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Saifi I, Bhat BA, Hamdani SS, Bhat UY, Lobato-Tapia CA, Mir MA, Dar TUH, Ganie SA. Artificial intelligence and cheminformatics tools: a contribution to the drug development and chemical science. J Biomol Struct Dyn 2024; 42:6523-6541. [PMID: 37434311 DOI: 10.1080/07391102.2023.2234039] [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: 02/12/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
In the ever-evolving field of drug discovery, the integration of Artificial Intelligence (AI) and Machine Learning (ML) with cheminformatics has proven to be a powerful combination. Cheminformatics, which combines the principles of computer science and chemistry, is used to extract chemical information and search compound databases, while the application of AI and ML allows for the identification of potential hit compounds, optimization of synthesis routes, and prediction of drug efficacy and toxicity. This collaborative approach has led to the discovery, preclinical evaluations and approval of over 70 drugs in recent years. To aid researchers in the pursuit of new drugs, this article presents a comprehensive list of databases, datasets, predictive and generative models, scoring functions and web platforms that have been launched between 2021 and 2022. These resources provide a wealth of information and tools for computer-assisted drug development, and are a valuable asset for those working in the field of cheminformatics. Overall, the integration of AI, ML and cheminformatics has greatly advanced the drug discovery process and continues to hold great potential for the future. As new resources and technologies become available, we can expect to see even more groundbreaking discoveries and advancements in these fields.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ifra Saifi
- Chaudhary Charan Singh University, Meerut, Uttar Pradesh, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Syed Suhail Hamdani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Umar Yousuf Bhat
- Department of Zoology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | | | - Mushtaq Ahmad Mir
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, KSA, Saudi Arabia
| | - Tanvir Ul Hasan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
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Xie S, Peng P, Dong X, Yuan J, Liang J. Novel gene signatures predicting and immune infiltration analysis in Parkinson's disease: based on combining random forest with artificial neural network. Neurol Sci 2024; 45:2681-2696. [PMID: 38265536 DOI: 10.1007/s10072-023-07299-2] [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: 11/09/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Parkinson's disease (PD) ranks as the second most prevalent neurodegenerative disorder globally, and its incidence is rapidly rising. The diagnosis of PD relies on clinical characteristics. Although current treatments aim to alleviate symptoms, they do not effectively halt the disease's progression. Early detection and intervention hold immense importance. This study aimed to establish a new PD diagnostic model. METHODS Data from a public database were adopted for the construction and validation of a PD diagnostic model with random forest and artificial neural network models. The CIBERSORT platform was applied for the evaluation of immune cell infiltration in PD. Quantitative real-time PCR was performed to verify the accuracy and reliability of the bioinformatics analysis results. RESULTS Leveraging existing gene expression data from the Gene Expression Omnibus (GEO) database, we sifted through differentially expressed genes (DEGs) in PD and identified 30 crucial genes through a random forest classifier. Furthermore, we successfully designed a novel PD diagnostic model using an artificial neural network and verified its diagnostic efficacy using publicly available datasets. Our research also suggests that mast cells may play a significant role in the onset and progression of PD. CONCLUSION This work developed a new PD diagnostic model with machine learning techniques and suggested the immune cells as a potential target for PD therapy.
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Affiliation(s)
- Shucai Xie
- Department of Critical Care Medicine, National Clinical Research Center for Genetic Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Pei Peng
- Department of Medicine Oncology, Changde Hospital, Xiangya School of Medicine, Central South University (The first people's hospital of Changde city), Changde, China
| | - Xingcheng Dong
- Department of Orthopedics, Changde Hospital, Xiangya School of Medicine, Central South University (The first people's hospital of Changde city), Changde, China
| | - Junxing Yuan
- Department of Neurology, Changde Hospital, Xiangya School of Medicine, Central South University (The first people's hospital of Changde city), No. 818 Renmin Road, Changde, 415000, Hunan, China
| | - Ji Liang
- Department of Neurology, Changde Hospital, Xiangya School of Medicine, Central South University (The first people's hospital of Changde city), No. 818 Renmin Road, Changde, 415000, Hunan, China.
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Zhang W, Song LN, You YF, Qi FN, Cui XH, Yi MX, Zhu G, Chang RA, Zhang HJ. Application of artificial intelligence in the prediction of immunotherapy efficacy in hepatocellular carcinoma: Current status and prospects. Artif Intell Gastroenterol 2024; 5:90096. [DOI: 10.35712/aig.v5.i1.90096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/28/2024] [Accepted: 03/12/2024] [Indexed: 04/29/2024] Open
Abstract
Artificial Intelligence (AI) has increased as a potent tool in medicine, with promising oncology applications. The emergence of immunotherapy has transformed the treatment terrain for hepatocellular carcinoma (HCC), offering new hope to patients with this challenging malignancy. This article examines the role and future of AI in forecasting the effectiveness of immunotherapy in HCC. We highlight the potential of AI to revolutionize the prediction of therapy response, thus improving patient selection and clinical outcomes. The article further outlines the challenges and future research directions in this emerging field.
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Affiliation(s)
- Wei Zhang
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Li-Ning Song
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Yun-Fei You
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Feng-Nan Qi
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Xiao-Hong Cui
- Department of General Surgery, Shanghai Electric Power Hospital, Shanghai 200050, China
| | - Ming-Xun Yi
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ren-An Chang
- Research Center of Clinical Medicine and Department of General Surgery, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Hai-Jian Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Research Center of Clinical Medicine, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
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Lv H, Liu L, He Y, Yang K, Fu Y, Bao Y. Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma. Front Pharmacol 2024; 15:1344755. [PMID: 38515849 PMCID: PMC10955143 DOI: 10.3389/fphar.2024.1344755] [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: 11/26/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Melanoma is the most lethal type of skin cancer with an increasing incidence. Cuproptosis is the most recently identified copper-dependent form of cell death that relies on mitochondrial respiration. The hippocampal (Hippo) pathway functions as a tumor suppressor by regulating Yes-associated protein/transcriptional coactivator with PDZ-binding motif (YAP/TAZ) activity. However, its role in cuproptosis remains unknown. In addition, the correlation of cuproptosis-related genes and Hippo pathway-related genes with tumor prognosis warrants further investigation. In the present study, we explored the correlation of cuproptosis-related genes and Hippo pathway-related genes with the prognosis of melanoma through analysis of data from a public database and experimental verification. We found eight Hippo pathway-related genes that were downregulated in melanoma and exhibited predictive value for prognosis. There was a significant positive correlation between cuproptosis-related genes and Hippo pathway-related genes in skin cutaneous melanoma. YAP1 expression was positively correlated with ferredoxin 1 (FDX1) expression in the GSE68599 dataset and A2058 cells. Moreover, YAP1 was positively and negatively correlated with M2 macrophages and regulatory T cell infiltration, respectively. In conclusion, the present study demonstrated the prognostic value of Hippo pathway-related genes (particularly YAP1) in melanoma, revealing the correlation between the expression of Hippo pathway-related genes and immune infiltration. Thus, the present findings may provide new clues on the prognostic assessment of patients with melanoma and a new target for the immunotherapy of this disease.
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Affiliation(s)
- Haozhen Lv
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Liu
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Yuexi He
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Kun Yang
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Fu
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Yingqiu Bao
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Dakilah I, Harb A, Abu-Gharbieh E, El-Huneidi W, Taneera J, Hamoudi R, Semreen MH, Bustanji Y. Potential of CDC25 phosphatases in cancer research and treatment: key to precision medicine. Front Pharmacol 2024; 15:1324001. [PMID: 38313315 PMCID: PMC10834672 DOI: 10.3389/fphar.2024.1324001] [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: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
The global burden of cancer continues to rise, underscoring the urgency of developing more effective and precisely targeted therapies. This comprehensive review explores the confluence of precision medicine and CDC25 phosphatases in the context of cancer research. Precision medicine, alternatively referred to as customized medicine, aims to customize medical interventions by taking into account the genetic, genomic, and epigenetic characteristics of individual patients. The identification of particular genetic and molecular drivers driving cancer helps both diagnostic accuracy and treatment selection. Precision medicine utilizes sophisticated technology such as genome sequencing and bioinformatics to elucidate genetic differences that underlie the proliferation of cancer cells, hence facilitating the development of customized therapeutic interventions. CDC25 phosphatases, which play a crucial role in governing the progression of the cell cycle, have garnered significant attention as potential targets for cancer treatment. The dysregulation of CDC25 is a characteristic feature observed in various types of malignancies, hence classifying them as proto-oncogenes. The proteins in question, which operate as phosphatases, play a role in the activation of Cyclin-dependent kinases (CDKs), so promoting the advancement of the cell cycle. CDC25 inhibitors demonstrate potential as therapeutic drugs for cancer treatment by specifically blocking the activity of CDKs and modulating the cell cycle in malignant cells. In brief, precision medicine presents a potentially fruitful option for augmenting cancer research, diagnosis, and treatment, with an emphasis on individualized care predicated upon patients' genetic and molecular profiles. The review highlights the significance of CDC25 phosphatases in the advancement of cancer and identifies them as promising candidates for therapeutic intervention. This statement underscores the significance of doing thorough molecular profiling in order to uncover the complex molecular characteristics of cancer cells.
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Affiliation(s)
- Ibraheem Dakilah
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Amani Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammed H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, Jordan
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Bhat BA, Algaissi A, Khamjan NA, Dar TUH, Dar SA, Varadharajan V, Qasir NA, Lohani M. Exploration of comprehensive marine natural products database against dengue viral non-structural protein 1 using high-throughput computational studies. J Biomol Struct Dyn 2024:1-10. [PMID: 38165485 DOI: 10.1080/07391102.2023.2297006] [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: 03/31/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential marine natural compounds against the NS1 of DENV. The structure of the NS1 protein was retrieved from Protein Data Bank with (PDB ID: 4O6B). Missing residues were added using modeler software. Molecular operating environment (MOE) programme was used to prepare the protein before docking. Virtual screening was performed on PyRx software to identify natural compounds retrieved from Comprehensive Marine Natural Products Database (CMNPD) against the NS1 protein, and best-docked compounds were examined by molecular docking and molecular dynamic (MD) simulation. Out of 31,561 marine compounds, the top 10 compounds showed docking scores lesser than -8.0 kcal/mol. One of the best hit compounds, CMNPD6802, was further analyzed using MD simulation study at 100 nanoseconds and Molecular Mechanics with Generalized Born and Surface Area Solvation (MM/GBSA). Based on its total binding energy, determined using the MM/GBSA approach, CMNPD6802 was ranked first. Its pharmacokinetic properties concerning the target protein NS1 were also evaluated. The results of the MD simulation showed that CMNPD6802 remained in close contact with the protein throughout the activation period, mapped using principal component analysis. These findings suggest that CMNPD6802 could serve as an NS1 inhibitor and may be a potential candidate for treating DENV infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Basharat Ahmad Bhat
- Department of BioResources, Amar Singh College Campus, Cluster University Srinagar, India
| | - Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Emerging and Epidemic Infectious Diseases Research Unit, Medical Research Centre, Jazan University, Jazan, Saudi Arabia
| | - Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan, Saudi Arabia
| | | | - Naif A Qasir
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohtashim Lohani
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
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Liu Y, Zhang Z, Lin W, Liang H, Lin M, Wang J, Chen L, Yang P, Liu M, Zheng Y. A novel FCTF evaluation and prediction model for food efficacy based on association rule mining. Front Nutr 2023; 10:1170084. [PMID: 37701374 PMCID: PMC10493461 DOI: 10.3389/fnut.2023.1170084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/16/2023] [Indexed: 09/14/2023] Open
Abstract
Introduction Food-components-target-function (FCTF) is an evaluation and prediction model based on association rule mining (ARM) and network interaction analysis, which is an innovative exploration of interdisciplinary integration in the food field. Methods Using the components as the basis, the targets and functions are comprehensively explored in various databases and platforms under the guidance of the ARM concept. The focused active components, key targets and preferred efficacy are then analyzed by different interaction calculations. The FCTF model is particularly suitable for preliminary studies of medicinal plants in remote and poor areas. Results The FCTF model of the local medicinal food Laoxianghuang focuses on the efficacy of digestive system cancers and neurological diseases, with key targets ACE, PTGS2, CYP2C19 and corresponding active components citronellal, trans-nerolidol, linalool, geraniol, α-terpineol, cadinene and α-pinene. Discussion Centuries of traditional experience point to the efficacy of Laoxianghuang in alleviating digestive disorders, and our established FCTF model of Laoxianghuang not only demonstrates this but also extends to its possible adjunctive efficacy in neurological diseases, which deserves later exploration. The FCTF model is based on the main line of components to target and efficacy and optimizes the research level from different dimensions and aspects of interaction analysis, hoping to make some contribution to the future development of the food discipline.
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Affiliation(s)
- Yaqun Liu
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Zhenxia Zhang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Wanling Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Hongxuan Liang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Junli Wang
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Lianghui Chen
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Peikui Yang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Mouquan Liu
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
| | - Yuzhong Zheng
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, China
- School of Laboratory Medicine, Youjiang Medical University for Nationalities, Baise, Guangxi, China
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Yang J, Nittala MR, Velazquez AE, Buddala V, Vijayakumar S. An Overview of the Use of Precision Population Medicine in Cancer Care: First of a Series. Cureus 2023; 15:e37889. [PMID: 37113463 PMCID: PMC10129036 DOI: 10.7759/cureus.37889] [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] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Advances in science and technology in the past century and a half have helped improve disease management, prevention, and early diagnosis and better health maintenance. These have led to a longer life expectancy in most developed and middle-income countries. However, resource- and infrastructure-scarce countries and populations have not enjoyed these benefits. Furthermore, in every society, including in developed nations, the lag time from new advances, either in the laboratory or from clinical trials, to using those findings in day-to-day medical practice often takes many years and sometimes close to or longer than a decade. A similar trend is seen in the application of "precision medicine" (PM) in terms of improving population health (PH). One of the reasons for such lack of application of precision medicine in population health is the misunderstanding of equating precision medicine with genomic medicine (GM) as if they are the same. Precision medicine needs to be recognized as encompassing genomic medicine in addition to other new developments such as big data analytics, electronic health records (EHR), telemedicine, and information communication technology. By leveraging these new developments together and applying well-tested epidemiological concepts, it can be posited that population/public health can be improved. In this paper, we take cancer as an example of the benefits of recognizing the potential of precision medicine in applying it to population/public health. Breast cancer and cervical cancer are taken as examples to demonstrate these hypotheses. There exists significant evidence already to show the importance of recognizing "precision population medicine" (PPM) in improving cancer outcomes not only in individual patients but also for its applications in early detection and cancer screening (especially in high-risk populations) and achieving those goals in a more cost-efficient manner that can reach resource- and infrastructure-scarce societies and populations. This is the first report of a series that will focus on individual cancer sites in the future.
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Affiliation(s)
- Johnny Yang
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | - Mary R Nittala
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
| | | | - Vedanth Buddala
- Radiation Oncology, University of Mississippi Medical Center, Jackson, USA
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Liu JY, Liu LP, Li Z, Luo YW, Liang F. The role of cuproptosis-related gene in the classification and prognosis of melanoma. Front Immunol 2022; 13:986214. [PMID: 36341437 PMCID: PMC9632664 DOI: 10.3389/fimmu.2022.986214] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background Melanoma, as one of the most aggressive and malignant cancers, ranks first in the lethality rate of skin cancers. Cuproptosis has been shown to paly a role in tumorigenesis, However, the role of cuproptosis in melanoma metastasis are not clear. Studying the correlation beteen the molecular subtypes of cuproptosis-related genes (CRGs) and metastasis of melanoma may provide some guidance for the prognosis of melanoma. Methods We collected 1085 melanoma samples in The Cancer Genome Atlas(TCGA) and Gene Expression Omnibus(GEO) databases, constructed CRGs molecular subtypes and gene subtypes according to clinical characteristics, and investigated the role of CRGs in melanoma metastasis. We randomly divide the samples into train set and validation set according to the ratio of 1:1. A prognostic model was constructed using data from the train set and then validated on the validation set. We performed tumor microenvironment analysis and drug sensitivity analyses for high and low risk groups based on the outcome of the prognostic model risk score. Finally, we established a metastatic model of melanoma. Results According to the expression levels of 12 cuproptosis-related genes, we obtained three subtypes of A1, B1, and C1. Among them, C1 subtype had the best survival outcome. Based on the differentially expressed genes shared by A1, B1, and C1 genotypes, we obtained the results of three gene subtypes of A2, B2, and C2. Among them, the B2 group had the best survival outcome. Then, we constructed a prognostic model consisting of 6 key variable genes, which could more accurately predict the 1-, 3-, and 5-year overall survival rates of melanoma patients. Besides, 98 drugs were screened out. Finally, we explored the role of cuproptosis-related genes in melanoma metastasis and established a metastasis model using seven key genes. Conclusions In conclusion, CRGs play a role in the metastasis and prognosis of melanoma, and also provide new insights into the underlying pathogenesis of melanoma.
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Affiliation(s)
- Jin-Ya Liu
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Le-Ping Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China,Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Li
- Department of Hematology and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Wei Luo
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China,*Correspondence: Fang Liang, ; Yan-Wei Luo,
| | - Fang Liang
- Department of Hematology and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Fang Liang, ; Yan-Wei Luo,
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Salvatori B, Linder T, Eppel D, Morettini M, Burattini L, Göbl C, Tura A. TyGIS: improved triglyceride-glucose index for the assessment of insulin sensitivity during pregnancy. Cardiovasc Diabetol 2022; 21:215. [PMID: 36258194 PMCID: PMC9580191 DOI: 10.1186/s12933-022-01649-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background The triglyceride-glucose index (TyG) has been proposed as a surrogate marker of insulin resistance, which is a typical trait of pregnancy. However, very few studies analyzed TyG performance as marker of insulin resistance in pregnancy, and they were limited to insulin resistance assessment at fasting rather than in dynamic conditions, i.e., during an oral glucose tolerance test (OGTT), which allows more reliable assessment of the actual insulin sensitivity impairment. Thus, first aim of the study was exploring in pregnancy the relationships between TyG and OGTT-derived insulin sensitivity. In addition, we developed a new version of TyG, for improved performance as marker of insulin resistance in pregnancy. Methods At early pregnancy, a cohort of 109 women underwent assessment of maternal biometry and blood tests at fasting, for measurements of several variables (visit 1). Subsequently (26 weeks of gestation) all visit 1 analyses were repeated (visit 2), and a subgroup of women (84 selected) received a 2 h-75 g OGTT (30, 60, 90, and 120 min sampling) with measurement of blood glucose, insulin and C-peptide for reliable assessment of insulin sensitivity (PREDIM index) and insulin secretion/beta-cell function. The dataset was randomly split into 70% training set and 30% test set, and by machine learning approach we identified the optimal model, with TyG included, showing the best relationship with PREDIM. For inclusion in the model, we considered only fasting variables, in agreement with TyG definition. Results The relationship of TyG with PREDIM was weak. Conversely, the improved TyG, called TyGIS, (linear function of TyG, body weight, lean body mass percentage and fasting insulin) resulted much strongly related to PREDIM, in both training and test sets (R2 > 0.64, p < 0.0001). Bland–Altman analysis and equivalence test confirmed the good performance of TyGIS in terms of association with PREDIM. Different further analyses confirmed TyGIS superiority over TyG. Conclusions We developed an improved version of TyG, as new surrogate marker of insulin sensitivity in pregnancy (TyGIS). Similarly to TyG, TyGIS relies only on fasting variables, but its performances are remarkably improved than those of TyG. Supplementary Information The online version contains supplementary material available at 10.1186/s12933-022-01649-8.
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Affiliation(s)
| | - Tina Linder
- Department of Obstetrics and Gynaecology, Medical University of Vienna, 1090, Vienna, Austria
| | - Daniel Eppel
- Department of Obstetrics and Gynaecology, Medical University of Vienna, 1090, Vienna, Austria
| | - Micaela Morettini
- Department of Information Engineering, Università Politecnica Delle Marche, 60131, Ancona, Italy
| | - Laura Burattini
- Department of Information Engineering, Università Politecnica Delle Marche, 60131, Ancona, Italy
| | - Christian Göbl
- Department of Obstetrics and Gynaecology, Medical University of Vienna, 1090, Vienna, Austria
| | - Andrea Tura
- CNR Institute of Neuroscience, Corso Stati Uniti 4, 35127, Padua, Italy.
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Han S, Cao Y, Guo T, Lin Q, Luo F. Targeting lncRNA/Wnt axis by flavonoids: A promising therapeutic approach for colorectal cancer. Phytother Res 2022; 36:4024-4040. [PMID: 36227024 DOI: 10.1002/ptr.7550] [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: 12/21/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Despite the dramatic advances in our understanding of the etiology of colorectal cancer (CRC) in recent decades, effective therapeutic strategies are still urgently needed. Oncogenic mutations in the Wnt/β-Catenin pathway are hallmarks of CRC. Moreover, long non-coding RNAs (lncRNAs) as molecular managers are involved in the initiation, progression, and metastasis of CRC. Therefore, it is important to further explore the interaction between lncRNAs and Wnt/β-Catenin signaling pathway for targeted therapy of CRC. Natural phytochemicals have not toxicity and can target carcinogenesis-related pathways. Growing evidences suggest that flavonoids are inversely associated with CRC risk. These bioactive compounds could target carcinogenesis pathways of CRC and reduced the side effects of anti-cancer drugs. The review systematically summarized the progress of flavonoids targeting lncRNA/Wnt axis in the investigations of CRC, which will provide a promising therapeutic approach for CRC and develop nutrition-oriented preventive strategies for CRC based on epigenetic mechanisms. In the field, more epidemiological and clinical trials are required in the future to verify feasibility of targeting lncRNA/Wnt axis by flavonoids in the therapy and prevention of CRC.
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Affiliation(s)
- Shuai Han
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
| | - Yunyun Cao
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
| | - Tianyi Guo
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
| | - Qinlu Lin
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
| | - Feijun Luo
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, People's Republic of China
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12
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Soni M, Pratap JV. Development of Novel Anti-Leishmanials: The Case for Structure-Based Approaches. Pathogens 2022; 11:pathogens11080950. [PMID: 36015070 PMCID: PMC9414883 DOI: 10.3390/pathogens11080950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
The neglected tropical disease (NTD) leishmaniasis is the collective name given to a diverse group of illnesses caused by ~20 species belonging to the genus Leishmania, a majority of which are vector borne and associated with complex life cycles that cause immense health, social, and economic burdens locally, but individually are not a major global health priority. Therapeutic approaches against leishmaniasis have various inadequacies including drug resistance and a lack of effective control and eradication of the disease spread. Therefore, the development of a rationale-driven, target based approaches towards novel therapeutics against leishmaniasis is an emergent need. The utilization of Artificial Intelligence/Machine Learning methods, which have made significant advances in drug discovery applications, would benefit the discovery process. In this review, following a summary of the disease epidemiology and available therapies, we consider three important leishmanial metabolic pathways that can be attractive targets for a structure-based drug discovery approach towards the development of novel anti-leishmanials. The folate biosynthesis pathway is critical, as Leishmania is auxotrophic for folates that are essential in many metabolic pathways. Leishmania can not synthesize purines de novo, and salvage them from the host, making the purine salvage pathway an attractive target for novel therapeutics. Leishmania also possesses an organelle glycosome, evolutionarily related to peroxisomes of higher eukaryotes, which is essential for the survival of the parasite. Research towards therapeutics is underway against enzymes from the first two pathways, while the third is as yet unexplored.
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Affiliation(s)
- Mohini Soni
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - J. Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence:
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13
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Prediction and Screening Model for Products Based on Fusion Regression and XGBoost Classification. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:4987639. [PMID: 35958779 PMCID: PMC9357736 DOI: 10.1155/2022/4987639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022]
Abstract
Performance prediction based on candidates and screening based on predicted performance value are the core of product development. For example, the performance prediction and screening of equipment components and parts are an important guarantee for the reliability of equipment products. The prediction and screening of drug bioactivity value and performance are the keys to pharmaceutical product development. The main reasons for the failure of pharmaceutical discovery are the low bioactivity of the candidate compounds and the deficiencies in their efficacy and safety, which are related to the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the compounds. Therefore, it is very necessary to quickly and effectively perform systematic bioactivity value prediction and ADMET property evaluation for candidate compounds in the early stage of drug discovery. In this paper, a data-driven pharmaceutical products screening prediction model is proposed to screen drug candidates with higher bioactivity value and better ADMET properties. First, a quantitative prediction method for bioactivity value is proposed using the fusion regression of LGBM and neural network based on backpropagation (BP-NN). Then, the ADMET properties prediction method is proposed using XGBoost. According to the predicted bioactivity value and ADMET properties, the BVAP method is defined to screen the drug candidates. And the screening model is validated on the dataset of antagonized Erα active compounds, in which the mean square error (MSE) of fusion regression is 1.1496, the XGBoost prediction accuracy of ADMET properties are 94.0% for Caco-2, 95.7% for CYP3A4, 89.4% for HERG, 88.6% for hob, and 96.2% for Mn. Compared with the commonly used methods for ADMET properties such as SVM, RF, KNN, LDA, and NB, the XGBoost in this paper has the highest prediction accuracy and AUC value, which has better guiding significance and can help screen pharmaceutical product candidates with good bioactivity, pharmacokinetic properties, and safety.
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14
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Cong Y, Endo T. Multi-Omics and Artificial Intelligence-Guided Drug Repositioning: Prospects, Challenges, and Lessons Learned from COVID-19. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:361-371. [PMID: 35759424 DOI: 10.1089/omi.2022.0068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Drug repurposing is of interest for therapeutics innovation in many human diseases including coronavirus disease 2019 (COVID-19). Methodological innovations in drug repurposing are currently being empowered by convergence of omics systems science and digital transformation of life sciences. This expert review article offers a systematic summary of the application of artificial intelligence (AI), particularly machine learning (ML), to drug repurposing and classifies and introduces the common clustering, dimensionality reduction, and other methods. We highlight, as a present-day high-profile example, the involvement of AI/ML-based drug discovery in the COVID-19 pandemic and discuss the collection and sharing of diverse data types, and the possible futures awaiting drug repurposing in an era of AI/ML and digital technologies. The article provides new insights on convergence of multi-omics and AI-based drug repurposing. We conclude with reflections on the various pathways to expedite innovation in drug development through drug repurposing for prompt responses to the current COVID-19 pandemic and future ecological crises in the 21st century.
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Affiliation(s)
- Yi Cong
- Laboratory of Information Biology, Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Toshinori Endo
- Laboratory of Information Biology, Information Science and Technology, Hokkaido University, Sapporo, Japan
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15
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Hassam M, Shamsi JA, Khan A, Al-Harrasi A, Uddin R. Prediction of inhibitory activities of small molecules against Pantothenate synthetase from Mycobacterium tuberculosis using Machine Learning models. Comput Biol Med 2022; 145:105453. [DOI: 10.1016/j.compbiomed.2022.105453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
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16
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Abstract
In this paper, we study the classification problem of large data with many features and strong feature dependencies. This type of problem has shortcomings when handled by machine learning models. Therefore, a classification model with cognitive reasoning ability is proposed. The core idea is to use cognitive reasoning mechanism proposed in this paper to solve the classification problem of large structured data with multiple features and strong correlation between features, and then implements cognitive reasoning for features. The model has three parts. The first part proposes a Feature-to-Image algorithm for converting structured data into image data. The algorithm quantifies the dependencies between features, so as to take into account the impact of individual independent features and correlations between features on the prediction results. The second part designs and implements low-level feature extraction of the quantified features using convolutional neural networks. With the relative symmetry of the capsule network, the third part proposes a cognitive reasoning mechanism to implement high-level feature extraction, feature cognitive reasoning, and classification tasks of the data. At the same time, this paper provides the derivation process and algorithm description of cognitive reasoning mechanism. Experiments show that our model is efficient and outperforms comparable models on the category prediction experiment of ADMET properties of five compounds.This work will provide a new way for cognitive computing of intelligent data analysis.
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17
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Yadav M, Abdalla M, Madhavi M, Chopra I, Bhrdwaj A, Soni L, Shaheen U, Prajapati L, Sharma M, Sikarwar MS, Albogami S, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR People’s Republic of China
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad, Telangana State, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Uzma Shaheen
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Megha Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | | | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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18
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Kondylakis H, Chicchi Giglioli IA, Katehakis DG, Aldemir H, Zikas P, Papagiannakis G, Hors-Fraile S, González-Sanz PL, Apostolakis KC, Stephanidis C, Núñez-Benjumea FJ, Baños-Rivera RM, Fernandez-Luque L, Kouroubali A. A Digital Health Intervention for Stress and Anxiety Relief in Perioperative Care: Protocol for a Feasibility Trial (Preprint). JMIR Res Protoc 2022; 11:e38536. [DOI: 10.2196/38536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/30/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
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19
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Mukherjee S, Abdalla M, Yadav M, Madhavi M, Bhrdwaj A, Khandelwal R, Prajapati L, Panicker A, Chaudhary A, Albrakati A, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation of VEGF inhibitors for the clinical treatment of Ovarian Cancer. J Mol Model 2022; 28:100. [PMID: 35325303 DOI: 10.1007/s00894-022-05081-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/08/2022] [Indexed: 11/28/2022]
Abstract
Vascular endothelial growth factor (VEGF) and its receptor play an important role both in physiologic and pathologic angiogenesis, which is identified in ovarian cancer progression and metastasis development. The aim of the present investigation is to identify a potential vascular endothelial growth factor inhibitor which is playing a crucial role in stimulating the immunosuppressive microenvironment in tumor cells of the ovary and to examine the effectiveness of the identified inhibitor for the treatment of ovarian cancer using various in silico approaches. Twelve established VEGF inhibitors were collected from various literatures. The compound AEE788 displays great affinity towards the target protein as a result of docking study. AEE788 was further used for structure-based virtual screening in order to obtain a more structurally similar compound with high affinity. Among the 80 virtual screened compounds, CID 88265020 explicates much better affinity than the established compound AEE788. Based on molecular dynamics simulation, pharmacophore and comparative toxicity analysis of both the best established compound and the best virtual screened compound displayed a trivial variation in associated properties. The virtual screened compound CID 88265020 has a high affinity with the lowest re-rank score and holds a huge potential to inhibit the VGFR and can be implemented for prospective future investigations in ovarian cancer.
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Affiliation(s)
- Sourav Mukherjee
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province, 250012, People's Republic of China
| | - Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad, 500001, Telangana, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Aravind Panicker
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Aashish Chaudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia.,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India. .,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia. .,Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh, India.
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.
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20
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Liu J, Guo W, Sakkiah S, Ji Z, Yavas G, Zou W, Chen M, Tong W, Patterson TA, Hong H. Machine Learning Models for Predicting Liver Toxicity. Methods Mol Biol 2022; 2425:393-415. [PMID: 35188640 DOI: 10.1007/978-1-0716-1960-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Liver toxicity is a major adverse drug reaction that accounts for drug failure in clinical trials and withdrawal from the market. Therefore, predicting potential liver toxicity at an early stage in drug discovery is crucial to reduce costs and the potential for drug failure. However, current in vivo animal toxicity testing is very expensive and time consuming. As an alternative approach, various machine learning models have been developed to predict potential liver toxicity in humans. This chapter reviews current advances in the development and application of machine learning models for prediction of potential liver toxicity in humans and discusses possible improvements to liver toxicity prediction.
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Affiliation(s)
- Jie Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Wenjing Guo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Sugunadevi Sakkiah
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Zuowei Ji
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Gokhan Yavas
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Wen Zou
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Minjun Chen
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Tucker A Patterson
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
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21
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Drug-Target Interaction Prediction Based on Multisource Information Weighted Fusion. CONTRAST MEDIA & MOLECULAR IMAGING 2021; 2021:6044256. [PMID: 34908912 PMCID: PMC8635946 DOI: 10.1155/2021/6044256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/22/2021] [Indexed: 01/08/2023]
Abstract
Recently, in most existing studies, it is assumed that there are no interaction relationships between drugs and targets with unknown interactions. However, unknown interactions mean the relationships between drugs and targets have just not been confirmed. In this paper, samples for which the relationship between drugs and targets has not been determined are considered unlabeled. A weighted fusion method of multisource information is proposed to screen drug-target interactions. Firstly, some drug-target pairs which may have interactions are selected. Secondly, the selected drug-target pairs are added to the positive samples, which are regarded as known to have interaction relationships, and the original interaction relationship matrix is revised. Finally, the revised datasets are used to predict the interaction derived from the bipartite local model with neighbor-based interaction profile inferring (BLM-NII). Experiments demonstrate that the proposed method has greatly improved specificity, sensitivity, precision, and accuracy compared with the BLM-NII method. In addition, compared with several state-of-the-art methods, the area under the receiver operating characteristic curve (AUC) and the area under the precision-recall curve (AUPR) of the proposed method are excellent.
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22
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Spjuth O, Frid J, Hellander A. The machine learning life cycle and the cloud: implications for drug discovery. Expert Opin Drug Discov 2021; 16:1071-1079. [PMID: 34057379 DOI: 10.1080/17460441.2021.1932812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Artificial intelligence (AI) and machine learning (ML) are increasingly used in many aspects of drug discovery. Larger data sizes and methods such as Deep Neural Networks contribute to challenges in data management, the required software stack, and computational infrastructure. There is an increasing need in drug discovery to continuously re-train models and make them available in production environments.Areas covered: This article describes how cloud computing can aid the ML life cycle in drug discovery. The authors discuss opportunities with containerization and scientific workflows and introduce the concept of MLOps and describe how it can facilitate reproducible and robust ML modeling in drug discovery organizations. They also discuss ML on private, sensitive and regulated data.Expert opinion: Cloud computing offers a compelling suite of building blocks to sustain the ML life cycle integrated in iterative drug discovery. Containerization and platforms such as Kubernetes together with scientific workflows can enable reproducible and resilient analysis pipelines, and the elasticity and flexibility of cloud infrastructures enables scalable and efficient access to compute resources. Drug discovery commonly involves working with sensitive or private data, and cloud computing and federated learning can contribute toward enabling collaborative drug discovery within and between organizations.Abbreviations: AI = Artificial Intelligence; DL = Deep Learning; GPU = Graphics Processing Unit; IaaS = Infrastructure as a Service; K8S = Kubernetes; ML = Machine Learning; MLOps = Machine Learning and Operations; PaaS = Platform as a Service; QC = Quality Control; SaaS = Software as a Service.
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Affiliation(s)
- Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala Sweden.,Scaleout Systems AB, Sweden
| | | | - Andreas Hellander
- Scaleout Systems AB, Sweden.,Department of Information Technology, Uppsala University, Sweden
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