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Ningthoujam SS, Nath R, Kityania S, Mazumder PB, Dutta Choudhury M, Talukdar AD, Nahar L, Sarker SD. R software for QSAR analysis in phytopharmacological studies. PHYTOCHEMICAL ANALYSIS : PCA 2023; 34:709-728. [PMID: 37392081 DOI: 10.1002/pca.3239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 07/02/2023]
Abstract
INTRODUCTION In recent decades, quantitative structure-activity relationship (QSAR) analysis has become an important method for drug design and natural product research. With the availability of bioinformatic and cheminformatic tools, a vast number of descriptors have been generated, making it challenging to select potential independent variables that are accurately related to the dependent response variable. OBJECTIVE The objective of this study is to demonstrate various descriptor selection procedures, such as the Boruta approach, all subsets regression, the ANOVA approach, the AIC method, stepwise regression, and genetic algorithm, that can be used in QSAR studies. Additionally, we performed regression diagnostics using R software to test parameters such as normality, linearity, residual histograms, PP plots, multicollinearity, and homoscedasticity. RESULTS The workflow designed in this study highlights the different descriptor selection procedures and regression diagnostics that can be used in QSAR studies. The results showed that the Boruta approach and genetic algorithm performed better than other methods in selecting potential independent variables. The regression diagnostics parameters tested using R software, such as normality, linearity, residual histograms, PP plots, multicollinearity, and homoscedasticity, helped in identifying and diagnosing model errors, ensuring the reliability of the QSAR model. CONCLUSION QSAR analysis is vital in drug design and natural product research. To develop a reliable QSAR model, it is essential to choose suitable descriptors and perform regression diagnostics. This study offers an accessible, customizable approach for researchers to select appropriate descriptors and diagnose errors in QSAR studies.
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Affiliation(s)
| | - Rajat Nath
- Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, India
| | - Sibashish Kityania
- Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, India
| | | | | | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, India
| | - Lutfun Nahar
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Palacký University, Olomouc, Czech Republic
| | - Satyajit D Sarker
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
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Zhang Q, Cui Q. Target protein identification of andrographolide based on isomer approach. J Pharm Biomed Anal 2023; 222:115111. [PMID: 36279844 DOI: 10.1016/j.jpba.2022.115111] [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: 08/23/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The target identification of natural products is one of the most challenging issues in the standardized application of traditional Chinese medicine. It is widely recognized that magnetic nanoparticles (MNPs) could function as a tool that capture the target proteins of active molecule. However, the false positives caused by non-specific adsorption should not be ignored. Here, we reported a functionalized MNPs technique that could enrich the target proteins of andrographolide (AG) based on isomers approach. We designed and characterized MNPs and isomers of AG. The combination of the two could be used as an ideal coupling, which provides a feasible method for the target proteins enrichment of AG. In addition, the target proteins were identified by HPLC-MS/MS. Moreover, bioinformatics analysis and systematic computational dockings were performed to search for the interactions between target proteins and AG. Six inflammation-related proteins, including CD4, IKBKB, PKN1, PKN2, YWHAB and YWHAH were proved to be the anti-inflammatory targets of AG. All of the results indicated this integrated system could benefit target identification of bioactive natural products.
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Affiliation(s)
- Qi Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Qingxin Cui
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
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Ahmed SS, Al-Mamun A, Hossain SI, Akter F, Ahammad I, Chowdhury ZM, Salimullah M. Virtual screening reveals liquiritigenin as a broad-spectrum inhibitor of SARS-CoV-2 variants of concern: an in silico study. J Biomol Struct Dyn 2022:1-19. [PMID: 35971968 DOI: 10.1080/07391102.2022.2111361] [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: 10/15/2022]
Abstract
The SARS-CoV-2 has severely impacted the lives of people worldwide. Global concern is on the rise due to a large number of unexpected mutations in the viral genome, resulting in new variants. Nature-based bioactive phytochemicals hold great promise as inhibitors against pathogenic viruses. The current study was aimed at evaluating some bioactive antiviral phytochemicals against SARS-CoV-2 variants of concern. A total of 46 phytochemicals were screened against the pathogenic spike protein of Alpha, Beta, Delta, Gamma, and Omicron variants. In addition to molecular docking, screening for favorable pharmacokinetic and pharmacodynamic properties such as absorption, distribution, metabolism, excretion, and toxicity was undertaken. For each of the aforementioned five SARS-CoV-2 variants of concern, a 100 ns molecular dynamics simulation was run to assess the stability of the complexes between their respective spike protein receptor-binding domain and the best-selected compound. From our current investigation, the natural compound liquiritigenin turned out to be the most promising potential lead compound against almost all the variants. These findings could pave the way for the development of effective medications against SARS-CoV-2 variants. However, in vivo trials in future studies are necessary for further validation of our results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Abdullah Al-Mamun
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Shah Imran Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Farzana Akter
- Department of Botany, University of Dhaka, Dhaka, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, Bangladesh
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Unraveling the Phytochemistry, Traditional Uses, and Biological and Pharmacological Activities of Thymus algeriensis Boiss. & Reut. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6487430. [PMID: 35663202 PMCID: PMC9159826 DOI: 10.1155/2022/6487430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 12/20/2022]
Abstract
Growing concern for public health has increased the need to change the paradigm towards a healthcare system that advocates holistic practices while reducing adverse effects. Herbal therapy is becoming an integral part of the therapeutic arsenal, and several successful plant-derived compounds/molecules are being introduced into the market. The medicinal plants belonging to the genus Thymus are among the most important species within the Lamiaceae family. One of them is Thymus algeriensis which is mainly distributed in the Mediterranean region. For a long time, this species has been used in traditional medicine to treat several disorders and diseases including inflammation, diabetes, rheumatism, digestive, and respiratory affections. This review describes the traditional uses, phytochemical composition, and biological and pharmacological activities of T. algeriensis extracts. Data were obtained using electronic databases such as SciFindern, ScienceDirect, Scopus, and Web of Science. Several plant-based extracts and a broad spectrum of identified secondary metabolites were highlighted and discussed with respective activities and modes of action. T. algeriensis represents a promising natural resource for the pharmaceutical industry mainly for antioxidant, anti-inflammatory, antimicrobial, and anticancer activities. Considering these findings, more research is needed to transmute the conventional uses of T. algeriensis into scientifically sound information. Moreover, extensive preclinical, clinical, toxicological, and pharmacokinetic trials on this species and its derivatives compounds are required to underpin the mechanisms of action and ensure its biosafety and efficiency. This comprehensive review provides a scientific basis for future investigations on the use of T. algeriensis and derived compounds in health maintenance and promotion and disease prevention.
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The Multifunctional Role of Herbal Products in the Management of Diabetes and Obesity: A Comprehensive Review. Molecules 2022; 27:molecules27051713. [PMID: 35268815 PMCID: PMC8911649 DOI: 10.3390/molecules27051713] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity and diabetes are the most demanding health problems today, and their prevalence, as well as comorbidities, is on the rise all over the world. As time goes on, both are becoming big issues that have a big impact on people’s lives. Diabetes is a metabolic and endocrine illness set apart by hyperglycemia and glucose narrow-mindedness because of insulin opposition. Heftiness is a typical, complex, and developing overall wellbeing worry that has for quite some time been connected to significant medical issues in individuals, all things considered. Because of the wide variety and low adverse effects, herbal products are an important hotspot for drug development. Synthetic compounds are not structurally diverse and lack drug-likeness properties. Thus, it is basic to keep on exploring herbal products as possible wellsprings of novel drugs. We conducted this review of the literature by searching Scopus, Science Direct, Elsevier, PubMed, and Web of Science databases. From 1990 until October 2021, research reports, review articles, and original research articles in English are presented. It provides top to bottom data and an examination of plant-inferred compounds that might be utilized against heftiness or potentially hostile to diabetes treatments. Our expanded comprehension of the systems of activity of phytogenic compounds, as an extra examination, could prompt the advancement of remedial methodologies for metabolic diseases. In clinical trials, a huge number of these food kinds or restorative plants, as well as their bioactive compounds, have been shown to be beneficial in the treatment of obesity.
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Computational strategies to model the interaction and the reactivity of biologically-relevant transition metal complexes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Rahman MM, Biswas S, Islam KJ, Paul AS, Mahato SK, Ali MA, Halim MA. Antiviral phytochemicals as potent inhibitors against NS3 protease of dengue virus. Comput Biol Med 2021; 134:104492. [PMID: 34022487 DOI: 10.1016/j.compbiomed.2021.104492] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
Dengue, a mosquito-borne disease, has appeared as a major infectious disease globally. The virus requires its proteins to replicate and reproduce in the host cell. The NS3 protease converts the polyprotein to functional proteins with the help of the NS2B cofactor. Thus, NS3 protease is a promising target to develop antiviral inhibitors against the dengue virus. A systematic screening including ADMET properties, molecular docking, molecular dynamics (MD) simulation, binding free energy calculation, and QSAR studies is carried out to predict potent inhibitors against the NS3 protease. From the screening of 40 antiviral phytochemicals, ADMET properties analysis was used to screen out ligands that violate ADME rules and have probable toxicity. Cyanidin 3-Glucoside, Dithymoquinone, and Glabridin were predicted to be potent inhibitors against the NS3 protease according to their binding affinity. These ligands showed several noncovalent interactions, including hydrogen bond, hydrophobic interaction, electrostatic interaction, pi-sulfur interactions. The ligand-protein complexes were further scrutinized using 250 ns molecular dynamics simulation. The MM-PBSA binding free energy calculation was conducted to investigate their binding stability in dynamic conditions. The calculated pIC50(mM) value was predicted using the QSAR model with 89.91% goodness of fit. The predicted biologocal activity value for the ligands indicates they might have good potency.
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Affiliation(s)
- Md Mahbubur Rahman
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Sourav Biswas
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Kazi Jahidul Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Archi Sundar Paul
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shiplob Kumar Mahato
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA.
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Begum S, Jaswanthi P, Venkata Lakshmi B, Bharathi K. QSAR studies on indole-azole Analogues using DTC tools; imidazole ring is more favorable for aromatase inhibition. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Chen ZD, Zhao L, Chen HY, Gong JN, Chen X, Chen CYC. A novel artificial intelligence protocol to investigate potential leads for Parkinson's disease. RSC Adv 2020; 10:22939-22958. [PMID: 35520357 PMCID: PMC9054719 DOI: 10.1039/d0ra04028b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/27/2020] [Indexed: 11/21/2022] Open
Abstract
Previous studies have shown that small molecule inhibitors of NLRP3 may be a potential treatment for Parkinson's disease (PD). NACHT, LRR and PYD domains-containing protein 3 (NLRP3), heat shock protein HSP 90-beta (HSP90AB1), caspase-1 (CASP1) and cellular tumor antigen p53 (TP53) have significant involvement in the pathogenesis pathway of PD. Molecular docking was used to screen the traditional Chinese medicine database TCM Database@Taiwan. Top traditional Chinese medicine (TCM) compounds with high affinities based on Dock Score were selected to form the drug-target interaction network to investigate potential candidates targeting NLRP3, HSP90AB1, CASP1, and TP53 proteins. Artificial intelligence model, 3D-Quantitative Structure-Activity Relationship (3D-QSAR) were constructed respectively utilizing training sets of inhibitors against the four proteins with known inhibitory activities (pIC50). The results showed that 2007_22057 (an indole derivative), 2007_22325 (a valine anhydride) and 2007_15317 (an indole derivative) might be a potential medicine formula for the treatment of PD. Then there are three candidate compounds identified by the result of molecular dynamics.
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Affiliation(s)
- Zhi-Dong Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China
- School of Pharmaceutical Sciences, Sun Yat-sen University Shenzhen 510275 China
| | - Lu Zhao
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University Guangzhou 510655 China
| | - Hsin-Yi Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China
| | - Jia-Ning Gong
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China
- School of Pharmaceutical Sciences, Sun Yat-sen University Shenzhen 510275 China
| | - Xu Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China
- School of Pharmaceutical Sciences, Sun Yat-sen University Shenzhen 510275 China
| | - Calvin Yu-Chian Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China
- Department of Medical Research, China Medical University Hospital Taichung 40447 Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University Taichung 41354 Taiwan
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QSAR-based molecular signatures of prenylated (iso)flavonoids underlying antimicrobial potency against and membrane-disruption in Gram positive and Gram negative bacteria. Sci Rep 2018; 8:9267. [PMID: 29915354 PMCID: PMC6006161 DOI: 10.1038/s41598-018-27545-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/05/2018] [Indexed: 12/27/2022] Open
Abstract
Prenylated flavonoids and isoflavonoids are phytochemicals with remarkable antibacterial activity. In this study, 30 prenylated (iso)flavonoids were tested against Listeria monocytogenes and Escherichia coli (the latter in combination with an efflux pump inhibitor). Minimum inhibitory concentrations of the most active compounds ranged between 6.3–15.0 µg/mL. Quantitative structure-activity relationships (QSAR) analysis was performed and linear regression models were proposed with R2 between 0.77–0.80, average R2m between 0.70–0.75, Q2LOO between 0.66–0.69, and relatively low amount of descriptors. Shape descriptors (related to flexibility and globularity), together with hydrophilic/hydrophobic volume and surface area descriptors, were identified as important molecular characteristics related to activity. A 3D pharmacophore model explaining the effect of the prenyl position on the activity of compounds was developed for each bacterium. These models predicted active compounds with an accuracy of 71–88%. With regard to the mode of action, good antibacterial prenylated (iso)flavonoids with low relative hydrophobic surface area caused remarkable membrane permeabilization, whereas those with higher relative hydrophobic surface area did not. Based on the QSAR and membrane permeabilization studies, the mode of action of antibacterial prenylated (iso)flavonoids was putatively rationalized.
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Arthur DE, Uzairu A, Mamza P, Abechi SE, Shallangwa G. In silico modelling of quantitative structure–activity relationship of multi-target anticancer compounds on k-562 cell line. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s13721-018-0168-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Muhammad U, Uzairu A, Ebuka Arthur D. Review on: quantitative structure activity relationship (QSAR) modeling. ACTA ACUST UNITED AC 2018. [DOI: 10.15406/japlr.2018.07.00232] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Evaluation of antibacterial, antioxidant and nootropic activities of Tiliacora racemosa Colebr. leaves: In vitro and in vivo approach. Biomed Pharmacother 2017; 86:662-668. [DOI: 10.1016/j.biopha.2016.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/23/2016] [Accepted: 12/04/2016] [Indexed: 01/05/2023] Open
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Kar S, Roy K, Leszczynski J. On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
It is widely accepted that modern QSAR began in the early 1960s. However, as long ago as 1816 scientists were making predictions about physical and chemical properties. The first investigations into the correlation of biological activities with physicochemical properties such as molecular weight and aqueous solubility began in 1841, almost 60 years before the important work of Overton and Meyer linking aquatic toxicity to lipid-water partitioning. Throughout the 20th century QSAR progressed, though there were many lean years. In 1962 came the seminal work of Corwin Hansch and co-workers, which stimulated a huge interest in the prediction of biological activities. Initially that interest lay largely within medicinal chemistry and drug design, but in the 1970s and 1980s, with increasing ecotoxicological concerns, QSAR modelling of environmental toxicities began to grow, especially once regulatory authorities became involved. Since then QSAR has continued to expand, with over 1400 publications annually from 2011 onwards.
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Posobiec LM, Clark RL, Bushdid PB, Laffan SB, Wang KF, White TEK. Dihydroartemisinin (DHA) Treatment Causes an Arrest of Cell Division and Apoptosis in Rat Embryonic Erythroblasts in Whole Embryo Culture. ACTA ACUST UNITED AC 2014; 98:445-58. [DOI: 10.1002/bdrb.21088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/14/2013] [Indexed: 12/25/2022]
Affiliation(s)
| | | | - Paul B. Bushdid
- Safety Assessment; GlaxoSmithKline; King of Prussia Pennsylvania
| | - Susan B. Laffan
- Safety Assessment; GlaxoSmithKline; King of Prussia Pennsylvania
| | - Kai-Fen Wang
- Safety Assessment; GlaxoSmithKline; King of Prussia Pennsylvania
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Janero DR. Relieving the cardiometabolic disease burden: a perspective on phytometabolite functional and chemical annotation for diabetes management. Expert Opin Pharmacother 2013; 15:5-10. [PMID: 24156826 DOI: 10.1517/14656566.2014.852538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Type 2 diabetes (T2D) is both a complex, multifactorial disease state and an unsolved, intensifying public-health problem. To help reduce disease burden, some T2D patients have embraced plant-derived substances for use with - if not in place of - prescription medicines, a trend based mainly upon historical precedent and anecdotal observations of human health benefit. Preclinical research has emphasized phytometabolite interactions with purported T2D pathogenic targets and the effects of botanical preparations on experimental T2D symptomology as induced in laboratory animals. More holistic, systems-oriented profiling of phytochemicals with functional-biology, omics, and chemical-fingerprinting tools now appears necessary to increase our appreciation of phytometabolite actions potentially beneficial to the T2D patient. The resultant, multidimensional view of phytometabolite pharmacology should help provide a more rational basis for evaluating the potential of natural plant products as T2D pharmacotherapy. Such information may also help substantiate and legitimize (pre)clinical demonstrations of phytochemical health benefits, advance our understanding of T2D pathogenesis, and offer scope for better T2D medicines. Public-private partnerships are invoked for conducting this research with the ultimate aim of improving the global cardiometabolic profile.
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Affiliation(s)
- David R Janero
- Northeastern University, Bouvé College of Health Sciences, Center for Drug Discovery, Department of Pharmaceutical Sciences, Health Sciences Entrepreneurs , 360 Huntington Avenue, 116 Mugar Life Sciences Hall, Boston, MA 02115-5000 , USA +1 617 373 2208 ; +1 617 373 7493 ;
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Stopa B, Jagusiak A, Konieczny L, Piekarska B, Rybarska J, Zemanek G, Król M, Piwowar P, Roterman I. The use of supramolecular structures as protein ligands. J Mol Model 2013; 19:4731-40. [PMID: 23296569 PMCID: PMC3825278 DOI: 10.1007/s00894-012-1744-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/17/2012] [Indexed: 11/30/2022]
Abstract
Congo red dye as well as other eagerly self-assembling organic molecules which form rod-like or ribbon-like supramolecular structures in water solutions, appears to represent a new class of protein ligands with possible wide-ranging medical applications. Such molecules associate with proteins as integral clusters and preferentially penetrate into areas of low molecular stability. Abnormal, partly unfolded proteins are the main binding target for such ligands, while well packed molecules are generally inaccessible. Of particular interest is the observation that local susceptibility for binding supramolecular ligands may be promoted in some proteins as a consequence of function-derived structural changes, and that such complexation may alter the activity profile of target proteins. Examples are presented in this paper.
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Affiliation(s)
- Barbara Stopa
- Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, 31-034, Kraków, Poland
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