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Guo Q, Fu B, Tian Y, Xu S, Meng X. Recent progress in artificial intelligence and machine learning for novel diabetes mellitus medications development. Curr Med Res Opin 2024:1-22. [PMID: 39083361 DOI: 10.1080/03007995.2024.2387187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 07/29/2024] [Indexed: 08/02/2024]
Abstract
Diabetes mellitus, stemming from either insulin resistance or inadequate insulin secretion, represents a complex ailment that results in prolonged hyperglycemia and severe complications. Patients endure severe ramifications such as kidney disease, vision impairment, cardiovascular disorders, and susceptibility to infections, leading to significant physical suffering and imposing substantial socio-economic burdens. This condition has evolved into an increasingly severe health crisis. There is an urgent need to develop new treatments with improved efficacy and fewer adverse effects to meet clinical demands. However, novel drug development is costly, time-consuming and often associated with side effects and suboptimal efficacy, making it a major challenge. Artificial Intelligence (AI) and Machine Learning (ML) have revolutionized drug development across its comprehensive lifecycle, spanning drug discovery, preclinical studies, clinical trials, and post-market surveillance. These technologies have significantly accelerated the identification of promising therapeutic candidates, optimized trial designs, and enhanced post-approval safety monitoring. Recent advances in AI, including data augmentation, interpretable AI, and integration of AI with traditional experimental methods, offer promising strategies for overcoming the challenges inherent in AI-based drug discovery. Despite these advancements, there exists a notable gap in comprehensive reviews detailing AI and ML applications throughout the entirety of developing medications for diabetes mellitus. This review aims to fill this gap by evaluating the impact and potential of AI and ML technologies at various stages of diabetes mellitus drug development. By synthesizing current research findings and technological advances so as to effectively control diabetes mellitus and mitigate its far-reaching social and economic impacts. The integration of AI and ML promises to revolutionize diabetes mellitus treatment strategies, offering hope for improved patient outcomes and reduced healthcare burdens worldwide.
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Affiliation(s)
- Qi Guo
- School of Pharmacy, Heilongjiang University of Chinese Medicine, NO.24 Heping Road, Harbin 150040, P. R. China
| | - Bo Fu
- School of Pharmacy, Heilongjiang University of Chinese Medicine, NO.24 Heping Road, Harbin 150040, P. R. China
| | - Yuan Tian
- School of Pharmacy, Heilongjiang University of Chinese Medicine, NO.24 Heping Road, Harbin 150040, P. R. China
| | - Shujun Xu
- School of Pharmacy, Heilongjiang University of Chinese Medicine, NO.24 Heping Road, Harbin 150040, P. R. China
| | - Xin Meng
- School of Pharmacy, Heilongjiang University of Chinese Medicine, NO.24 Heping Road, Harbin 150040, P. R. China
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Snanoudj S, Derambure C, Zhang C, Hai Yen NT, Lesueur C, Coutant S, Abily-Donval L, Marret S, Yang H, Mardinoglu A, Bekri S, Tebani A. Genome-wide expression analysis in a Fabry disease human podocyte cell line. Heliyon 2024; 10:e34357. [PMID: 39100494 PMCID: PMC11295972 DOI: 10.1016/j.heliyon.2024.e34357] [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: 03/14/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 08/06/2024] Open
Abstract
Fabry disease (FD) is an X-linked lysosomal disease caused by an enzyme deficiency of alpha-galactosidase A (α-gal A). This deficiency leads to the accumulation of glycosphingolipids in lysosomes, resulting in a range of clinical symptoms. The complex pathogenesis of FD involves lysosomal dysfunction, altered autophagy, and mitochondrial abnormalities. Omics sciences, particularly transcriptomic analysis, comprehensively understand molecular mechanisms underlying diseases. This study focuses on genome-wide expression analysis in an FD human podocyte model to gain insights into the underlying mechanisms of podocyte dysfunction. Human control and GLA-edited podocytes were used. Gene expression data was generated using RNA-seq analysis, and differentially expressed genes were identified using DESeq2. Principal component analysis and Spearman correlation have explored gene expression trends. Functional enrichment and Reporter metabolite analyses were conducted to identify significantly affected metabolites and metabolic pathways. Differential expression analysis revealed 247 genes with altered expression levels in GLA-edited podocytes compared to control podocytes. Among these genes, 136 were underexpressed, and 111 were overexpressed in GLA-edited cells. Functional analysis of differentially expressed genes showed their involvement in various pathways related to oxidative stress, inflammation, fatty acid metabolism, collagen and extracellular matrix homeostasis, kidney injury, apoptosis, autophagy, and cellular stress response. The study provides insights into molecular mechanisms underlying Fabry podocyte dysfunction. Integrating transcriptomics data with genome-scale metabolic modeling further unveiled metabolic alterations in GLA-edited podocytes. This comprehensive approach contributes to a better understanding of Fabry disease and may lead to identifying new biomarkers and therapeutic targets for this rare lysosomal disorder.
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Affiliation(s)
- Sarah Snanoudj
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Metabolic Biochemistry, Referral Center for Lysosomal Diseases, Filière G2M, 76000, Rouen, France
| | - Céline Derambure
- Normandie Univ, UNIROUEN, INSERM U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nguyen Thi Hai Yen
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Metabolic Biochemistry, Referral Center for Lysosomal Diseases, Filière G2M, 76000, Rouen, France
| | - Céline Lesueur
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Metabolic Biochemistry, Referral Center for Lysosomal Diseases, Filière G2M, 76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, INSERM U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Lénaïg Abily-Donval
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Neonatal Pediatrics, Intensive Care, and Neuropediatrics, 76000, Rouen, France
| | - Stéphane Marret
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Neonatal Pediatrics, Intensive Care, and Neuropediatrics, 76000, Rouen, France
| | - Hong Yang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Soumeya Bekri
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Metabolic Biochemistry, Referral Center for Lysosomal Diseases, Filière G2M, 76000, Rouen, France
| | - Abdellah Tebani
- Normandie Univ, UNIROUEN, INSERM, U1245, CHU Rouen, Department of Metabolic Biochemistry, Referral Center for Lysosomal Diseases, Filière G2M, 76000, Rouen, France
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Alruhaimi RS, Mahmoud AM, Elbagory I, Ahmeda AF, El-Bassuony AA, Lamsabhi AM, Kamel EM. Unveiling the tyrosinase inhibitory potential of phenolics from Centaurium spicatum: Bridging in silico and in vitro perspectives. Bioorg Chem 2024; 147:107397. [PMID: 38691905 DOI: 10.1016/j.bioorg.2024.107397] [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: 03/19/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Phenolics, abundant in plants, constitute a significant portion of phytoconstituents consumed in the human diet. The phytochemical screening of the aerial parts of Centaurium spicatum led to the isolation of five phenolics. The anti-tyrosinase activities of the isolated compounds were assessed through a combination of in vitro experiments and multiple in silico approaches. Docking and molecular dynamics (MD) simulation techniques were utilized to figure out the binding interactions of the isolated phytochemicals with tyrosinase. The findings from molecular docking analysis revealed that the isolated phenolics were able to bind effectively to tyrosinase and potentially inhibit substrate binding, consequently diminishing the catalytic activity of tyrosinase. Among isolated compounds, cichoric acid displayed the lowest binding energy and the highest extent of polar interactions with the target enzyme. Analysis of MD simulation trajectories indicated that equilibrium was reached within 30 ns for all complexes of tyrosinase with the isolated phenolics. Among the five ligands studied, cichoric acid exhibited the lowest interaction energies, rendering its complex with tyrosinase the most stable. Considering these collective findings, cichoric acid emerges as a promising candidate for the design and development of a potential tyrosinase inhibitor. Furthermore, the in vitro anti-tyrosinase activity assay unveiled significant variations among the isolated compounds. Notably, cichoric acid exhibited the most potent inhibitory effect, as evidenced by the lowest IC50 value (7.92 ± 1.32 µg/ml), followed by isorhamnetin and gentiopicrin. In contrast, sinapic acid demonstrated the least inhibitory activity against tyrosinase, with the highest IC50 value. Moreover, cichoric acid exhibited a mixed inhibition mode against the hydrolysis of l-DOPA catalyzed by tyrosinase, with Ki value of 1.64. Remarkably, these experimental findings align well with the outcomes of docking and MD simulations, underscoring the consistency and reliability of our computational predictions with the actual inhibitory potential observed in vitro.
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Affiliation(s)
- Reem S Alruhaimi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ayman M Mahmoud
- Department of Life Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester M1 5GD, UK; Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Ibrahim Elbagory
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Rafha 76321, Saudi Arabia
| | - Ahmad F Ahmeda
- Department of Basic Medical Sciences, College of Medicine, Ajman University, Ajman 346, United Arab Emirates; Center of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates
| | - Ashraf A El-Bassuony
- Organic Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, Madrid 28049, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Emadeldin M Kamel
- Organic Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef 62514, Egypt
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Sadeghi M, Seyedebrahimi S, Ghanadian M, Miroliaei M. Identification of cholinesterases inhibitors from flavonoids derivatives for possible treatment of Alzheimer's disease: In silico and in vitro approaches. Curr Res Struct Biol 2024; 7:100146. [PMID: 38707547 PMCID: PMC11070244 DOI: 10.1016/j.crstbi.2024.100146] [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: 01/21/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Nowadays, one of the methods to prevent the progress of Alzheimer's disease (AD) is to prescribe compounds that inhibit the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes. Researchers are actively pursuing compounds, particularly of natural origin, that exhibit enhanced efficacy and reduced side effects. The inhibition of AChE and BChE using natural flavonoids represents a promising avenue for regulating AD. This study aims to identify alternative flavonoids capable of modulating AD by down-regulating AChE and BChE activity through a molecular docking approach. Molecular docking analysis identified Ginkgetin and Kolaflavanone as potent inhibitors of AChE and BChE, respectively, among the selected flavonoids. Asn87 and Ala127 involved in the interactions of AChE-Ginkgetin complex through conventional hydrogen bonds. While in the BChE-Kolaflavanone complex, Asn83, Ser79, Gln 47, and Ser287 are involved. In vitro analysis further corroborated the inhibitory potential, with Ginkgetin exhibiting an IC50 of 3.2 mM against AChE, and Kolaflavanone displaying an IC50 of 3.6 mM against BChE. These findings underscore the potential of Ginkgetin and Kolaflavanone as candidate inhibitors for the treatment of AD through the inhibition of AChE and BChE enzymes. Nevertheless, additional in vitro and in vivo studies are imperative to validate the efficacy of these compounds.
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Affiliation(s)
- Morteza Sadeghi
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
| | - Seyedehmasoumeh Seyedebrahimi
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
| | - Mustafa Ghanadian
- Department of Pharmacognosy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehran Miroliaei
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
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Ušjak L, Stojković D, Carević T, Milutinović V, Soković M, Niketić M, Petrović S. Chemical Analysis and Investigation of Antimicrobial and Antibiofilm Activities of Prangos trifida (Apiaceae). Antibiotics (Basel) 2024; 13:41. [PMID: 38247600 PMCID: PMC10812483 DOI: 10.3390/antibiotics13010041] [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: 11/09/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Plants of the genus Prangos are intensively investigated as potential new sources of bioactive isolated products. In this work, the chemical composition of volatile constituents (essential oils and headspace volatiles) and dichloromethane extracts, as well as antimicrobial and antibiofilm activities of essential oils and MFDEs (methanol fractions of dichloromethane extracts) of Prangos trifida from Serbia, were investigated. Volatiles of roots, leaves, stems and fruits, and fatty acids and phytosterols in dichloromethane extracts of roots and fruits were analyzed by GC-FID-MS, whereas coumarins in MFDEs by LC-MS and some isolated coumarins by 1H-NMR. Minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations/minimum fungicidal concentrations (MBCs/MFCs) of essential oils and MFDEs were determined against 13 microorganisms. Antibiofilm activity was assessed against four microorganisms. Additionally, congo red and ergosterol binding assays were conducted to elucidate selected mechanisms of antibiofilm action in the case of Candida albicans. Total of 52 volatile constituents, 16 fatty acids, eight phytosterols and 10 coumarins were identified. Essential oils demonstrated significant activity, surpassing that of commercial food preservatives, against six tested molds from the Aspergillus, Penicillium and Trichoderma genera, as well as against bacteria Staphylococcus aureus and Bacillus cereus. Most of the oils strongly inhibited the formation of biofilms by S. aureus, Listeria monocytogenes and Escherichia coli. MFDEs exhibited noteworthy effects against B. cereus and the tested Aspergillus species, particularly A. niger, and significantly inhibited C. albicans biofilm formation. This inhibition was linked to a marked reduction in exopolysaccharide production, while antifungal mechanisms associated with ergosterol remained unaffected.
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Affiliation(s)
- Ljuboš Ušjak
- Department of Pharmacognosy, University of Belgrade-Faculty of Pharmacy, Vojvode Stepe 450, 11221 Belgrade, Serbia; (L.U.); (V.M.)
| | - Dejan Stojković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”-National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (T.C.); (M.S.)
| | - Tamara Carević
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”-National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (T.C.); (M.S.)
| | - Violeta Milutinović
- Department of Pharmacognosy, University of Belgrade-Faculty of Pharmacy, Vojvode Stepe 450, 11221 Belgrade, Serbia; (L.U.); (V.M.)
| | - Marina Soković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”-National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (T.C.); (M.S.)
| | - Marjan Niketić
- Natural History Museum, Njegoševa 51, 11000 Belgrade, Serbia;
- Serbian Academy of Sciences and Arts, Kneza Mihaila 35/II, 11000 Belgrade, Serbia
| | - Silvana Petrović
- Department of Pharmacognosy, University of Belgrade-Faculty of Pharmacy, Vojvode Stepe 450, 11221 Belgrade, Serbia; (L.U.); (V.M.)
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Niazi SK, Mariam Z. Computer-Aided Drug Design and Drug Discovery: A Prospective Analysis. Pharmaceuticals (Basel) 2023; 17:22. [PMID: 38256856 PMCID: PMC10819513 DOI: 10.3390/ph17010022] [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: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
In the dynamic landscape of drug discovery, Computer-Aided Drug Design (CADD) emerges as a transformative force, bridging the realms of biology and technology. This paper overviews CADDs historical evolution, categorization into structure-based and ligand-based approaches, and its crucial role in rationalizing and expediting drug discovery. As CADD advances, incorporating diverse biological data and ensuring data privacy become paramount. Challenges persist, demanding the optimization of algorithms and robust ethical frameworks. Integrating Machine Learning and Artificial Intelligence amplifies CADDs predictive capabilities, yet ethical considerations and scalability challenges linger. Collaborative efforts and global initiatives, exemplified by platforms like Open-Source Malaria, underscore the democratization of drug discovery. The convergence of CADD with personalized medicine offers tailored therapeutic solutions, though ethical dilemmas and accessibility concerns must be navigated. Emerging technologies like quantum computing, immersive technologies, and green chemistry promise to redefine the future of CADD. The trajectory of CADD, marked by rapid advancements, anticipates challenges in ensuring accuracy, addressing biases in AI, and incorporating sustainability metrics. This paper concludes by highlighting the need for proactive measures in navigating the ethical, technological, and educational frontiers of CADD to shape a healthier, brighter future in drug discovery.
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Affiliation(s)
| | - Zamara Mariam
- Centre for Health and Life Sciences, Coventry University, Coventry City CV1 5FB, UK
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