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Viswanathan S, Arumugam T, Subramanian K, Sivaraj R, Ramesh V, Vasanthi AHR. Molecular docking analysis of flavonoids with AChE and BACE-1. Bioinformation 2024; 20:103-109. [PMID: 38497082 PMCID: PMC10941774 DOI: 10.6026/973206300200103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Flavonoids are promising therapeutics for the treatment of Alzheimer's disease (AD). Therefore, it is of interest to study the anti-AD potential of 35 flavonoids towards the inhibition of AchE and BACE-1. Hence, the physicochemical, pharmacokinetic parameters, toxicity risk and drug-likeliness of the selected 35 flavonoids were computed. Further, the molecular docking analysis of flavonoids with AChE and BACE-1 were completed. A binding energy of -10.42 kcal/mol Epicatechin gallate, -10.16 kcal/mol sterubin and -10.11 kcal/mol Fisetin was observed with AchE as potential inhibitors. Similarly, Biochainin-A -9.81kcal/mol, Sterubin -8.96 kcal/mol and Epicatechin gallate -7.4 7 kcal/mol showed with BACE-1. Thus, these flavonoids are potential leads for structure-based design of effective anti-Alzheimer's agents.
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Affiliation(s)
- Sittarthan Viswanathan
- Department of Pharmacology, Mother Theresa Post Graduate & Research Institute of Health Sciences (Government of Puducherry Institution), Puducherry - 605006, India
| | - Thennavan Arumugam
- Department of Pharmacology, Central Animal House, JIPMER, Puducherry - 605006
| | - Kavimani Subramanian
- Department of Pharmacology, Mother Theresa Post Graduate & Research Institute of Health Sciences (Government of Puducherry Institution), Puducherry - 605006, India
| | - Rengaraj Sivaraj
- Department of Pharmacology, Aarupadai Veedu Medical College & Hospital, Puducherry 607402
| | - Vimalavathini Ramesh
- Department of Pharmacology, Mother Theresa Post Graduate & Research Institute of Health Sciences (Government of Puducherry Institution), Puducherry - 605006, India
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Hassan HA, Abdelwahab SF, Al-Khdhairawi A, Al Zrkani MK, Rehman HM, Abdel-Rahman IM, El-Sheikh AAK, Abdelhamid MM. Exploring the therapeutic potential of galidesivir analogs against Zaire ebolavirus protein 24 (V24): database screening, molecular docking, drug-relevant property evaluation and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-11. [PMID: 37477257 DOI: 10.1080/07391102.2023.2236720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The recent outbreak of the Ebola virus (EBOV) has marked it as one of the most severe health threats globally. Among various anti-EBOV inhibitors studied, galidesivir (BCX4430) has shown remarkable efficacy. This study aims to identify novel potential anti-EBOV drugs among galidesivir analogs, focusing on the Zaire ebolavirus (Z-EBOV), which exhibits a mortality rate of 90%. We subjected 200 candidate compounds to molecular docking calculations, followed by an evaluation of the bioactivity of the top 25 compounds using the OSIRIS Property Explorer. Initial 50 ns molecular dynamics (MD) simulations were then performed. According to our findings, only six compounds exhibited positive drug scores. We further performed molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations of binding energy over 50 ns, selecting the two top-performing compounds for extended 150 ns MD simulations. CID 117698807 and CID 117712809 showed higher binding stability compared to galidesivir, with ΔGbinding values of -36.7 and -53.4 kcal/mol, respectively. Both compounds demonstrated high stability within the Z-EBOV-V24 active site over the 150 ns MD simulations. Hence, our study proposes CID 117698807 and CID 117712809 as potential anti-Z-EBOV-V24 drug candidates, warranting further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, Egypt
| | - Sayed F Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Al-Khdhairawi
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mrtatha K Al Zrkani
- Institute of Genetic Engineering & Biotechnology Research, Baghdad University, Iraq
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Islam M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New-Minia, Egypt
| | - Azza A K El-Sheikh
- Basic Health Sciences Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mahmoud M Abdelhamid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Maliar T, Maliarová M, Purdešová A, Jankech T, Gerhardtová I, Beňovič P, Dvořáček V, Jágr M, Viskupičová J. The Adapted POM Analysis of Avenanthramides In Silico. Pharmaceuticals (Basel) 2023; 16:ph16050717. [PMID: 37242500 DOI: 10.3390/ph16050717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
POM analysis and related approaches are significant tools based on calculating various physico-chemical properties and predicting biological activity, ADME parameters, and toxicity of a molecule. These methods are used to evaluate a molecule's potential to become a drug candidate. Avenanthramides (AVNs) are promising secondary metabolites specific to Avena spp. (oat). They comprise the amides of anthranilic acid linked to various polyphenolic acids with or without post-condensation molecule transformation. These natural compounds have been reported to exert numerous biological effects, including antioxidant, anti-inflammatory, hepatoprotective, antiatherogenic, and antiproliferative properties. To date, almost 50 various AVNs have been identified. We performed a modified POM analysis of 42 AVNs using MOLINSPIRATION, SWISSADME, and OSIRIS software. The evaluation of primary in silico parameters revealed significant differences among individual AVNs, highlighting the most promising candidates. These preliminary results may help coordinate and initiate other research projects focused on particular AVNs, especially those with predicted bioactivity, low toxicity, optimal ADME parameters, and promising perspectives.
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Affiliation(s)
- Tibor Maliar
- Department of Chemistry, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Námestie J. Herdu 2, 917 01 Trnava, Slovakia
| | - Mária Maliarová
- Department of Chemistry, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Námestie J. Herdu 2, 917 01 Trnava, Slovakia
| | - Andrea Purdešová
- Department of Chemistry, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Námestie J. Herdu 2, 917 01 Trnava, Slovakia
| | - Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ivana Gerhardtová
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Patrik Beňovič
- Department of Chemistry, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Námestie J. Herdu 2, 917 01 Trnava, Slovakia
| | - Václav Dvořáček
- Crop Research Institute, Drnovská 507/73, 161 06 Prague, Czech Republic
| | - Michal Jágr
- Crop Research Institute, Drnovská 507/73, 161 06 Prague, Czech Republic
| | - Jana Viskupičová
- Centre of Experimental Medicine SAS, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dúbravská Cesta 9, 841 04 Bratislava, Slovakia
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Goor RM, Hoffman D, Riley GR. Novel Method for Accurately Assessing Pull-up Artifacts in STR Analysis. Forensic Sci Int Genet 2020; 51:102410. [PMID: 33373910 DOI: 10.1016/j.fsigen.2020.102410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/13/2020] [Accepted: 10/18/2020] [Indexed: 11/26/2022]
Abstract
OSIRIS is a mathematically-based software tool for Short Tandem Repeat (STR) and DNA fragment analysis (https://www.ncbi.nlm.nih.gov/osiris/). As part of its routine sample analyses, OSIRIS computes unique quality metrics that can be used for sample quality assessment. A common artifact of STR analysis is cross-channel pull-up or pull-down (negative pull-up). This occurs because of the spectral overlap between the dyes used with the marker set, and the failure of the color deconvolution matrix to isolate the colors in the dye set adequately. This paper describes a mathematical method for analyzing and quantifying the pull-up patterns across sample channels and effectively identifying and correcting the pull-up artifacts, as implemented in OSIRIS. Unlike approaches to pull-up that require a training set composed of previous samples, the algorithm described here uses a mathematical model of the underlying causes of pull-up. It is based solely on the information intrinsic to the sample it is analyzing and therefore incorporates the effects of the ambient conditions and the specific procedures used in creating the sample. These conditions are the physical determinants of the level of pull-up in the sample and are not likely to be represented in a training set consisting of past samples.
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Affiliation(s)
- Robert M Goor
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Douglas Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - George R Riley
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Bailey RM, van der Grient JMA. OSIRIS: A model for integrating the effects of multiple stressors on marine ecosystems. J Theor Biol 2020; 493:110211. [PMID: 32097609 DOI: 10.1016/j.jtbi.2020.110211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 11/23/2022]
Abstract
While much has been learnt about the impacts of specific stressors on individual marine organisms, considerable debate exists over the nature and impact of multiple simultaneous stressors on both individual species and marine ecosystems. We describe a modelling tool (OSIRIS) for integrating the effects of multiple simultaneous stressors. The model is relatively computationally light, and demonstrated using a coarse-grained, non-spatial and simplified representation of a temperate marine ecosystem. This version is capable of reproducing a wide range of dynamic responses. Results indicate the degree to which interactions are synergistic is crucial in determining sensitivity to forcing, particularly for the higher trophic levels, which can respond non-linearly to stronger forcing. Stronger synergistic interactions sensitize the system to variability in forcing, and combinations of stronger forcing, noise and synergies between effects are particularly potent. This work also underlines the significant potential risk incurred in treating stressors on ecosystems as individual and additive.
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