-3 displayed higher activity for inhibiting cell growth and migration, and for inducing G1-phase cell cycle arrest and apoptosis. Collectively, these findings demonstrate the utility of a computational framework for independent validation of drugs being tested in CRPC clinical trials, and for nominating drugs with enhanced biological activity in models of enzalutamide-resistant CRPC. The efficiency of this method relative to traditional drug development approaches indicates a high potential for accelerating drug development for CRPC.
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Affiliation(s)
- Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN55455
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Adam M. Lee
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Sampreeti Jena
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Yingbo Huang
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Yeung Ho
- Department of Laboratory Medicine and Pathology, The University of Minnesota Medical School, Minneapolis, MN55455
| | - Kiel T. Tietz
- Department of Laboratory Medicine and Pathology, The University of Minnesota Medical School, Minneapolis, MN55455
| | - Conor R. Miller
- Department of Laboratory Medicine and Pathology, The University of Minnesota Medical School, Minneapolis, MN55455
| | - Mei-Chi Su
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Joshua Mentzer
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Alexander L. Ling
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
| | - Yingming Li
- Department of Laboratory Medicine and Pathology, The University of Minnesota Medical School, Minneapolis, MN55455
| | - Scott M. Dehm
- Department of Laboratory Medicine and Pathology, The University of Minnesota Medical School, Minneapolis, MN55455
| | - R. Stephanie Huang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN55455
- The Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN55455
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Yuan Y, Zhang Y, Meng X, Liu Z, Wang B, Miao R, Zhang R, Su W, Liu L. EDC-DTI: An end-to-end deep collaborative learning model based on multiple information for drug-target interactions prediction. J Mol Graph Model 2023; 122:108498. [PMID: 37126908 DOI: 10.1016/j.jmgm.2023.108498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Innovations in drug-target interactions (DTIs) prediction accelerate the progression of drug development. The introduction of deep learning models has a dramatic impact on DTIs prediction, with a distinct influence on saving time and money in drug discovery. This study develops an end-to-end deep collaborative learning model for DTIs prediction, called EDC-DTI, to identify new targets for existing drugs based on multiple drug-target-related information including homogeneous information and heterogeneous information by the way of deep learning. Our end-to-end model is composed of a feature builder and a classifier. Feature builder consists of two collaborative feature construction algorithms that extract the molecular properties and the topology property of networks, and the classifier consists of a feature encoder and a feature decoder which are designed for feature integration and DTIs prediction, respectively. The feature encoder, mainly based on the improved graph attention network, incorporates heterogeneous information into drug features and target features separately. The feature decoder is composed of multiple neural networks for predictions. Compared with six popular baseline models, EDC-DTI achieves highest predictive performance in the case of low computational costs. Robustness tests demonstrate that EDC-DTI is able to maintain strong predictive performance on sparse datasets. As well, we use the model to predict the most likely targets to interact with Simvastatin (DB00641), Nifedipine (DB01115) and Afatinib (DB08916) as examples. Results show that most of the predictions can be confirmed by literature with clear evidence.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China.
| | - Yuhao Zhang
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Xiangbo Meng
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Zhenyu Liu
- School of Cyberspace Security, Gansu University of Political Science and Law, Anning West Road, Lanzhou, 730070, Gansu, China
| | - Bohan Wang
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Ruidong Miao
- School of Life Science, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Ruisheng Zhang
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Wei Su
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Lei Liu
- Duzhe Publishing Group Co. Ltd., DuZhe Road, Lanzhou, 730000, Gansu, China
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Molecular-evaluated and explainable drug repurposing for COVID-19 using ensemble knowledge graph embedding. Sci Rep 2023; 13:3643. [PMID: 36871056 PMCID: PMC9985643 DOI: 10.1038/s41598-023-30095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
The search for an effective drug is still urgent for COVID-19 as no drug with proven clinical efficacy is available. Finding the new purpose of an approved or investigational drug, known as drug repurposing, has become increasingly popular in recent years. We propose here a new drug repurposing approach for COVID-19, based on knowledge graph (KG) embeddings. Our approach learns "ensemble embeddings" of entities and relations in a COVID-19 centric KG, in order to get a better latent representation of the graph elements. Ensemble KG-embeddings are subsequently used in a deep neural network trained for discovering potential drugs for COVID-19. Compared to related works, we retrieve more in-trial drugs among our top-ranked predictions, thus giving greater confidence in our prediction for out-of-trial drugs. For the first time to our knowledge, molecular docking is then used to evaluate the predictions obtained from drug repurposing using KG embedding. We show that Fosinopril is a potential ligand for the SARS-CoV-2 nsp13 target. We also provide explanations of our predictions thanks to rules extracted from the KG and instanciated by KG-derived explanatory paths. Molecular evaluation and explanatory paths bring reliability to our results and constitute new complementary and reusable methods for assessing KG-based drug repurposing.
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39
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Singh D, Singh A, Chawla PA. An overview of current strategies and future prospects in drug repurposing in tuberculosis. EXPLORATION OF MEDICINE 2023. [DOI: 10.37349/emed.2023.00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
A large number of the population faces mortality as an effect of tuberculosis (TB). The line of treatment in the management of TB faces a jolt with ever-increasing multi-drug resistance (DR) cases. Further, the drugs engaged in the treatment of TB are associated with different toxicities, such as renal and hepatic toxicity. Different combinations are sought for effective anti-tuberculosis (anti-TB) effects with a decrease in toxicity. In this regard, drug repurposing has been very promising in improving the efficacy of drugs by enhancement of bioavailability and widening the safety margin. The success in drug repurposing lies in specified binding and inhibition of a particular target in the drug molecule. Different drugs have been repurposed for various ailments like cancer, Alzheimer’s disease, acquired immunodeficiency syndrome (AIDS), hair loss, etc. Repurposing in anti-TB drugs holds great potential too. The use of whole-cell screening assays and the availability of large chemical compounds for testing against Mycobacterium tuberculosis poses a challenge in this development. The target-based discovery of sites has emerged in the form of phenotypic screening as ethionamide R (EthR) and malate synthase inhibitors are similar to pharmaceuticals. In this review, the authors have thoroughly described the drug repurposing techniques on the basis of pharmacogenomics and drug metabolism, pathogen-targeted therapy, host-directed therapy, and bioinformatics approaches for the identification of drugs. Further, the significance of repurposing of drugs elaborated on large databases has been revealed. The role of genomics and network-based methods in drug repurposing has been also discussed in this article.
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Affiliation(s)
- Dilpreet Singh
- Department of Pharmaceutics, ISF College of Pharmacy, Moga 142001, Punjab, India
| | - Amrinder Singh
- Department of Pharmaceutics, ISF College of Pharmacy, Moga 142001, Punjab, India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, Punjab, India
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40
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Bhanu1 P, Setlur AS, K C, Niranjan V, Hemandhar Kumar N, Buchke S, Kumar J, Rani A, Tiwari SM, Mishra V. Repurposing of known drugs for COVID-19 using molecular docking and simulation analysis. Bioinformation 2023; 19:149-159. [PMID: 37814677 PMCID: PMC10560309 DOI: 10.6026/97320630019149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 10/11/2023] Open
Abstract
We selected fifty one drugs already known for their potential disease treatment roles in various studies and subjected to docking and molecular docking simulation (MDS) analyses. Five of them showed promising features that are discussed and suggested as potential candidates for repurposing for COVID-19. These top five compounds were boswellic acid, pimecrolimus, GYY-4137, BMS-345541 and triamcinolone hexacetonide that interacted with the chosen receptors 1R42, 4G3D, 6VW1, 6VXX and 7MEQ, respectively with binding energies of -9.2 kcal/mol, -9.1 kcal/mol, -10.3 kcal/mol, -10.1 kcal/mol and -8.7 kcal/mol, respectively. The MDS studies for the top 5 best complexes revealed binding features for the chosen receptor, human NF-kappa B transcription factor as an important drug target in COVID-19-based drug development strategies.
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Affiliation(s)
- Piyush Bhanu1
- Xome Life Sciences, Bangalore Bio Innovation Centre (BBC), Helix Biotech Park, Bengaluru, Karnataka- 560100, India
| | - Anagha S Setlur
- Department of Biotechnology, RV College of Engineering, RV Vidyanikethan Post, Mysuru Road, Bengaluru 560059, India
| | - Chandrashekar K
- Department of Biotechnology, RV College of Engineering, RV Vidyanikethan Post, Mysuru Road, Bengaluru 560059, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, RV Vidyanikethan Post, Mysuru Road, Bengaluru 560059, India
| | - Nisha Hemandhar Kumar
- Institute of Neuro and Sensory Physiology, University Medical Centre, Goettiengen - 37075, Germany
| | - Sakshi Buchke
- Xome Life Sciences, Bangalore Bio Innovation Centre (BBC), Helix Biotech Park, Bengaluru, Karnataka- 560100, India
| | - Jitendra Kumar
- Bangalore Bio Innovation Centre (BBC), Helix Biotech Park, Electronics City Phase- 1, Bengaluru-560100, Karnataka, India
| | - Anita Rani
- Department of Botany, Dyal Singh College, University of Delhi, New Delhi 110003, India
| | - Sushil M Tiwari
- Department of Botany, Hansraj College, University of Delhi, Delhi 110007, India
| | - Vachaspati Mishra
- Department of Botany, Deen Dayal Upadhyay College, University of Delhi, Delhi 110078, India
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41
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Franco-Trepat E, Alonso-Pérez A, Guillán-Fresco M, López-Fagúndez M, Pazos-Pérez A, Crespo-Golmar A, Belén Bravo S, López-López V, Jorge-Mora A, Cerón-Carrasco JP, Lois Iglesias A, Gómez R. β Boswellic Acid Blocks Articular Innate Immune Responses: An In Silico and In Vitro Approach to Traditional Medicine. Antioxidants (Basel) 2023; 12:antiox12020371. [PMID: 36829930 PMCID: PMC9952103 DOI: 10.3390/antiox12020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Osteoarthritis (OA) is hallmarked as a silent progressive rheumatic disease of the whole joint. The accumulation of inflammatory and catabolic factors such as IL6, TNFα, and COX2 drives the OA pathophysiology into cartilage degradation, synovia inflammation, and bone destruction. There is no clinical available OA treatment. Although traditional ayurvedic medicine has been using Boswellia serrata extracts (BSE) as an antirheumatic treatment for a millennium, none of the BSE components have been clinically approved. Recently, β boswellic acid (BBA) has been shown to reduce in vivo OA-cartilage loss through an unknown mechanism. We used computational pharmacology, proteomics, transcriptomics, and metabolomics to present solid evidence of BBA therapeutic properties in mouse and primary human OA joint cells. Specifically, BBA binds to the innate immune receptor Toll-like Receptor 4 (TLR4) complex and inhibits both TLR4 and Interleukin 1 Receptor (IL1R) signaling in OA chondrocytes, osteoblasts, and synoviocytes. Moreover, BBA inhibition of TLR4/IL1R downregulated reactive oxygen species (ROS) synthesis and MAPK p38/NFκB, NLRP3, IFNαβ, TNF, and ECM-related pathways. Altogether, we present a solid bulk of evidence that BBA blocks OA innate immune responses and could be transferred into the clinic as an alimentary supplement or as a therapeutic tool after clinical trial evaluations.
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Affiliation(s)
- Eloi Franco-Trepat
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Ana Alonso-Pérez
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - María Guillán-Fresco
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Miriam López-Fagúndez
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Andrés Pazos-Pérez
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Antía Crespo-Golmar
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Susana Belén Bravo
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Verónica López-López
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Alberto Jorge-Mora
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - José P. Cerón-Carrasco
- Centro Universitario de la Defensa, Universidad Politécnica de Cartagena, C/Coronel López Peña S/N, Base Aérea de San Javier, Santiago de La Ribera, 30720 Murcia, Spain
| | - Ana Lois Iglesias
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
| | - Rodolfo Gómez
- Musculoskeletal Pathology Group, Institute IDIS, Santiago University Clinical Hospital, 15706 Santiago de Compostela, Spain
- Correspondence:
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Sarkar C, Das B, Rawat VS, Wahlang JB, Nongpiur A, Tiewsoh I, Lyngdoh NM, Das D, Bidarolli M, Sony HT. Artificial Intelligence and Machine Learning Technology Driven Modern Drug Discovery and Development. Int J Mol Sci 2023; 24:ijms24032026. [PMID: 36768346 PMCID: PMC9916967 DOI: 10.3390/ijms24032026] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/22/2023] Open
Abstract
The discovery and advances of medicines may be considered as the ultimate relevant translational science effort that adds to human invulnerability and happiness. But advancing a fresh medication is a quite convoluted, costly, and protracted operation, normally costing USD ~2.6 billion and consuming a mean time span of 12 years. Methods to cut back expenditure and hasten new drug discovery have prompted an arduous and compelling brainstorming exercise in the pharmaceutical industry. The engagement of Artificial Intelligence (AI), including the deep-learning (DL) component in particular, has been facilitated by the employment of classified big data, in concert with strikingly reinforced computing prowess and cloud storage, across all fields. AI has energized computer-facilitated drug discovery. An unrestricted espousing of machine learning (ML), especially DL, in many scientific specialties, and the technological refinements in computing hardware and software, in concert with various aspects of the problem, sustain this progress. ML algorithms have been extensively engaged for computer-facilitated drug discovery. DL methods, such as artificial neural networks (ANNs) comprising multiple buried processing layers, have of late seen a resurgence due to their capability to power automatic attribute elicitations from the input data, coupled with their ability to obtain nonlinear input-output pertinencies. Such features of DL methods augment classical ML techniques which bank on human-contrived molecular descriptors. A major part of the early reluctance concerning utility of AI in pharmaceutical discovery has begun to melt, thereby advancing medicinal chemistry. AI, along with modern experimental technical knowledge, is anticipated to invigorate the quest for new and improved pharmaceuticals in an expeditious, economical, and increasingly compelling manner. DL-facilitated methods have just initiated kickstarting for some integral issues in drug discovery. Many technological advances, such as "message-passing paradigms", "spatial-symmetry-preserving networks", "hybrid de novo design", and other ingenious ML exemplars, will definitely come to be pervasively widespread and help dissect many of the biggest, and most intriguing inquiries. Open data allocation and model augmentation will exert a decisive hold during the progress of drug discovery employing AI. This review will address the impending utilizations of AI to refine and bolster the drug discovery operation.
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Affiliation(s)
- Chayna Sarkar
- Department of Pharmacology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Mawdiangdiang, Shillong 793018, Meghalaya, India
| | - Biswadeep Das
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Virbhadra Road, Rishikesh 249203, Uttarakhand, India
- Correspondence: ; Tel./Fax: +91-135-708-856-0009
| | - Vikram Singh Rawat
- Department of Psychiatry, All India Institute of Medical Sciences (AIIMS), Virbhadra Road, Rishikesh 249203, Uttarakhand, India
| | - Julie Birdie Wahlang
- Department of Pharmacology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Mawdiangdiang, Shillong 793018, Meghalaya, India
| | - Arvind Nongpiur
- Department of Psychiatry, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Mawdiangdiang, Shillong 793018, Meghalaya, India
| | - Iadarilang Tiewsoh
- Department of Medicine, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Mawdiangdiang, Shillong 793018, Meghalaya, India
| | - Nari M. Lyngdoh
- Department of Anesthesiology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences (NEIGRIHMS), Mawdiangdiang, Shillong 793018, Meghalaya, India
| | - Debasmita Das
- Department of Computer Science and Engineering, Vellore Institute of Technology, Vellore Campus, Tiruvalam Road, Katpadi, Vellore 632014, Tamil Nadu, India
| | - Manjunath Bidarolli
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Virbhadra Road, Rishikesh 249203, Uttarakhand, India
| | - Hannah Theresa Sony
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Virbhadra Road, Rishikesh 249203, Uttarakhand, India
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Cheng J, Hao Y, Shi Q, Hou G, Wang Y, Wang Y, Xiao W, Othman J, Qi J, Wang Y, Chen Y, Yu G. Discovery of Novel Chinese Medicine Compounds Targeting 3CL Protease by Virtual Screening and Molecular Dynamics Simulation. Molecules 2023; 28:molecules28030937. [PMID: 36770604 PMCID: PMC9921503 DOI: 10.3390/molecules28030937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/23/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
The transmission and infectivity of COVID-19 have caused a pandemic that has lasted for several years. This is due to the constantly changing variants and subvariants that have evolved rapidly from SARS-CoV-2. To discover drugs with therapeutic potential for COVID-19, we focused on the 3CL protease (3CLpro) of SARS-CoV-2, which has been proven to be an important target for COVID-19 infection. Computational prediction techniques are quick and accurate enough to facilitate the discovery of drugs against the 3CLpro of SARS-CoV-2. In this paper, we used both ligand-based virtual screening and structure-based virtual screening to screen the traditional Chinese medicine small molecules that have the potential to target the 3CLpro of SARS-CoV-2. MD simulations were used to confirm these results for future in vitro testing. MCCS was then used to calculate the normalized free energy of each ligand and the residue energy contribution. As a result, we found ZINC15676170, ZINC09033700, and ZINC12530139 to be the most promising antiviral therapies against the 3CLpro of SARS-CoV-2.
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Affiliation(s)
- Jin Cheng
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Yixuan Hao
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Qin Shi
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Guanyu Hou
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yanan Wang
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Yong Wang
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Wen Xiao
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Joseph Othman
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Junnan Qi
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
- Correspondence: (Y.W.); (Y.C.); (G.Y.); Tel.: +86-2362563190 (Y.W.); +86-57188813483 (Y.C.); +86-13401772896 (G.Y.)
| | - Yan Chen
- College of Pharmacology Sciences, Zhejiang University of Technology, Hangzhou 310014, China
- Correspondence: (Y.W.); (Y.C.); (G.Y.); Tel.: +86-2362563190 (Y.W.); +86-57188813483 (Y.C.); +86-13401772896 (G.Y.)
| | - Guanghua Yu
- School of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng 224005, China
- Correspondence: (Y.W.); (Y.C.); (G.Y.); Tel.: +86-2362563190 (Y.W.); +86-57188813483 (Y.C.); +86-13401772896 (G.Y.)
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Kozawa S, Yokoyama H, Urayama K, Tejima K, Doi H, Takagi S, Sato TN. Latent disease similarities and therapeutic repurposing possibilities uncovered by multi-modal generative topic modeling of human diseases. BIOINFORMATICS ADVANCES 2023; 3:vbad047. [PMID: 37123453 PMCID: PMC10133403 DOI: 10.1093/bioadv/vbad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/14/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023]
Abstract
Motivation Human diseases are characterized by multiple features such as their pathophysiological, molecular and genetic changes. The rapid expansion of such multi-modal disease-omics space provides an opportunity to re-classify diverse human diseases and to uncover their latent molecular similarities, which could be exploited to repurpose a therapeutic-target for one disease to another. Results Herein, we probe this underexplored space by soft-clustering 6955 human diseases by multi-modal generative topic modeling. Focusing on chronic kidney disease and myocardial infarction, two most life-threatening diseases, unveiled are their previously underrecognized molecular similarities to neoplasia and mental/neurological-disorders, and 69 repurposable therapeutic-targets for these diseases. Using an edit-distance-based pathway-classifier, we also find molecular pathways by which these targets could elicit their clinical effects. Importantly, for the 17 targets, the evidence for their therapeutic usefulness is retrospectively found in the pre-clinical and clinical space, illustrating the effectiveness of the method, and suggesting its broader applications across diverse human diseases. Availability and implementation The code reported in this article is available at: https://github.com/skozawa170301ktx/MultiModalDiseaseModeling. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Satoshi Kozawa
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- ERATO Sato-Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Hirona Yokoyama
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- V-iCliniX Laboratory, Nara Medical University, Nara 634-8521, Japan
| | - Kyoji Urayama
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- ERATO Sato-Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Kengo Tejima
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- ERATO Sato-Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Hotaka Doi
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- V-iCliniX Laboratory, Nara Medical University, Nara 634-8521, Japan
| | - Shunki Takagi
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
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Mteremko D, Chilongola J, Paluch AS, Chacha M. Targeting human thymidylate synthase: Ensemble-based virtual screening for drug repositioning and the role of water. J Mol Graph Model 2023; 118:108348. [PMID: 36257147 DOI: 10.1016/j.jmgm.2022.108348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022]
Abstract
A drug repositioning computational approach was carried to search inhibitors for human thymidylate synthase. An ensemble-based virtual screening of FDA-approved drugs showed the drugs Imatinib, Lumacaftor and Naldemedine to be likely candidates for repurposing. The role of water in the drug-receptor interactions was revealed by the application of an extended AutoDock scoring function that included the water forcefield. The binding affinity scores when hydrated ligands were docked were improved in the drugs considered. Further binding free energy calculations based on the Molecular Mechanics Poisson-Boltzmann Surface Area method revealed that Imatinib, Lumacaftor and Naldemedine scored -130.7 ± 28.1, -210.6 ± 29.9 and -238.0 ± 25.4 kJ/mol, respectively, showing good binding affinity for the candidates considered. Overall, the analysis of the molecular dynamics trajectory of the receptor-drug complexes revealed stable structures for Imatinib, Lumacaftor and Naldemedine, for the entire simulation time.
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Affiliation(s)
- Denis Mteremko
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Jaffu Chilongola
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Musa Chacha
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; Arusha Technical College, Arusha, Tanzania
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Wang L, Chen X, Zhang L, Li L, Huang Y, Sun Y, Yuan X. Artificial intelligence in clinical decision support systems for oncology. Int J Med Sci 2023; 20:79-86. [PMID: 36619220 PMCID: PMC9812798 DOI: 10.7150/ijms.77205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Artificial intelligence (AI) has been widely used in various medical fields, such as image diagnosis, pathological classification, selection of treatment schemes, and prognosis analysis. Especially in the image-aided diagnosis of tumors, the cooperation of human-computer interactions has become mature. However, the ethics of the application of AI as an emerging technology in clinical decision-making have not been fully supported, so the clinical decision support system (CDSS) based on AI technology has not fully realized human-computer interactions in clinical practice as the image-aided diagnosis system. The CDSS was currently used and promoted worldwide including Watson for Oncology, Chinese society of clinical oncology-artificial intelligence (CSCO AI) and so on. This paper summarized the applications and clarified the principle of AI in CDSS, analyzed the difficulties of AI in oncology decisions, and provided a reference scheme for the application of AI in oncology decisions in the future.
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Affiliation(s)
- Lu Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xinyi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Lu Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - YongBiao Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yinan Sun
- Department of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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Maghsoudi S, Taghavi Shahraki B, Rameh F, Nazarabi M, Fatahi Y, Akhavan O, Rabiee M, Mostafavi E, Lima EC, Saeb MR, Rabiee N. A review on computer-aided chemogenomics and drug repositioning for rational COVID-19 drug discovery. Chem Biol Drug Des 2022; 100:699-721. [PMID: 36002440 PMCID: PMC9539342 DOI: 10.1111/cbdd.14136] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/07/2022] [Accepted: 08/21/2022] [Indexed: 11/29/2022]
Abstract
Application of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment-either experimentally or computationally-to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development of unprecedented drugs. The expensive and time-consuming process of traditional drug discovery is no longer feasible, for nowadays the identification of potential drug candidates is much easier for therapeutic targets through elaborate in silico approaches, allowing the prediction of the toxicity of drugs, such as drug repositioning (DR) and chemical genomics (chemogenomics). Coronaviruses (CoVs) are cross-species viruses that are able to spread expeditiously from the into new host species, which in turn cause epidemic diseases. In this sense, this review furnishes an outline of computational strategies and their applications in drug discovery. A special focus is placed on chemogenomics and DR as unique and emerging system-based disciplines on CoV drug and target discovery to model protein networks against a library of compounds. Furthermore, to demonstrate the special advantages of CADD methods in rapidly finding a drug for this deadly virus, numerous examples of the recent achievements grounded on molecular docking, chemogenomics, and DR are reported, analyzed, and interpreted in detail. It is believed that the outcome of this review assists developers of energy harvesting materials and systems for detection of future unexpected kinds of CoVs or other variants.
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Affiliation(s)
- Saeid Maghsoudi
- Faculty of Medicine, Department of Physiology and PathophysiologyUniversity of ManitobaWinnipegManitobaCanada
- Biology of Breathing Group, Children's Hospital Research Institute of Manitoba (CHRIM), University of ManitobaWinnipegManitobaCanada
| | | | | | - Masoomeh Nazarabi
- Faculty of Organic Chemistry, Department of ChemistryUniversity of KashanKashanIran
| | - Yousef Fatahi
- Department of Pharmaceutical Nanotechnology, Faculty of PharmacyTehran University of Medical SciencesTehranIran
- Nanotechnology Research Center, Faculty of PharmacyTehran University of Medical SciencesTehranIran
| | - Omid Akhavan
- Department of PhysicsSharif University of TechnologyTehranIran
| | - Mohammad Rabiee
- Biomaterials Group, Department of Biomedical EngineeringAmirkabir University of TechnologyTehranIran
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of MedicineStanfordCaliforniaUSA
- Department of MedicineStanford University School of MedicineStanfordCaliforniaUSA
| | - Eder C. Lima
- Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS)Porto AlegreBrazil
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of ChemistryGdańsk University of TechnologyGdańskPoland
| | - Navid Rabiee
- Department of PhysicsSharif University of TechnologyTehranIran
- School of EngineeringMacquarie UniversitySydneyNew South WalesAustralia
- Department of Materials Science and EngineeringPohang University of Science and Technology (POSTECH)PohangSouth Korea
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Fossa P, Uggeri M, Orro A, Urbinati C, Rondina A, Milanesi M, Pedemonte N, Pesce E, Padoan R, Ford RC, Meng X, Rusnati M, D’Ursi P. Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing. Int J Mol Sci 2022; 23:ijms232012274. [PMID: 36293130 PMCID: PMC9602983 DOI: 10.3390/ijms232012274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. Cystic fibrosis remains a potentially fatal disease, but it has become treatable as a chronic condition due to some CFTR-rescuing drugs that, when used in combination, increase in their therapeutic effect due to a synergic action. Also, dietary supplementation of natural compounds in combination with approved drugs could represent a promising strategy to further alleviate cystic fibrosis symptoms. On these bases, we screened by in silico drug repositioning 846 small synthetic or natural compounds from the AIFA database to evaluate their capacity to interact with the highly druggable lumacaftor binding site of F508del-CFTR. Among the identified hits, nicotinamide (NAM) was predicted to accommodate into the lumacaftor binding region of F508del-CFTR without competing against the drug but rather stabilizing its binding. The effective capacity of NAM to bind F508del-CFTR in a lumacaftor-uncompetitive manner was then validated experimentally by surface plasmon resonance analysis. Finally, the capacity of NAM to synergize with lumacaftor increasing its CFTR-rescuing activity was demonstrated in cell-based assays. This study suggests the possible identification of natural small molecules devoid of side effects and endowed with the capacity to synergize with drugs currently employed for the treatment of cystic fibrosis, which hopefully will increase the therapeutic efficacy with lower doses.
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Affiliation(s)
- Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, 16132 Genoa, Italy
| | - Matteo Uggeri
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, 16132 Genoa, Italy
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Alessandro Orro
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Chiara Urbinati
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alessandro Rondina
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
| | - Maria Milanesi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | | | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Rita Padoan
- Department of Pediatrics, Regional Support Centre for Cystic Fibrosis, Children’s Hospital—ASST Spedali Civili, University of Brescia, 25123 Brescia, Italy
| | - Robert C. Ford
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Xin Meng
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Correspondence: (M.R.); (P.D.)
| | - Pasqualina D’Ursi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, Italy
- Correspondence: (M.R.); (P.D.)
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Nian Y, Hu X, Zhang R, Feng J, Du J, Li F, Bu L, Zhang Y, Chen Y, Tao C. Mining on Alzheimer's diseases related knowledge graph to identity potential AD-related semantic triples for drug repurposing. BMC Bioinformatics 2022; 23:407. [PMID: 36180861 PMCID: PMC9523633 DOI: 10.1186/s12859-022-04934-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study the relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep via SemMedDB. We used both a BERT-based classifier and rule-based methods during data preprocessing to exclude noise while preserving most AD-related semantic triples. The 1,672,110 filtered triples were used to train with knowledge graph completion algorithms (i.e., TransE, DistMult, and ComplEx) to predict candidates that might be helpful for AD treatment or prevention. RESULTS Among three knowledge graph completion models, TransE outperformed the other two (MR = 10.53, Hits@1 = 0.28). We leveraged the time-slicing technique to further evaluate the prediction results. We found supporting evidence for most highly ranked candidates predicted by our model which indicates that our approach can inform reliable new knowledge. CONCLUSION This paper shows that our graph mining model can predict reliable new relationships between AD and other entities (i.e., dietary supplements, chemicals, and drugs). The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses.
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Affiliation(s)
- Yi Nian
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030 USA
| | - Xinyue Hu
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030 USA
| | - Rui Zhang
- Department of Pharmaceutical Care & Health System (PCHS) and the Institute for Health Informatics (IHI), University of Minnesota, 7-115A Weaver-Densford Hall, Minneapolis, MN 55455 USA
| | - Jingna Feng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030 USA
| | - Jingcheng Du
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030 USA
| | - Fang Li
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030 USA
| | - Larry Bu
- University of Maryland School of Medicine, 655 W Baltimore St S, Baltimore, MD 21201 USA
| | - Yuji Zhang
- University of Maryland School of Medicine, 655 W Baltimore St S, Baltimore, MD 21201 USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology and Informatics (DBEI), the Perelman School of Medicine, University of Pennsylvania, 602 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Cui Tao
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St, Houston, TX 77030 USA
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50
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Literature-based drug-drug similarity for drug repurposing: impact of Medical Subject Headings term refinement and hierarchical clustering. Future Med Chem 2022; 14:1309-1323. [PMID: 36017692 DOI: 10.4155/fmc-2022-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: We describe herein, an improved procedure for drug repurposing based on refined Medical Subject Headings (MeSH) terms and hierarchical clustering method. Materials & methods: In the present study, we have employed MeSH data from MEDLINE (2019), 1669 US FDA approved drugs from Open FDA and a refined set of MeSH terms. Refinement of MeSH terms was performed to include terms related to mechanistic information of drugs and diseases. Results and Conclusions: In-depth analysis of the results obtained, demonstrated greater efficiency of the proposed approach, based on refined MeSH terms and hierarchical clustering, in terms of number of selected drug candidates for repurposing. Further, analysis of misclustering and size of noise clusters suggest that the proposed approach is reliable and can be employed in drug repurposing.
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