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Lei G, Gao G, Zhou M, Guo J, Chen Y. Water-soluble essential oil components of flowers of Paeonia × suffruticosa cultivars and in silico analysis with antidepressant targets. Nat Prod Res 2024; 38:1776-1779. [PMID: 37254836 DOI: 10.1080/14786419.2023.2217706] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023]
Abstract
The present study focused on water-soluble essential oil recovered from the hydrolate of ten Paeonia × suffruticosa cultivars. Thirty-seven components, mostly oxygenated compounds (94.6-99.6%), were detected by gas chromatography-mass spectrometry (GC-MS) and GC-flame ionisation detector (GC-FID). The geranic acid chemotype was discovered (in cultivar 'Lan BaoShi'). Eight key oxygenated components were analysed in silico with antidepressant targets sodium-dependent serotonin transporter (SERT), 5-hydroxytryptamine receptor 1 A (5-HT1A), and monoamine oxidase type A (MAO-A). Geraniol, nerol, citronellol, and geranic acid presented superior docking properties. Phenylethyl alcohol and 1,3,5-trimethoxybenzene were also well docked. These molecules were bound to the active sites successfully (with partial occupancy in SERT). They might increase serotonin level or mimic its effect in central nervous system. (Z)-3-Hexen-1-ol and 1-hexanol showed weak binding. The in silico analysis revealed for the first time that the key water-soluble essential oil components of P. × suffruticosa potentially targeted antidepressant targets.
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Affiliation(s)
- Gaoming Lei
- Department of Pharmaceutical Sciences, College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Guoyu Gao
- Department of Pharmaceutical Sciences, College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Mengke Zhou
- Department of Pharmaceutical Sciences, College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Jianqi Guo
- Department of Pharmaceutical Sciences, College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
| | - Yuting Chen
- Department of Pharmaceutical Sciences, College of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
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2
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Espinosa Prieto A, Hardion L, Debortoli N, Beisel JN. Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13937. [PMID: 38363053 DOI: 10.1111/1755-0998.13937] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
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Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Laurent Hardion
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Nicolas Debortoli
- Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium
- E-BIOM SA, Namur, Belgium
| | - Jean-Nicolas Beisel
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
- École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France
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3
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Liu Y, Lawless M, Li M, Fairman K, Embry MR, Mitchell CA. Prediction of physicochemical and pharmacokinetic properties of botanical constituents by computational models. J Appl Toxicol 2024. [PMID: 38655841 DOI: 10.1002/jat.4617] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Botanicals contain complex mixtures of chemicals most of which lack pharmacokinetic data in humans. Since physicochemical and pharmacokinetic properties dictate the in vivo exposure of botanical constituents, these parameters greatly impact the pharmacological and toxicological effects of botanicals in consumer products. This study sought to use computational (i.e., in silico) models, including quantitative structure-activity relationships (QSAR) and physiologically based pharmacokinetic (PBPK) modeling, to predict properties of botanical constituents. One hundred and three major constituents (e.g., withanolides, mitragynine, and yohimbine) in 13 botanicals (e.g., ashwagandha, kratom, and yohimbe) were investigated. The predicted properties included biopharmaceutical classification system (BCS) classes based on aqueous solubility and permeability, oral absorption, liver microsomal clearance, oral bioavailability, and others. Over half of these constituents fell into BCS classes I and II at dose levels no greater than 100 mg per day, indicating high permeability and absorption (%Fa > 75%) in the gastrointestinal tract. However, some constituents such as glycosides in ashwagandha and Asian ginseng showed low bioavailability after oral administration due to poor absorption (BCS classes III and IV, %Fa < 40%). These in silico results fill data gaps for botanical constituents and could guide future safety studies. For example, the predicted human plasma concentrations may help select concentrations for in vitro toxicity testing. Additionally, the in silico data could be used in tiered or batteries of assays to assess the safety of botanical products. For example, highly absorbed botanical constituents indicate potential high exposure in the body, which could lead to toxic effects.
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Affiliation(s)
- Yitong Liu
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | | | - Miao Li
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Kiara Fairman
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Michelle R Embry
- Health and Environmental Sciences Institute, Washington, DC, USA
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Hasan K, Baroroh U, Madhani IN, Muscifa ZS, Novianti MT, Abidin M, Yusuf M, Subroto T. Enzymatic Performance of Aspergillus oryzae α-Amylase in the Presence of Organic Solvents: Activity, Stability, and Bioinformatic Studies. Bioinform Biol Insights 2024; 18:11779322241234767. [PMID: 38660393 PMCID: PMC11041543 DOI: 10.1177/11779322241234767] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 02/07/2024] [Indexed: 04/26/2024] Open
Abstract
Enzymatic reactions can be modulated by the incorporation of organic solvents, leading to alterations in enzyme stability, activity, and reaction rates. These solvents create a favorable microenvironment that enables hydrophobic reactions, facilities enzyme-substrate complex formation, and reduces undesirable water-dependent side reactions. However, it is crucial to understand the impact of organic solvents on enzymatic activity, as they can also induce enzyme inactivation. In this study, the enzymatic performance of Aspergillus oryzae α-amylase (Taka-amylase) in various organic solvents both experimentally and computationally was investigated. The results demonstrated that ethanol and ether sustain Taka-amylase activity up to 20% to 25% of the organic solvents, with ether providing twice the stability of ethanol. Molecular dynamics simulations further revealed that Taka-amylase has a more stable structure in ether and ethanol relative to other organic solvents. In addition, the analysis showed that the loop located near the active site in the AB-domain is a vulnerable site for enzyme destabilization when exposed to organic solvents. The ability of Taka-amylase to preserve the secondary loop structure in ether and ethanol contributed to the enzyme's activity. In addition, the solvent accessibility surface area of Taka-amylase is distributed throughout all enzyme structures, thereby contributing to the instability of Taka-amylase in the presence of most organic solvents.
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Affiliation(s)
- Khomaini Hasan
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Jenderal Achmad Yani, Cimahi, Indonesia
| | - Umi Baroroh
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Bandung, Indonesia
| | - Indri Novia Madhani
- Department of Chemistry, Universitas Jenderal Achmad Yani, Cimahi, Indonesia
| | - Zahra Silmi Muscifa
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Mia Tria Novianti
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhamad Abidin
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Yusuf
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, Indonesia
| | - Toto Subroto
- Research Centre for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, Indonesia
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Defo Deeh PB, Sathiyaseelan A, Vishven Naveen K, Wang MH. Phytochemical analysis and antioxidant potential of Mondia whitei and Guibourtia tessmannii against H 2O 2-induced cytotoxicity in PC3 cells. J Biomol Struct Dyn 2024:1-15. [PMID: 38651748 DOI: 10.1080/07391102.2024.2335299] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
The management of oxidative stress-related disorders has garnered significant interest, particularly in the exploration of medicinal plants possessing potent antioxidant activities. This study was undertaken to evaluate the antioxidant activity of Mondia whitei (MW) and Guibourtia tessmannii (GT) against H2O2-induced cytotoxicity in PC3 cells. The phytochemical composition of MW and GT was determined by GC-MS analysis. Total phenolic (TP) and total flavonoid (TF) contents were quantified by Folin Ciocalteu and AlCl3 methods, respectively. The antioxidant potential of the extracts was determined using the DPPH and ABTS+ radicals scavenging method, as well as cupric and ferric reducing capacity assay. Moreover, all phytocompounds were docked against acetylcholinesterase (AChE) and glutathione S-transferase (GST) using ArgusLab, and results were analyzed using the BIOVIA Discovery Studio Visualizer 2021 client. MW and GT comprised 20 and 22 compounds, respectively. GT exhibited higher TP and TF contents (210.70 ± 12.7; 12.61 ± 1.3 GAE/g DW) compared to MW (132.59 ± 12.59; 5.53 ± 1.3 mg of GAE/g DW). Both MW and GT demonstrated substantial antioxidant activity, with GT proving to be more effective in preventing H2O2-induced cytotoxicity. For instance, MW and GT significantly (p < .001) increased the DPPH, ABTS+, and cupric activity, compared with the H2O2 group. All compounds identified in MW and GT exhibited a strong binding affinity against AChE and GST. Drug likeness and toxicity of all phytocompounds were under the acceptable norms of Lipinski's rule. In conclusion, these plants could be effective candidates for the management/treatment of oxidative stress-related disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrick Brice Defo Deeh
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | | | - Kumar Vishven Naveen
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Myeong-Hyeon Wang
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
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Pasala PK, Rudrapal M, Challa RR, Ahmad SF, Vallamkonda B, R RB. Anti-Parkinson potential of hesperetin nanoparticles: in vivo and in silico investigations. Nat Prod Res 2024:1-10. [PMID: 38646872 DOI: 10.1080/14786419.2024.2344740] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/14/2024] [Indexed: 04/23/2024]
Abstract
Parkinson's disease (PD) is characterised by the gradual demise of dopaminergic neurons. In recent years, there has been significant interest in herbal treatments. In this study, hesperetin nanoparticles (HTN) were developed and compared their anti-PD potential with hesperetin (HT) on rotenone induced PD rats. Molecular docking was also performed to evaluate the binding affinity of hesperetin on pathological protein, i.e. D2 dopamine receptors (DR2), using Auto Dock Vina tools. The results showed a higher binding relationship of HTN on dopamine receptors (-7.2 kcal/mol) compared to L-dopa (-6.4 kcal/mol), supporting their potential as drug candidates for PD therapy. HTN was effectively synthesised using the fabrication technique and characterised by zeta potential and SEM analysis. HTN had favourable characteristics, including a size of 249.8 ± 14.9 nm and a Z-potential of -32.9 mV. After being administered orally, HTN demonstrated a notable anti-Parkinsonian effects, indicated by the significant improvement in motor function as assessed by the rota rod test (p < .001***), pole test (p < .001***), stair test (p < .01**), wood walk test (p < .01**) and an increase in substantia nigra (SN) antioxidant levels, CAT (p < .001***), SOD (p < .001***), GSH (p < .01**). Additionally, HTN led to increased dopamine levels (p < .01**) and a decrease in the oxidant system, MDA levels (p < .01**). Furthermore, histopathological examination revealed decreased SN neuronal necrosis in diseased animals treated with HTN compared to those treated with HT in a rat model of Parkinson's disease. Therefore, HTN can be regarded as a viable platform for efficient therapy of PD.
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Affiliation(s)
- Praveen Kumar Pasala
- Department of Pharmacology, Raghavendra Institute of Pharmaceutical Education and Research, JNTUA, Anantapur, Andhra Pradesh, India
| | - Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology and Pharmaceutical Sciences, Vignan's Foundation for Science, Technology & Research (Deemed to be University), Guntur, Andhra Pradesh, India
| | | | - Sheikh F Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | | | - Ram Babu R
- Department of Pharmacology, Santhiram College of Pharmacy, JNTUA, Nandyal, Andhra Pradesh, India
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7
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Chun SJ, Jang BS, Choi HS, Chang JH, Shin KH. Prediction of Overall Disease Burden in (y)pN1 Breast Cancer Using Knowledge-Based Machine Learning Model. Cancers (Basel) 2024; 16:1494. [PMID: 38672575 PMCID: PMC11048634 DOI: 10.3390/cancers16081494] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND We aimed to construct an expert knowledge-based Bayesian network (BN) model for assessing the overall disease burden (ODB) in (y)pN1 breast cancer patients and compare ODB across arms of ongoing trials. METHODS Utilizing institutional data and expert surveys, we developed a BN model for (y)pN1 breast cancer. Expert-derived probabilities and disability weights for radiotherapy-related benefit (e.g., 7-year disease-free survival [DFS]) and toxicities were integrated into the model. ODB was defined as the sum of disability weights multiplied by probabilities. In silico predictions were conducted for Alliance A011202, PORT-N1, RAPCHEM, and RT-CHARM trials, comparing ODB, 7-year DFS, and side effects. RESULTS In the Alliance A011202 trial, 7-year DFS was 80.1% in both arms. Axillary lymph node dissection led to higher clinical lymphedema and ODB compared to sentinel lymph node biopsy with full regional nodal irradiation (RNI). In the PORT-N1 trial, the control arm (whole-breast irradiation [WBI] with RNI or post-mastectomy radiotherapy [PMRT]) had an ODB of 0.254, while the experimental arm (WBI alone or no PMRT) had an ODB of 0.255. In the RAPCHEM trial, the radiotherapy field did not impact the 7-year DFS in ypN1 patients. However, there was a mild ODB increase with a larger irradiation field. In the RT-CHARM trial, we identified factors associated with the major complication rate, which ranged from 18.3% to 22.1%. CONCLUSIONS The expert knowledge-based BN model predicted ongoing trial outcomes, validating reported results and assumptions. In addition, the model demonstrated the ODB in different arms, with an emphasis on quality of life.
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Affiliation(s)
- Seok-Joo Chun
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Radiation Oncology, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang 10326, Republic of Korea
| | - Bum-Sup Jang
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hyeon Seok Choi
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyung Hwan Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
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Liu JX, Zhang X, Huang YQ, Hao GF, Yang GF. Multi-level bioinformatics resources support drug target discovery of protein-protein interactions. Drug Discov Today 2024; 29:103979. [PMID: 38608830 DOI: 10.1016/j.drudis.2024.103979] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Drug discovery often begins with a new target. Protein-protein interactions (PPIs) are crucial to multitudinous cellular processes and offer a promising avenue for drug-target discovery. PPIs are characterized by multi-level complexity: at the protein level, interaction networks can be used to identify potential targets, whereas at the residue level, the details of the interactions of individual PPIs can be used to examine a target's druggability. Much great progress has been made in target discovery through multi-level PPI-related computational approaches, but these resources have not been fully discussed. Here, we systematically survey bioinformatics tools for identifying and assessing potential drug targets, examining their characteristics, limitations and applications. This work will aid the integration of the broader protein-to-network context with the analysis of detailed binding mechanisms to support the discovery of drug targets.
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Affiliation(s)
- Jia-Xin Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China
| | - Xiao Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
| | - Yuan-Qin Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China.
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.
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Syaifie PH, Ibadillah D, Jauhar MM, Reninta R, Ningsih S, Ramadhan D, Arda AG, Ningrum DWC, Kaswati NMN, Rochman NT, Mardliyati E. Phytochemical Profile, Antioxidant, Enzyme Inhibition, Acute Toxicity, In Silico Molecular Docking and Dynamic Analysis of Apis mellifera Propolis as Antidiabetic Supplement. Chem Biodivers 2024:e202400433. [PMID: 38584139 DOI: 10.1002/cbdv.202400433] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
This study aims to identification of phytochemical profile of Apis mellifera propolis and explore potential of its anti-diabetic activity through inhibition on α-amylase (α-AE), α-glucosidase(α-GE) and finally identified the novel antidiabetic compounds from propolis. Apis mellifera propolis extract (AMPE) exhibited elevated polyphenol 33.26 ± 0.17 (mg GAE/g) and flavonoid (15.45 ± 0.13 mg RE/g), while its also indicated moderate strong antioxidant activity (EC50 793.09 ±1.94 µg/ml). This study found that AMPE displayed promising α-AE and α-GE inhibition through in vitro study. Based on LC-MS/MS screening, 18 unique AMPE compounds were identified, majorly belonging to anthraquinone and flavonoid compounds. In silico study determined that 8 compounds of AMPE compounds exhibited strong binding to α-AE, interacting to catalytic residue of ASP197. Moreover, 2 compounds exhibit potential inhibition of α-AG, by interacting to crucial amino acids of ARG315, ASP352, and ASP69. Finally, we suggested 2,7-Dihydroxy-1-(p-hydroxybenzyl)-4-methoxy-9,10-dihydrophenanthrene and 3(3-(3,4-Dihydroxybenzyl)-7-hydroxychroman-4-one as novel inhibitors of α-AE and α-GE. Notably, these compounds were initially discovered in Apis mellifera propolis, and molecular dynamic analysis confirmed their stable binding with both enzymes over 100 ns simulations. In vivo acute toxicity test reveals AMPE as a practically non-toxic product with LD50 value of 16050mg/kg.
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Affiliation(s)
- Putri Hawa Syaifie
- Nano Center Indonesia, Center of Excellence Life Sciences, Setu, 15343, Tangerang Selatan, INDONESIA
| | - Delfritama Ibadillah
- Nano Center Indonesia, Center of Excellence Life Sciences, Setu, Tangerang Selatan, 15343, Tangerang Selatan, INDONESIA
| | - Muhammad Miftah Jauhar
- Nano Center Indonesia, Center of Excellence Life Sciences, Setu, Tangerang Selatan, 15343, Tangerang Selatan, INDONESIA
| | - Rikania Reninta
- BRIN, Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Cibinong, Bogor, INDONESIA
| | - Sri Ningsih
- BRIN, Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong, Bogor, INDONESIA
| | - Donny Ramadhan
- RISTEK-BRIN, Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong, Bogor, Bogor, INDONESIA
| | - Adzani Gaisani Arda
- Nano Center Indonesia, Center of Excellence Life Sciences, Setu, Tangerang Selatan, 15343, Tangerang Selatan, INDONESIA
| | - Dhecella Winy Cintya Ningrum
- Nano Center Indonesia, Center of Excellence Life Sciences, Setu, Tangerang Selatan, 15343, Tangerang Selatan, INDONESIA
| | - Nofa Mardia Ningsih Kaswati
- Nano Center Indonesia, Center of Excellence Life Sciences, Setu, Tangerang Selatan, 15343, Tangerang Selatan, INDONESIA
| | - Nurul Taufiqu Rochman
- BRIN, Research Center for Advanced Materials, National Research and Innovation Agency (BRIN), Setu, Tangerang Selatan, Tangerang Selatan, INDONESIA
| | - Etik Mardliyati
- BRIN, Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), Cibinong, Bogor, Bogor, INDONESIA
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Garrido-Palazuelos LI, Aguirre-Sánchez JR, Castro-Del Campo N, López-Cuevas O, González-Torres B, Chaidez C, Medrano-Félix JA. Genomic characteristics of Salmonella Montevideo and Pomona: impact of isolation source on antibiotic resistance, virulence and metabolic capacity. Int J Environ Health Res 2024:1-16. [PMID: 38576268 DOI: 10.1080/09603123.2024.2336597] [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] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Salmonella enterica is known for its disease-causing serotypes, including Montevideo and Pomona. These serotypes have been found in various environments, including river water, sediments, food, and animals. However, the global spread of these serotypes has increased, leading to many reported infections and outbreaks. The goal of this study was the genomic analysis of 48 strains of S. Montevideo and S. Pomona isolated from different sources, including clinical. Results showed that environmental strains carried more antibiotic resistance genes than the clinical strains, such as genes for resistance to aminoglycosides, chloramphenicol, and sulfonamides. Additionally, the type 4 secretion system, was only found in environmental strains. .Also many phosphotransferase transport systems were identified and the presence of genes for the alternative pathway Entner-Doudoroff. The origin of isolation may have a significant impact on the ability of Salmonella isolates to adapt and survive in different environments, leading to genomic flexibility and a selection advantage.
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Affiliation(s)
- Lennin Isaac Garrido-Palazuelos
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Roberto Aguirre-Sánchez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Osvaldo López-Cuevas
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Berenice González-Torres
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Cristóbal Chaidez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Andrés Medrano-Félix
- Investigadoras e investigadores por México Centro de Investigación En Alimentación y Desarrollo A.C. Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán, México
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11
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Polat C, Ayhan N, Ergünay K, Charrel RN. Comprehensive evaluation of nucleic acid amplification methods widely used for generic detection of sandfly-borne phleboviruses. Microbiol Spectr 2024; 12:e0342823. [PMID: 38456695 DOI: 10.1128/spectrum.03428-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/13/2024] [Indexed: 03/09/2024] Open
Abstract
Sandfly-borne phleboviruses (SBPs), which cause sandfly fever, aseptic meningitis, encephalitis, and meningoencephalitis, are emerging pathogens of major public health concern. Virus nucleic acid testing is essential for SBP diagnosis, especially in the early stages of infection, and for the discovery of novel SBPs. The efficacy of utilizing generic primers that target conserved nucleotide sequences for the detection of both known and novel SBPs has not been extensively evaluated. We aimed to compare and evaluate the performance of five generic primer sets, widely used to detect S- and L-segments of arthropod-borne phleboviruses and designed as singleplex (n = 3) and nested (n = 2) formats, including both well-known and recently characterized 15 Old World virus strains. Furthermore, we performed in silico analysis to assess the detection capabilities of these generic primer sets. The initial evaluation of previously published generic primer sets for SBP detection yielded two singleplex primer sets with the potential to be adapted for use in real-time or high-throughput detection settings. Studies are ongoing to develop and further optimize a preliminary assay and test various hosts and vectors to assess their capacity to detect known and novel viruses. IMPORTANCE Virus nucleic acid testing is the primary diagnostic method, particularly in the early stages of illness. Virus-specific or syndromic tests are widely used for this purpose. The use of generic primers has had a considerable impact on the discovery, identification, and detection of Old World sandfly-borne phleboviruses (OWSBP). The study is significant because it is the first to carry out a comparative evaluation of all published OWSBP generic primer sets.
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Affiliation(s)
- Ceylan Polat
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
| | - Nazli Ayhan
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
- National Reference Center for Arboviruses, National Institute of Health, and Medical Research (Inserm) and French Armed Forces Biomedical Research Institute (IRBA), Marseille, France
| | - Koray Ergünay
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, Maryland, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, Maryland, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, USA
| | - Remi N Charrel
- Unité des Virus Emergents, Aix Marseille University, Marseille, France
- Laboratoire des Infections Virales Aigues et Tropicales, Pole des Maladies Infectieuses, AP-HM Hopitaux Universitaires de Marseille, Marseille, France
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12
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Larrea‐Sebal A, Sasiain I, Jebari‐Benslaiman S, Galicia‐Garcia U, Uribe KB, Benito‐Vicente A, Gracia‐Rubio I, Bediaga‐Bañeres H, Arrasate S, Cenarro A, Civeira F, González‐Díaz H, Martín C. OptiMo-LDLr: An Integrated In Silico Model with Enhanced Predictive Power for LDL Receptor Variants, Unraveling Hot Spot Pathogenic Residues. Adv Sci (Weinh) 2024; 11:e2305177. [PMID: 38258479 PMCID: PMC10987110 DOI: 10.1002/advs.202305177] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/11/2023] [Indexed: 01/24/2024]
Abstract
Familial hypercholesterolemia (FH) is an inherited metabolic disease affecting cholesterol metabolism, with 90% of cases caused by mutations in the LDL receptor gene (LDLR), primarily missense mutations. This study aims to integrate six commonly used predictive software to create a new model for predicting LDLR mutation pathogenicity and mapping hot spot residues. Six predictive-software are selected: Polyphen-2, SIFT, MutationTaster, REVEL, VARITY, and MLb-LDLr. Software accuracy is tested with the characterized variants annotated in ClinVar and, by bioinformatic and machine learning techniques all models are integrated into a more accurate one. The resulting optimized model presents a specificity of 96.71% and a sensitivity of 98.36%. Hot spot residues with high potential of pathogenicity appear across all domains except for the signal peptide and the O-linked domain. In addition, translating this information into 3D structure of the LDLr highlights potentially pathogenic clusters within the different domains, which may be related to specific biological function. The results of this work provide a powerful tool to classify LDLR pathogenic variants. Moreover, an open-access guide user interface (OptiMo-LDLr) is provided to the scientific community. This study shows that combination of several predictive software results in a more accurate prediction to help clinicians in FH diagnosis.
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Affiliation(s)
- Asier Larrea‐Sebal
- Biofisika Institute (UPV/EHU, CSIC)Barrio Sarriena s/n.LeioaBizkaia48940Spain
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
- Fundación Biofisika BizkaiaBarrio Sarriena s/n.LeioaBizkaia48940Spain
| | - Iñaki Sasiain
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
| | - Shifa Jebari‐Benslaiman
- Biofisika Institute (UPV/EHU, CSIC)Barrio Sarriena s/n.LeioaBizkaia48940Spain
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
| | - Unai Galicia‐Garcia
- Biofisika Institute (UPV/EHU, CSIC)Barrio Sarriena s/n.LeioaBizkaia48940Spain
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
| | - Kepa B. Uribe
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
| | - Asier Benito‐Vicente
- Biofisika Institute (UPV/EHU, CSIC)Barrio Sarriena s/n.LeioaBizkaia48940Spain
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
| | - Irene Gracia‐Rubio
- Lipid Unit, Hospital Universitario Miguel Servet, IIS Aragon, CIBERCVUniversidad de ZaragozaZaragoza50009Spain
| | | | - Sonia Arrasate
- Department of Organic and ChemistryUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Ana Cenarro
- Lipid Unit, Hospital Universitario Miguel Servet, IIS Aragon, CIBERCVUniversidad de ZaragozaZaragoza50009Spain
| | - Fernando Civeira
- Lipid Unit, Hospital Universitario Miguel Servet, IIS Aragon, CIBERCVUniversidad de ZaragozaZaragoza50009Spain
| | - Humberto González‐Díaz
- Biofisika Institute (UPV/EHU, CSIC)Barrio Sarriena s/n.LeioaBizkaia48940Spain
- Ikerbasque, Basque Foundation for ScienceBilbaoBizkaia48013Spain
| | - Cesar Martín
- Biofisika Institute (UPV/EHU, CSIC)Barrio Sarriena s/n.LeioaBizkaia48940Spain
- Department of Biochemistry and Molecular BiologyUniversidad del País Vasco UPV/EHULeioaBizkaia48940Spain
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13
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Pieper C, Engel N, Wend K, Kneuer C, Martin S. In Vitro Human Dermal Absorption Studies on Pesticides in Complex Mixtures: Investigation of Guidance Criteria and Possible Impact Parameters. Toxics 2024; 12:248. [PMID: 38668471 PMCID: PMC11054108 DOI: 10.3390/toxics12040248] [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] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024]
Abstract
Pesticides must not pose unacceptable risks to human health, so risk assessments are conducted before products are authorised. Dermal exposure is often the main route of intake, so estimating realistic and trustworthy dermal absorption values is crucial for risk assessment. Although there are agreed test guidelines for in vitro dermal absorption studies, not every product is tested due to cost reasons. The present dataset consists of 945 individual in vitro experiments on the dermal absorption of human skin with 179 active substances of pesticides in 353 different mixtures, including concentrates and dilutions. The dataset was evaluated to identify the possible impacts of experimental conditions and physico-chemical properties on dermal absorption. The dataset was also analysed to assess the appropriateness of the pro rata correction for untested dilutions, and the set concentration cut-off to decide on the dilution status for choosing a default value on dermal absorption. The study found that the implementation of specific guidelines improved the harmonisation of study conduct, with support for approaches such as pro rata correction and default values. Further analysis of the specific co-formulants may identify influencing factors that may be more important than the experimental variables.
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Affiliation(s)
- Christina Pieper
- Department of Pesticides Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany (K.W.)
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024; 25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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15
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Sengupta A, Lago MA, Badano A. In situtumor model for longitudinal in silico imaging trials. Phys Med Biol 2024; 69:075029. [PMID: 38471177 DOI: 10.1088/1361-6560/ad3322] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/14/2024]
Abstract
Objective.In this article, we introduce a computational model for simulating the growth of breast cancer lesions accounting for the stiffness of surrounding anatomical structures.Approach.In our model, ligaments are classified as the most rigid structures while the softer parts of the breast are occupied by fat and glandular tissues As a result of these variations in tissue elasticity, the rapidly proliferating tumor cells are met with differential resistance. It is found that these cells are likely to circumvent stiffer terrains such as ligaments, instead electing to proliferate preferentially within the more yielding confines of the breast's soft topography. By manipulating the interstitial tumor pressure in direct proportion to the elastic constants of the tissues surrounding the tumor, this model thus creates the potential for realizing a database of unique lesion morphology sculpted by the distinctive topography of each local anatomical infrastructure. We modeled the growth of simulated lesions within volumes extracted from fatty breast models, developed by Graffet alwith a resolution of 50μm generated with the open-source and readily available Virtual Imaging Clinical Trials for Regulatory Evaluation (VICTRE) imaging pipeline. To visualize and validate the realism of the lesion models, we leveraged the imaging component of the VICTRE pipeline, which replicates the siemens mammomat inspiration mammography system in a digital format. This system was instrumental in generating digital mammogram (DM) images for each breast model containing the simulated lesions.Results.By utilizing the DM images, we were able to effectively illustrate the imaging characteristics of the lesions as they integrated with the anatomical backgrounds. Our research also involved a reader study that compared 25 simulated DM regions of interest (ROIs) with inserted lesions from our models with DM ROIs from the DDSM dataset containing real manifestations of breast cancer. In general the simulation time for the lesions was approximately 2.5 hours, but it varied depending on the lesion's local environment.Significance.The lesion growth model will facilitate and enhance longitudinal in silico trials investigating the progression of breast cancer.
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Affiliation(s)
- Aunnasha Sengupta
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD 2099, United States of America
| | - Miguel A Lago
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD 2099, United States of America
| | - Aldo Badano
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD 2099, United States of America
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Sass JO, Johnson K, Darques JB, Buerstenbinder L, Soodmand I, Bader R, Kebbach M. Influence of posterior cruciate ligament tension on tibiofemoral and patellofemoral joint contact mechanics in cruciate-retaining total knee replacement: a combined musculoskeletal multibody and finite-element simulation. Comput Methods Biomech Biomed Engin 2024:1-13. [PMID: 38511844 DOI: 10.1080/10255842.2024.2329946] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
The influence of posterior cruciate ligament (PCL) tension on the clinical outcome of cruciate-retaining total knee replacement (CR-TKR) remains controversial. Various numerical approaches have been used to study this influence systematically, but the models used are limited by certain assumptions and simplifications. Therefore, the objective of this computational study was to develop a combined musculoskeletal multibody and finite-element simulation during a squat motion to 90° knee flexion with a CR-TKR design to overcome previous limitations regarding model inputs. In addition, different PCL tensions (tight, lax, resected) were modeled and the influence on tibiofemoral and resurfaced patellofemoral joint dynamics and contact stresses was evaluated. The effect of the PCL on knee joint dynamics and contact stresses was more pronounced at higher flexion angles. Tibiofemoral joint dynamics were influenced and a tight PCL induced increased posterior femoral translation during flexion. The maximum contact stress in the tibial insert increased from 20.6 MPa to 22.5 MPa for the resected and tightest PCL at 90° knee flexion. Patellofemoral joint dynamics were only slightly affected by PCL tension. However, the maximum contact stress in the patellar component decreased from 58.0 MPa to 53.7 MPa for the resected and tightest PCL at 90° knee flexion. The combination of musculoskeletal multibody and finite-element simulation is a sufficient method to comprehensively investigate knee joint dynamics and contact stresses in CR-TKR. The PCL tension after CR-TKR affects joint dynamics and contact stresses at the articulating implant surfaces.
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Affiliation(s)
- Jan-Oliver Sass
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
| | - Kurt Johnson
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
| | - Jean-Baptiste Darques
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
- Polytech Marseille, école d'ingénieurs d'Aix Marseille Université, Marseille, France
| | - Lucas Buerstenbinder
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
| | - Iman Soodmand
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
| | - Rainer Bader
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
| | - Maeruan Kebbach
- Biomechanics and Implant Technology Research Laboratory, Department of Orthopedics, Rostock University Medical Center, Rostock, Germany
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Silva AC, Loizou GD, McNally K, Osborne O, Potter C, Gott D, Colbourne JK, Viant MR. A novel method to derive a human safety limit for PFOA by gene expression profiling and modelling. Front Toxicol 2024; 6:1368320. [PMID: 38577564 PMCID: PMC10991825 DOI: 10.3389/ftox.2024.1368320] [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: 01/10/2024] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Perfluorooctanoic acid (PFOA) is a persistent environmental contaminant that can accumulate in the human body due to its long half-life. This substance has been associated with liver, pancreatic, testicular and breast cancers, liver steatosis and endocrine disruption. PFOA is a member of a large group of substances also known as "forever chemicals" and the vast majority of substances of this group lack toxicological data that would enable their effective risk assessment in terms of human health hazards. This study aimed to derive a health-based guidance value for PFOA intake (ng/kg BW/day) from in vitro transcriptomics data. To this end, we developed an in silico workflow comprising five components: (i) sourcing in vitro hepatic transcriptomics concentration-response data; (ii) deriving molecular points of departure using BMDExpress3 and performing pathway analysis using gene set enrichment analysis (GSEA) to identify the most sensitive molecular pathways to PFOA exposure; (iii) estimating freely-dissolved PFOA concentrations in vitro using a mass balance model; (iv) estimating in vivo doses by reverse dosimetry using a PBK model for PFOA as part of a quantitative in vitro to in vivo extrapolation (QIVIVE) algorithm; and (v) calculating a tolerable daily intake (TDI) for PFOA. Fourteen percent of interrogated genes exhibited in vitro concentration-response relationships. GSEA pathway enrichment analysis revealed that "fatty acid metabolism" was the most sensitive pathway to PFOA exposure. In vitro free PFOA concentrations were calculated to be 2.9% of the nominal applied concentrations, and these free concentrations were input into the QIVIVE workflow. Exposure doses for a virtual population of 3,000 individuals were estimated, from which a TDI of 0.15 ng/kg BW/day for PFOA was calculated using the benchmark dose modelling software, PROAST. This TDI is comparable to previously published values of 1.16, 0.69, and 0.86 ng/kg BW/day by the European Food Safety Authority. In conclusion, this study demonstrates the combined utility of an "omics"-derived molecular point of departure and in silico QIVIVE workflow for setting health-based guidance values in anticipation of the acceptance of in vitro concentration-response molecular measurements in chemical risk assessment.
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Affiliation(s)
- Arthur de Carvalho e Silva
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Environmental Research and Justice (CERJ), University of Birmingham, Birmingham, United Kingdom
| | | | | | - Olivia Osborne
- Science Evidence and Research Division, Food Standards Agency, London, United Kingdom
| | - Claire Potter
- Science Evidence and Research Division, Food Standards Agency, London, United Kingdom
| | - David Gott
- Science Evidence and Research Division, Food Standards Agency, London, United Kingdom
| | - John K. Colbourne
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Environmental Research and Justice (CERJ), University of Birmingham, Birmingham, United Kingdom
| | - Mark R. Viant
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Environmental Research and Justice (CERJ), University of Birmingham, Birmingham, United Kingdom
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Su H, Fan W, Xu Y, Tang S, Yue D, Liao Z. Preparation, identification, and molecular docking of novel angiotensin-converting enzyme inhibitory peptides derived from rice-based distillers' spent cakes. J Sci Food Agric 2024. [PMID: 38507298 DOI: 10.1002/jsfa.13474] [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] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Rice-based distillers' spent cake (RDSC), a by-product of the Chinese liquor (Baijiu) industry, is a potential source of ACE inhibitory peptide. Since angiotensin-converting enzyme (ACE) plays a crucial role in controlling hypertension, inhibition of ACE has been widely emphasized. The ACE inhibitory active peptide derived from by-products of food has been recognized as safer and cheaper inhibitors. RESULTS Aimed to discover ACE-inhibiting active peptides in RDSC. Hydrolysis of RDSC by alcalase for 4 h followed by ultrafiltration yielded low-molecular-weight (< 3 kDa) fractions. Subsequently, a comprehensive method that using a combination of LC-Q-TOF-MS and LC-Q Exactive-MS to identify the novel short- (3-5 amino acids residues; n = 7) and medium-sized peptides (more than 6 amino acids residues; n = 6). In vitro activity assay showed that the peptides KPFFPGL, GFPRPLL, GPPGVF, and VGK exhibited the highest activity with IC50 of 11.63, 12.34, 19.55, and 33.54 μM. Molecular docking reveal that the active and inactive sites (Glu123, Asp121, Arg522, and Lys118) play important roles in enhancing the ACE inhibitory activity of peptides. CONCLUSION Here we report a comprehensive method that effectively extracted and identified the bioactive peptides from RDSC. Four highly active novel peptides may be the most promising candidates for functional foods to against hypertension, provide significant information for enhancing value of rice-based distilled by-products. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hanxing Su
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China
| | - Wenlai Fan
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Wuxi 214122, Jiangsu, China
| | - Shaopei Tang
- Baijiu Fermentation Technology Research Center of Jiangnan University-Kweichow Zhen Distillery Co. Ltd., 1800 Lihu Ave, Wuxi 214122, Jiangsu, China
| | - Dehong Yue
- Baijiu Fermentation Technology Research Center of Jiangnan University-Kweichow Zhen Distillery Co. Ltd., 1800 Lihu Ave, Wuxi 214122, Jiangsu, China
| | - Zuyue Liao
- Baijiu Fermentation Technology Research Center of Jiangnan University-Kweichow Zhen Distillery Co. Ltd., 1800 Lihu Ave, Wuxi 214122, Jiangsu, China
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Sun R, Zheng P, Chen P, Wu D, Zheng J, Liu X, Hu Y. Enhancing the Catalytic Efficiency of D-lactonohydrolase through the Synergy of Tunnel Engineering, Evolutionary Analysis, and Force-Field Calculations. Chemistry 2024; 30:e202304164. [PMID: 38217521 DOI: 10.1002/chem.202304164] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/15/2024]
Abstract
Computational design advances enzyme evolution and their use in biocatalysis in a faster and more efficient manner. In this study, a synergistic approach integrating tunnel engineering, evolutionary analysis, and force-field calculations has been employed to enhance the catalytic activity of D-lactonohydrolase (D-Lac), which is a pivotal enzyme involved in the resolution of racemic pantolactone during the production of vitamin B5. The best mutant, N96S/A271E/F274Y/F308G (M3), was obtained and its catalytic efficiency (kcat/KM) was nearly 23-fold higher than that of the wild-type. The M3 whole-cell converted 20 % of DL-pantolactone into D-pantoic acid (D-PA, >99 % e.e.) with a conversion rate of 47 % and space-time yield of 107.1 g L-1 h-1, demonstrating its great potential for industrial-scale D-pantothenic acid production. Molecular dynamics (MD) simulations revealed that the reduction in the steric hindrance within the substrate tunnel and conformational reconstruction of the distal loop resulted in a more favourable"catalytic" conformation, making it easier for the substrate and enzyme to enter their pre-reaction state. This study illustrates the potential of the distal residue on the pivotal loop at the entrance of the D-Lac substrate tunnel as a novel modification hotspot capable of reshaping energy patterns and consequently influencing the enzymatic activity.
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Affiliation(s)
- Ruobin Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Pu Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Pengcheng Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Dan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Jiangmei Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Xueyu Liu
- Hangzhou Xinfu Technology Co., Ltd., Hangzhou, 311301, P. R. China
| | - Yunxiang Hu
- Hangzhou Xinfu Technology Co., Ltd., Hangzhou, 311301, P. R. China
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William JNG, Dhar R, Gundamaraju R, Sahoo OS, Pethusamy K, Raj AFPAM, Ramasamy S, Alqahtani MS, Abbas M, Karmakar S. SKping cell cycle regulation: role of ubiquitin ligase SKP2 in hematological malignancies. Front Oncol 2024; 14:1288501. [PMID: 38559562 PMCID: PMC10978726 DOI: 10.3389/fonc.2024.1288501] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
SKP2 (S-phase kinase-associated protein 2) is a member of the F-box family of substrate-recognition subunits in the SCF ubiquitin-protein ligase complexes. It is associated with ubiquitin-mediated degradation in the mammalian cell cycle components and other target proteins involved in cell cycle progression, signal transduction, and transcription. Being an oncogene in solid tumors and hematological malignancies, it is frequently associated with drug resistance and poor disease outcomes. In the current review, we discussed the novel role of SKP2 in different hematological malignancies. Further, we performed a limited in-silico analysis to establish the involvement of SKP2 in a few publicly available cancer datasets. Interestingly, our study identified Skp2 expression to be altered in a cancer-specific manner. While it was found to be overexpressed in several cancer types, few cancer showed a down-regulation in SKP2. Our review provides evidence for developing novel SKP2 inhibitors in hematological malignancies. We also investigated the effect of SKP2 status on survival and disease progression. In addition, the role of miRNA and its associated families in regulating Skp2 expression was explored. Subsequently, we predicted common miRNAs against Skp2 genes by using miRNA-predication tools. Finally, we discussed current approaches and future prospective approaches to target the Skp2 gene by using different drugs and miRNA-based therapeutics applications in translational research.
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Affiliation(s)
- Jonahunnatha Nesson George William
- Department of Medical, Oral and Biotechnological Sciences (DSMOB), Ageing Research Center and Translational Medicine-CeSI-MeT, “G. d’Annunzio” University Chieti-Pescara, Chieti, Italy
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Intestinal Mucosal Biology Lab, School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Om Saswat Sahoo
- Department of Biotechnology, National Institute of Technology, Durgapur, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Subbiah Ramasamy
- Cardiac Metabolic Disease Laboratory, Department Of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, University of Leicester, Leicester, United Kingdom
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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21
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Balakrishnan S, Rahman RNZRA, Noor NDM, Latip W, Ali MSM. Expression and functional analysis of a recombinant aquaporin Z from Antarctic Pseudomonas sp. AMS3. Proteins 2024. [PMID: 38477414 DOI: 10.1002/prot.26680] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/14/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Aquaporin (AQP) is a water channel protein from the family of transmembrane proteins which facilitates the movement of water across the cell membrane. It is ubiquitous in nature, however the understanding of the water transport mechanism, especially for AQPs in microbes adapted to low temperatures, remains limited. AQP also has been recognized for its ability to be used for water filtration, but knowledge of the biochemical features necessary for its potential applications in industrial processes has been lacking. Therefore, this research was conducted to express, extract, solubilize, purify, and study the functional adaptations of the aquaporin Z family from Pseudomonas sp. AMS3 via molecular approaches. In this study, AqpZ1 AMS3 was successfully subcloned and expressed in E. coli BL21 (DE3) as a recombinant protein. The AqpZ1 AMS3 gene was expressed under optimized conditions and the best optimized condition for the AQP was in 0.5 mM IPTG incubated at 25°C for 20 h induction time. A zwitterionic mild detergent [(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate was the suitable surfactant for the protein solubilization. The protein was then purified via affinity chromatography. Liposome and proteoliposome was reconstituted to determine the particle size using dynamic light scattering. This information obtained from this psychrophilic AQP identified provides new insights into the structural adaptation of this protein at low temperatures and could be useful for low temperature application and molecular engineering purposes in the future.
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Affiliation(s)
- S Balakrishnan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - R N Z R A Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - N D M Noor
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - W Latip
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - M S M Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Enzyme Technology Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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22
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Boulay E, Troncy E, Jacquemet V, Huang H, Pugsley MK, Downey AM, Venegas Baca R, Authier S. In Silico Human Cardiomyocyte Action Potential Modeling: Exploring Ion Channel Input Combinations. Int J Toxicol 2024:10915818241237988. [PMID: 38477622 DOI: 10.1177/10915818241237988] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
In silico modeling offers an opportunity to supplement and accelerate cardiac safety testing. With in silico modeling, computational simulation methods are used to predict electrophysiological interactions and pharmacological effects of novel drugs on critical physiological processes. The O'Hara-Rudy's model was developed to predict the response to different ion channel inhibition levels on cardiac action potential duration (APD) which is known to directly correlate with the QT interval. APD data at 30% 60% and 90% inhibition were derived from the model to delineate possible ventricular arrhythmia scenarios and the marginal contribution of each ion channel to the model. Action potential values were calculated for epicardial, myocardial, and endocardial cells, with action potential curve modeling. This study assessed cardiac ion channel inhibition data combinations to consider when undertaking in silico modeling of proarrhythmic effects as stipulated in the Comprehensive in Vitro Proarrhythmia Assay (CiPA). As expected, our data highlight the importance of the delayed rectifier potassium channel (IKr) as the most impactful channel for APD prolongation. The impact of the transient outward potassium channel (Ito) inhibition on APD was minimal while the inward rectifier (IK1) and slow component of the delayed rectifier potassium channel (IKs) also had limited APD effects. In contrast, the contribution of fast sodium channel (INa) and/or L-type calcium channel (ICa) inhibition resulted in substantial APD alterations supporting the pharmacological relevance of in silico modeling using input from a limited number of cardiac ion channels including IKr, INa, and ICa, at least at an early stage of drug development.
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Affiliation(s)
- Emmanuel Boulay
- GREPAQ (Groupe de Recherche en Pharmacologie Animale du Québec), Université de Montréal, Saint-Hyacinthe, QC, Canada
- Charles River Laboratories, Laval, QC, Canada
| | - Eric Troncy
- GREPAQ (Groupe de Recherche en Pharmacologie Animale du Québec), Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Vincent Jacquemet
- Département de Pharmacologie et Physiologie, Université de Montréal, Faculté de Médecine, Montréal, QC, Canada
- Centre de Recherche, Hôpital du Sacré-Cœur, Montréal, QC, Canada
- Institut de Génie Biomédical, Université de Montréal, Montréal, QC, Canada
| | - Hai Huang
- Charles River Laboratories, Laval, QC, Canada
| | - Michael K Pugsley
- Toxicology & Safety Pharmacology, Cytokinetics, San Francisco, CA, USA
| | | | | | - Simon Authier
- GREPAQ (Groupe de Recherche en Pharmacologie Animale du Québec), Université de Montréal, Saint-Hyacinthe, QC, Canada
- Charles River Laboratories, Laval, QC, Canada
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23
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Sarhadi M, Pahlavani E, Hosseini Razavi N, Ghadyani F, Abdollahi Z, Sarhadi S, Sabeti Akbar Abad M, Shahriari H, Majidpour M. IL-18 and CD14 variants in chronic HBV predisposition: a case-control study with in silico analyses focused on transcription and splicing. Nucleosides Nucleotides Nucleic Acids 2024:1-21. [PMID: 38459706 DOI: 10.1080/15257770.2024.2326132] [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] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
Hepatitis B virus (HBV), a vaccine-avoidable infection, is a health concern worldwide, leading to liver disorders such as acute self-constraint and chronic hepatitis, liver failure, hepatic cirrhosis, and even hepatocellular carcinoma if untreated. 'Immunogeneticprofiling', genetic variations of the pro- and anti-inflammatory cytokines responsible for regulating the immune responses, cause person-to-person differences and impact the clinical manifestation of the disease. The current experimental-bioinformatics research was conducted to examine whether promoteric IL-18-rs187238 C > G and -rs1946518 T > G and intronic CD14-rs2569190 A > G variations are associated with chronic HBV. A total of 400 individuals (200 in each case and control group) participated in the study and were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. The data was also assessed bioinformatics-wise for conservation, genomic transcription and splicing, and protein interactions. Findings proposed that unlike the IL-18-rs1946518 T > G and CD14-rs2569190 A > G, the IL-18-rs187238 C > G is a protector against chronic HBV (odds ratio [OR] = 0.62, 95% confidence intervals [CI]: 0.46-0.83, and p = 0.002). The TG/CC/AA, TG/CC/AG, TT/CC/AG, and GG/CC/AA combined genotypes significantly increased chronic HBV risk (p < 0.05), while the IL-18 G/T and G/G haplotypes lessened it (p < 0.05). Moreover, IL-18-rs1946518 T > G is in the protected genomic regions across mammalian species. In contrast to the IL-18-rs1946518 T > G, IL-18-rs187238 C > G is likely to create novel binding sites for transcription factors, and the CD14-rs2569190 A > G presumably changed the ribonucleic acid splicing pattern. More research on larger populations and other ethnicities is required to authenticate these results.
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Affiliation(s)
- Mohammad Sarhadi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Elham Pahlavani
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Niloufar Hosseini Razavi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fatemeh Ghadyani
- Department of Cellular and Molecular, Faculty of Biology Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Zahra Abdollahi
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Somayeh Sarhadi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahboobeh Sabeti Akbar Abad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hossein Shahriari
- Clinical Immunology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdi Majidpour
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, Zahedan University of Medical Sciences, Zahedan, Iran
- Clinical Immunology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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24
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Jain NK, Tailang M, Chandrasekaran B, Khazaleh N, Thangavel N, Makeen HA, Albratty M, Najmi A, Alhazmi HA, Zoghebi K, Alagusundaram M, Jain HK. Integrating network pharmacology with molecular docking to rationalize the ethnomedicinal use of Alchornea laxiflora (Benth.) Pax & K. Hoffm. for efficient treatment of depression. Front Pharmacol 2024; 15:1290398. [PMID: 38505421 PMCID: PMC10949534 DOI: 10.3389/fphar.2024.1290398] [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: 09/08/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024] Open
Abstract
Background: Alchornea laxiflora (Benth.) Pax & K. Hoffm. (A. laxiflora) has been indicated in traditional medicine to treat depression. However, scientific rationalization is still lacking. Hence, this study aimed to investigate the antidepressant potential of A. laxiflora using network pharmacology and molecular docking analysis. Materials and methods: The active compounds and potential targets of A. laxiflora and depression-related targets were retrieved from public databases, such as PubMed, PubChem, DisGeNET, GeneCards, OMIM, SwissTargetprediction, BindingDB, STRING, and DAVID. Essential bioactive compounds, potential targets, and signaling pathways were predicted using in silico analysis, including BA-TAR, PPI, BA-TAR-PATH network construction, and GO and KEGG pathway enrichment analysis. Later on, with molecular docking analysis, the interaction of essential bioactive compounds of A. laxiflora and predicted core targets of depression were verified. Results: The network pharmacology approach identified 15 active compounds, a total of 219 compound-related targets, and 14,574 depression-related targets with 200 intersecting targets between them. SRC, EGFR, PIK3R1, AKT1, and MAPK1 were the core targets, whereas 3-acetyloleanolic acid and 3-acetylursolic acid were the most active compounds of A. laxiflora with anti-depressant potential. GO functional enrichment analysis revealed 129 GO terms, including 82 biological processes, 14 cellular components, and 34 molecular function terms. KEGG pathway enrichment analysis yielded significantly enriched 108 signaling pathways. Out of them, PI3K-Akt and MAPK signaling pathways might have a key role in treating depression. Molecular docking analysis results exhibited that core targets of depression, such as SRC, EGFR, PIK3R1, AKT1, and MAPK1, bind stably with the analyzed bioactive compounds of A. laxiflora. Conclusion: The present study elucidates the bioactive compounds, potential targets, and pertinent mechanism of action of A. laxiflora in treating depression. A. laxiflora might exert an antidepressant effect by regulating PI3K-Akt and MAPK signaling pathways. However, further investigations are required to validate.
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Affiliation(s)
- Nem Kumar Jain
- School of Pharmacy, ITM University, Gwalior, Madhya Pradesh, India
- School of Studies in Pharmaceutical Sciences, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Mukul Tailang
- School of Studies in Pharmaceutical Sciences, Jiwaji University, Gwalior, Madhya Pradesh, India
| | | | | | - Neelaveni Thangavel
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Hafiz A. Makeen
- Pharmacy Practice Research Unit, Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Hassan Ahmad Alhazmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - M. Alagusundaram
- School of Pharmacy, ITM University, Gwalior, Madhya Pradesh, India
| | - Hemant Kumar Jain
- Department of General Medicine, Government Medical College, Datia, Madhya Pradesh, India
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25
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Yang Z, Wang C, Huang B, Chen Y, Liu Z, Chen H, Chen J. Biodirected Screening and Preparation of Larimichthys crocea Angiotensin-I-Converting Enzyme-Inhibitory Peptides by a Combined In Vitro and In Silico Approach. Molecules 2024; 29:1134. [PMID: 38474646 DOI: 10.3390/molecules29051134] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Food-derived angiotensin-I-converting enzyme (ACE)-inhibitory peptides have gained attention for their potent and safe treatment of hypertensive disorders. However, there are some limitations of conventional methods for preparing ACE-inhibitory peptides. In this study, in silico hydrolysis, the quantitative structure-activity relationship (QSAR) model, LC-MS/MS, inhibition kinetics, and molecular docking were used to investigate the stability, hydrolyzability, in vitro activity, and inhibition mechanism of bioactive peptides during the actual hydrolysis process. Six novel ACE-inhibitory peptides were screened from the Larimichthys crocea protein (LCP) and had low IC50 values (from 0.63 ± 0.09 µM to 10.26 ± 0.21 µM), which were close to the results of the QSAR model. After in vitro gastrointestinal simulated digestion activity of IPYADFK, FYEPFM and NWPWMK were found to remain almost unchanged, whereas LYDHLGK, INEMLDTK, and IHFGTTGK were affected by gastrointestinal digestion. Meanwhile, the inhibition kinetics and molecular docking results were consistent in that ACE-inhibitory peptides of different inhibition forms could effectively bind to the active or non-central active centers of ACE through hydrogen bonding. Our proposed method has better reproducibility, accuracy, and higher directivity than previous methods. This study can provide new approaches for the deep processing, identification, and preparation of Larimichthys crocea.
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Affiliation(s)
- Zhizhi Yang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changrong Wang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baote Huang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yihui Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhiyu Liu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, National Research and Development Center for Marine Fish Processing (Xiamen), Xiamen 361013, China
| | - Hongbin Chen
- Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou Normal University, Quanzhou 362000, China
| | - Jicheng Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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26
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Jani NA, Maarof NI, Zahari MMFM, Jamil M, Zakaria II, Mohamad Zobir SZ, Kasim N, Salin NH, Mohamad Ali NA, Khalid WEFW, Pungot NH. Phytochemical profiling of the essential oils from three Curcuma species and their in vitro and in silico dengue protease inhibition activity. Nat Prod Res 2024; 38:926-932. [PMID: 37144399 DOI: 10.1080/14786419.2023.2208256] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
The chemical compositions, in vitro and in silico anti-dengue activity of the essential oils of the rhizomes of Curcuma longa Linn., C. aeruginosa Roxb., and C. xanthorrhiza Roxb. had been investigated. The C. longa oil was mainly composed of ar-turmerone (54.0%) and curlone (17.7%), while the C. aeruginosa oil was rich in curzerenone (23.4%), 1,8-cineole (21.2%), and camphor (7.1%). Xanthorrhizol (21.6%), β-curcumene (19.5%), ar-curcumene (14.2%), and camphor (9.2%) were the major compounds in the C. xanthorrhiza oil. Among the oils, the C. longa oil was found to be the most active NSB-NS3 protease inhibitor (IC50 1.98 μg/mL). PLS biplot disclosed that the essential oils were classified into three separated clusters based on their characteristic chemical compositions, with C. longa positioned closest to the in vitro anti-dengue activity. Four compounds from the C. longa oil have both hydrogen and hydrophobic bonds that could be responsible for the DENV-2 NS2B-NS3 inhibitory effect.
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Affiliation(s)
- Nor Akmalazura Jani
- Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, Kuala Pilah, Negeri Sembilan, Malaysia
| | - Noor Inani Maarof
- Universiti Teknologi MARA, Cawangan Negeri Sembilan, Kampus Kuala Pilah, Kuala Pilah, Negeri Sembilan, Malaysia
| | | | - Mailina Jamil
- Herbal Product Development Programme, Natural Products Division, Forest Research Institute Malaysia (FRIM), Kepong, Kuala Lumpur, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Siti Zuraidah Mohamad Zobir
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Halaman Bukit Gambir, Gelugor, Pulau Pinang, Malaysia
| | - Noraini Kasim
- Universiti Teknologi MARA, Shah Alam, Selangor, Malaysia
| | - Nurul Hanim Salin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Halaman Bukit Gambir, Gelugor, Pulau Pinang, Malaysia
| | - Nor Azah Mohamad Ali
- Herbal Product Development Programme, Natural Products Division, Forest Research Institute Malaysia (FRIM), Kepong, Kuala Lumpur, Malaysia
| | | | - Noor Hidayah Pungot
- Organic Synthesis Laboratory, Institute of Science, Universiti Teknologi MARA, Bandar Puncak Alam, Selangor, Malaysia
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27
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Tyagi S, Mishra R, Mazumder A, Mazumder R, Singh G, Pandey P. Synthesis, in silico screening, and biological evaluation of novel pyridine congeners as anti-epileptic agents targeting AMPA (α-amino-3-hydroxy-5-methylisoxazole) receptors. Chem Biol Drug Des 2024; 103:e14498. [PMID: 38453241 DOI: 10.1111/cbdd.14498] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/23/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024]
Abstract
The research involves the synthesis of a series of new pyridine analogs 5(i-x) and their evaluation for anti-epileptic potential using in silico and in vivo models. Synthesis of the compounds was accomplished by using the Vilsmeier-Haack reaction principle. AutoDock 4.2 was used for their in silico screening against AMPA (-amino-3-hydroxy-5-methylisoxazole) receptor (PDB ID:3m3f). For in vivo testing, the maximal electroshock seizure (MES) model was used. The physicochemical, pharmacokinetic, drug-like, and drug-score features of all synthesized compounds were assessed using the online Swiss ADME and Protein Plus software. The in silico results showed that all the synthesized compounds 5(i-x) had 1-3 interactions and affinities ranging from -6.5 to -8.0 kJ/mol with the targeted receptor compared to the binding affinities of the standard drug phenytoin and the original ligand of the target (P99), which were -7.6 and -6.8 kJ/mol, respectively. In vivo study results showed that the compound 5-Carbamoyl-2-formyl-1-[2-(4-nitrophenyl)-2-oxo-ethyl]-pyridinium gave 60% protection against epileptic seizures compared to 59% protection afforded by regular phenytoin. All of them met Lipinski's rule of five and had drug-likeness and drug score values of 0.55 and 0.8, respectively, making them chemically and functionally like phenytoin. According to the findings of the studies, the synthesized derivatives have the potential to be employed as a stepping stone in the development of novel anti-epileptic drugs.
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Affiliation(s)
- Shivani Tyagi
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Rakhi Mishra
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Avijit Mazumder
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Rupa Mazumder
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
| | - Gurvinder Singh
- School of Pharmaceutical Science, Lovely Professional University, Phagwara, Punjab, India
| | - Pratibha Pandey
- Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, Uttar Pradesh, India
- Noida Institute of Engineering and Technology, Biotechnology Department, Greater Noida, Uttar Pradesh, India
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28
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Shahriar S, Shermin SA, Hasnat H, Hossain F, Han A, Geng P, Alam S, Mamun AA. Chemico-pharmacological evaluation of the methanolic leaf extract of Catharanthus ovalis: GC-MS/MS, in vivo, in vitro, and in silico approaches. Front Pharmacol 2024; 15:1347069. [PMID: 38495091 PMCID: PMC10940508 DOI: 10.3389/fphar.2024.1347069] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/10/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction: Natural plant-based medicines have gained popularity recently as a major source of inventive, risk-free, and more potent secondary bioactive compounds with medicinal potential. Catharanthus ovalis is a perennial shrub containing various indole alkaloids cultivated extensively for local medical purposes. Methods: This research is conducted to identify the phytocompounds present in the leaves of C. ovalis and its central and peripheral analgesic, thrombolytic, and membrane-stabilizing activities through tail immersion, acetic acid-induced writhing, human blood clot lysis, and erythrocyte lysis by heat and hypotonic solution methods, respectively. Results and discussion: A total of 39 compounds were identified using GC-MS/MS techniques, including hexadecanoic acid, methyl ester (56.749%), methyl stearate (29.782%), carvacrol and its TBDMS derivative (12.586%), and 9-octadecenoic acid, methyl ester, (E)-] (9.297%) presented in high quantity. The highest tail immersion latency was observed for the 600 mg/kg extract of C. ovalis crude extract. Both 400 and 600 mg/kg doses of C. ovalis crude extract exhibited prominent peripheral analgesic activity. The maximum thrombolytic effect was observed by DCM soluble fraction extract by inhibiting 54.87% of the clot. However, the aqueous-soluble fraction of this extract manifested an excellent membrane-stabilizing effect by showing 73.98% and 87.51% hemolysis against heat- and hypotonic-induced hemolysis, respectively. Some of the compounds were identified as active agents against different receptors related to these diseases, which supported the findings of in vitro and in vivo tests. Conclusion: Further investigation needs to be conducted to specify and identify the exact mechanism of action of these compounds.
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Affiliation(s)
- Saimon Shahriar
- Department of Pharmacy, School of Pharmaceutical Sciences, State University of Bangladesh, Dhaka, Bangladesh
| | - Samia Akter Shermin
- Department of Pharmacy, School of Pharmaceutical Sciences, State University of Bangladesh, Dhaka, Bangladesh
| | - Hasin Hasnat
- Department of Pharmacy, School of Pharmaceutical Sciences, State University of Bangladesh, Dhaka, Bangladesh
| | - Faisal Hossain
- Department of Pharmacy, School of Pharmaceutical Sciences, State University of Bangladesh, Dhaka, Bangladesh
| | - Aixia Han
- Central Laboratory of The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People’s Hospital, Lishui, Zhejiang, China
| | - Peiwu Geng
- Central Laboratory of The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People’s Hospital, Lishui, Zhejiang, China
| | - Safaet Alam
- Drugs and Toxins Research Division, BCSIR Laboratories Rajshahi, Bangladesh Council of Scientific and Industrial Research, Rajshahi, Bangladesh
| | - Abdullah Al Mamun
- Central Laboratory of The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People’s Hospital, Lishui, Zhejiang, China
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Kim MJ, Kulkarni V, Goode MA, Hernandez J, Graham S, Sivesind TE, Manchadi ML. Utilizing systems genetics to enhance understanding into molecular targets of skin cancer. Exp Dermatol 2024; 33:e15043. [PMID: 38459629 PMCID: PMC11018140 DOI: 10.1111/exd.15043] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/10/2024]
Abstract
Despite progress made with immune checkpoint inhibitors and targeted therapies, skin cancer remains a significant public health concern in the United States. The intricacies of the disease, encompassing genetics, immune responses, and external factors, call for a comprehensive approach. Techniques in systems genetics, including transcriptional correlation analysis, functional pathway enrichment analysis, and protein-protein interaction network analysis, prove valuable in deciphering intricate molecular mechanisms and identifying potential diagnostic and therapeutic targets for skin cancer. Recent studies demonstrate the efficacy of these techniques in uncovering molecular processes and pinpointing diagnostic markers for various skin cancer types, highlighting the potential of systems genetics in advancing innovative therapies. While certain limitations exist, such as generalizability and contextualization of external factors, the ongoing progress in AI technologies provides hope in overcoming these challenges. By providing protocols and a practical example involving Braf, we aim to inspire early-career experimental dermatologists to adopt these tools and seamlessly integrate these techniques into their skin cancer research, positioning them at the forefront of innovative approaches in combating this devastating disease.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | | | - Micah A Goode
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Jacob Hernandez
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Sean Graham
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Kemelbekov U, Volynkin V, Zhumakova S, Orynbassarova K, Papezhuk M, Yu V. Comparative Analysis of the Structure and Pharmacological Properties of Some Piperidines and Host-Guest Complexes of β-Cyclodextrin. Molecules 2024; 29:1098. [PMID: 38474609 DOI: 10.3390/molecules29051098] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Pain and anesthesia are a problem for all physicians. Scientists from different countries are constantly searching for new anesthetic agents and methods of general anesthesia. In anesthesiology, the role and importance of local anesthesia always remain topical. In the present work, a comparative analysis of the results of pharmacological studies on models of the conduction and terminal anesthesia, as well as acute toxicity studies of the inclusion complex of 1-methyl-4-ethynyl-4-hydroxypiperidine (MEP) with β-cyclodextrin, was carried out. A virtual screening and comparative analysis of pharmacological activity were also performed on a number of the prepared piperidine derivatives and their host-guest complexes of β-cyclodextrin to identify the structure-activity relationship. Various programs were used to study biological activity in silico. For comparative analysis of chemical and pharmacological properties, data from previous works were used. For some piperidine derivatives, new dosage forms were prepared as beta-cyclodextrin host-guest complexes. Some compounds were recognized as promising local anesthetics. Pharmacological studies have shown that KFCD-7 is more active than reference drugs in terms of local anesthetic activity and acute toxicity but is less active than host-guest complexes, based on other piperidines. This fact is in good agreement with the predicted results of biological activity.
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Affiliation(s)
- Ulan Kemelbekov
- South Kazakhstan Medical Academy, 1 Al-Farabi Square, Shymkent 160019, Kazakhstan
- A.B. Bekturov Institute of Chemical Sciences, 106 Ualikhanov St., Almaty 050010, Kazakhstan
| | - Vitaly Volynkin
- Faculty of Chemistry, Kuban State University, Krasnodar 350040, Russia
| | - Symbat Zhumakova
- A.B. Bekturov Institute of Chemical Sciences, 106 Ualikhanov St., Almaty 050010, Kazakhstan
| | - Kulpan Orynbassarova
- South Kazakhstan Medical Academy, 1 Al-Farabi Square, Shymkent 160019, Kazakhstan
| | - Marina Papezhuk
- Faculty of Chemistry, Kuban State University, Krasnodar 350040, Russia
| | - Valentina Yu
- A.B. Bekturov Institute of Chemical Sciences, 106 Ualikhanov St., Almaty 050010, Kazakhstan
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Yunos NM, Al-Thiabat MG, Sallehudin NJ, A Wahab H. Quassinoids from Eurycoma longifolia as Potential Dihydrofolate Reductase Inhibitors: A Computational Study. Curr Pharm Biotechnol 2024; 25:CPB-EPUB-138868. [PMID: 38425119 DOI: 10.2174/0113892010273336240221101506] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/01/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Quassinoids are degraded triterpene compounds that can be obtained from various species of the Simaroubaceae plant family, including Eurycoma longifolia. Quassinoids are the major compounds in E. longifolia, and they are known to have various medicinal potentials, such as anticancer and antimalarial properties. Dihydrofolate reductase (DHFR) was reported to be one of the important targets for certain anticancer and antimalarial drugs. Twelve quassinoids from E. longifolia were identified to have anticancer effects based on their IC50 values. This study aimed to evaluate the interactions of these twelve quassinoids with DHFR via Autodock 4.2 software and Biovia Discovery Studio Visualiser. METHODS Twelve quassinoids from E. longifolia and their interactions with DHFR were evaluated via Autodock 4.2 software and Biovia Discovery Studio Visualiser. Their drug-likeness and pharmacokinetic properties were also assessed using the ADMETlab 2.0 program. RESULTS The molecular docking results showed that eleven quassinoids showed better docking scores than methotrexate, in which the binding energy (BE) of these quassinoids ranged from - 7.87 to -9.58 kcal/mol. Their inhibition constant (Ki) ranged from 0.095 to 1.71 μM. At the same time, the BE and Ki values for methotrexate were -7.80 kcal/mol and 1.64 μM, respectively. CONCLUSION From the analysis, 6-dehydrolongilactone and eurycomalide B are among the twelve compounds that showed great potential as hit-to-lead compounds based on the docking score on DHFR, drug-likeness, and ADMET properties. These results suggest a great potential to pursue validation studies via in vitro and in vivo models.
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Affiliation(s)
- Nurhanan Murni Yunos
- Natural Products Division, Forest Research Institute Malaysia (FRIM), Kepong 52109 Selangor, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | | | - Nor Jannah Sallehudin
- Natural Products Division, Forest Research Institute Malaysia (FRIM), Kepong 52109 Selangor, Malaysia
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
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Segatto NV, Simões LD, Bender CB, Sousa FS, Oliveira TL, Paschoal JDF, Pacheco BS, Lopes I, Seixas FK, Qazi A, Thomas FM, Chaki S, Robertson N, Newsom J, Patel S, Rund LA, Jordan LR, Bolt C, Schachtschneider KM, Schook LB, Collares TV. Oncopig bladder cancer cells recapitulate human bladder cancer treatment responses in vitro. Front Oncol 2024; 14:1323422. [PMID: 38469237 PMCID: PMC10926022 DOI: 10.3389/fonc.2024.1323422] [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: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Bladder cancer is a common neoplasia of the urinary tract that holds the highest cost of lifelong treatment per patient, highlighting the need for a continuous search for new therapies for the disease. Current bladder cancer models are either imperfect in their ability to translate results to clinical practice (mouse models), or rare and not inducible (canine models). Swine models are an attractive alternative to model the disease due to their similarities with humans on several levels. The Oncopig Cancer Model has been shown to develop tumors that closely resemble human tumors. However, urothelial carcinoma has not yet been studied in this platform. Methods We aimed to develop novel Oncopig bladder cancer cell line (BCCL) and investigate whether these urothelial swine cells mimic human bladder cancer cell line (5637 and T24) treatment-responses to cisplatin, doxorubicin, and gemcitabine in vitro. Results Results demonstrated consistent treatment responses between Oncopig and human cells in most concentrations tested (p>0.05). Overall, Oncopig cells were more predictive of T24 than 5637 cell therapeutic responses. Microarray analysis also demonstrated similar alterations in expression of apoptotic (GADD45B and TP53INP1) and cytoskeleton-related genes (ZMYM6 and RND1) following gemcitabine exposure between 5637 (human) and Oncopig BCCL cells, indicating apoptosis may be triggered through similar signaling pathways. Molecular docking results indicated that swine and humans had similar Dg values between the chemotherapeutics and their target proteins. Discussion Taken together, these results suggest the Oncopig could be an attractive animal to model urothelial carcinoma due to similarities in in vitro therapeutic responses compared to human cells.
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Affiliation(s)
- Natália V. Segatto
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Lucas D. Simões
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Camila B. Bender
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fernanda S. Sousa
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Thais L. Oliveira
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Júlia D. F. Paschoal
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Bruna S. Pacheco
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Isadora Lopes
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabiana K. Seixas
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Aisha Qazi
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Faith M. Thomas
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Sulalita Chaki
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | | | | | - Shovik Patel
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Laurie A. Rund
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Luke R. Jordan
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Sus Clinicals Inc., Chicago, IL, United States
| | - Courtni Bolt
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Sus Clinicals Inc., Chicago, IL, United States
| | | | - Lawrence B. Schook
- Department of Animal Sciences, University of Illinois, Urbana, IL, United States
- Sus Clinicals Inc., Chicago, IL, United States
| | - Tiago V. Collares
- Technology Development Center, Laboratory of Cancer Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
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Wong YH, Lee SH. Short Fragmented Peptides from Pardachirus Marmoratus Exhibit Stronger Anticancer Activities in In Silico Residue Replacement and Analyses. Curr Drug Discov Technol 2024; 21:CDDT-EPUB-138703. [PMID: 38409702 DOI: 10.2174/0115701638290855240207114727] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Cancer is a worldwide issue. It has been observed that conventional therapies face many problems, such as side effects and drug resistance. Recent research reportedly used marine-derived products to treat various diseases and explored their potential in treating cancers. OBJECTIVE This study aims to discover short-length anticancer peptides derived from pardaxin 6 through an in silico approach. METHODS Fragmented peptides ranging from 5 to 15 amino acids were derived from the pardaxin 6 parental peptide. These peptides were further replaced with one residue and, along with the original fragmented peptides, were predicted for their SVM scores and physicochemical properties. The top 5 derivative peptides were further examined for their toxicity, hemolytic probability, peptide structures, docking models, and energy scores using various web servers. The trend of in silico analysis outputs across 5 to 15 amino acid fragments was further analyzed. RESULTS Results showed that when the amino acids were increased, SVM scores of the original fragmented peptides were also increased. Designed peptides had increased SVM scores, which was aligned with previous studies where the single residue replacement transformed the non-anticancer peptide into an anticancer agent. Moreover, in vitro studies validated that the designed peptides retained or enhanced anticancer effects against different cancer cell lines. Interestingly, a decreasing trend was observed in those fragmented derivative peptides. CONCLUSION Single residue replacement in fragmented pardaxin 6 was found to produce stronger anticancer agents through in silico predictions. Through bioinformatics tools, fragmented peptides improved the efficiency of marine-derived drugs with higher efficacy and lower hemolytic effects in treating cancers.
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Affiliation(s)
- Yong Hui Wong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, 47500, Malaysia
| | - Sau Har Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, 47500, Malaysia
- Medical Advancement for Better Quality of Life Impact Lab, Taylor's University, Subang Jaya, 47500, Malaysia
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Alharthi NS, Alwethaynani MS, Alhazmi AY, Alawam AS, Alshehri FF, Alotaibi F, Rehman ZU, Alkhayl FFA, Al-Bazi MM, Khan FR. In silico assessment of a natural small molecule as an inhibitor of programmed death ligand 1 for cancer immunotherapy: a computational approach. J Biomol Struct Dyn 2024:1-21. [PMID: 38385444 DOI: 10.1080/07391102.2024.2317980] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Programmed cell death ligand 1 (PD-L1) is a crucial target for cancer therapy. Here, an in silico study investigates PD-L1 to inhibit its interaction with PD1, thereby promoting an immune response to eliminate cancer cells. The study employed machine learning (ML) -based QSAR to detect PDL1 inhibitors. Morgan's fingerprint with docking score showed a 0.83 correlation with the experimental IC50, enabling the screening of 3200 natural compounds. The top three compounds, considered 2819, 2821 and 3188, were selected from the ML-based QSAR and subjected to molecular docking and simulation. The binding scores for 2819, 2821 and 3188 were -7.0, -9.0 and -8.9 kcal/mol, respectively. The stability of the ligands during a 100 ns simulation was assessed using RMSD, showing that 2819 and 2821 maintained stable patterns comparable to the control inhibitor. Notably, 2819 exhibited a consistent stable pattern throughout the simulation, while 2821 showed stability in the last 40 ns. The control compound showed the highest number of hydrogen bonds with proteins, whereas compounds 2819 and 2821 formed continuous H-bonds. 3188 was separated from the protein in later phases and is not regarded as a potential PD-L1-binding molecule. MMGBSA binding free energy for complexes was computed. Control had the lowest binding free energy, while 2819 and 2821 also had lower binding energies. In contrast, 3188 showed poor binding free energy, causing protein separation. Principal component analysis showed a loss of entropy and reduced protein conformational variation. Overall, 2819 and 2821 are potential binders for PD-L1 inhibition and immune response triggering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nahed S Alharthi
- Department of Medical Laboratory. College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudia Arabia
| | - Maher S Alwethaynani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Abdulfattah Y Alhazmi
- Pharmaceutical Practices Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abdullah S Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Faez Falah Alshehri
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Saudi Arabia
| | - Faisal Alotaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Saudi Arabia
| | - Zia Ur Rehman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Maha M Al-Bazi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, AlQuwayiyah, Shaqra University, Saudi Arabia
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Teber R, Asakawa S. In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes. Int J Mol Sci 2024; 25:2566. [PMID: 38473813 DOI: 10.3390/ijms25052566] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.
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Affiliation(s)
- Rabeb Teber
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
- Signal Peptidome Research Laboratory, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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Gomes SF, Alvarenga ES, Baia VC, Oliveira DF. N-Phenylnorbornenesuccinimide derivatives, agricultural defensive, and enzymatic target selection. Pest Manag Sci 2024. [PMID: 38372427 DOI: 10.1002/ps.8031] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND Faced with the need to develop new herbicides with modes of action different to those observed for existing agrochemicals, one of the most promising strategies employed by synthetic chemists involves the structural modification of molecules found in natural products. Molecules containing amides, imides, and epoxides as functional groups are prevalent in nature and find extensive application in synthesizing more intricate compounds due to their biological properties. In this context, this paper delineates the synthesis of N-phenylnorbornenesuccinimide derivatives, conducts biological assays, and carries out in silico investigation of the protein target associated with the most potent compound in plant organisms. The phytotoxic effects of the synthesized compounds (2-29) were evaluated on Allium cepa, Bidens pilosa, Cucumis sativus, Sorghum bicolor, and Solanum lycopersicum. RESULTS Reaction of endo-bicyclo[2.2.1]hept-5-ene-3a,7a-dicarboxylic anhydride (1) with aromatic amines led to the N-phenylnorbornenesuccinic acids (2-11) with yields ranging from 75% to 90%. Cyclization of compounds (2-11) in the presence of acetic anhydride and sodium acetate afforded N-phenylnorbornenesuccinimides (12-20) with yields varying from 65% to 89%. Those imides were then subjected to epoxidation reaction to afford N-phenylepoxynorbornanesuccimides (21-29) with yields from 60% to 90%. All compounds inhibited the growth of seedlings of the plants evaluated. Substance 23 was the most active against the plants tested, inhibiting 100% the growth of all species in all concentrations. Cyclophilin was found to be the enzymatic target of compound 23. CONCLUSION These findings suggest that derivatives of N-phenylnorbornenesuccinimide are promising compounds in the quest for more selective and stable agrochemicals. This perspective reinforces the significance of these derivatives as potential innovative herbicides and emphasizes the importance of further exploring their biological activity on weeds. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Sabriny F Gomes
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elson S Alvarenga
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Vitor C Baia
- Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
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Habib A, Liang Y, Xu X, Zhu N, Xie J. Immunoinformatic Identification of Multiple Epitopes of gp120 Protein of HIV-1 to Enhance the Immune Response against HIV-1 Infection. Int J Mol Sci 2024; 25:2432. [PMID: 38397105 PMCID: PMC10889372 DOI: 10.3390/ijms25042432] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Acquired Immunodeficiency Syndrome is caused by the Human Immunodeficiency Virus (HIV), and a significant number of fatalities occur annually. There is a dire need to develop an effective vaccine against HIV-1. Understanding the structural proteins of viruses helps in designing a vaccine based on immunogenic peptides. In the current experiment, we identified gp120 epitopes using bioinformatic epitope prediction tools, molecular docking, and MD simulations. The Gb-1 peptide was considered an adjuvant. Consecutive sequences of GTG, GSG, GGTGG, and GGGGS linkers were used to bind the B cell, Cytotoxic T Lymphocytes (CTL), and Helper T Lymphocytes (HTL) epitopes. The final vaccine construct consisted of 315 amino acids and is expected to be a recombinant protein of approximately 35.49 kDa. Based on docking experiments, molecular dynamics simulations, and tertiary structure validation, the analysis of the modeled protein indicates that it possesses a stable structure and can interact with Toll-like receptors. The analysis demonstrates that the proposed vaccine can provoke an immunological response by activating T and B cells, as well as stimulating the release of IgA and IgG antibodies. This vaccine shows potential for HIV-1 prophylaxis. The in-silico design suggests that multiple-epitope constructs can be used as potentially effective immunogens for HIV-1 vaccine development.
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Affiliation(s)
- Arslan Habib
- Laboratory of Molecular Immunology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; (A.H.); (X.X.); (N.Z.)
| | - Yulai Liang
- Laboratory of Molecular Immunology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; (A.H.); (X.X.); (N.Z.)
| | - Xinyi Xu
- Laboratory of Molecular Immunology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; (A.H.); (X.X.); (N.Z.)
| | - Naishuo Zhu
- Laboratory of Molecular Immunology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; (A.H.); (X.X.); (N.Z.)
- Institute of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Xie
- Laboratory of Molecular Immunology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; (A.H.); (X.X.); (N.Z.)
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Aljedaie MM, Alam P. In silico identification of human microRNAs pointing centrin genes in Leishmania donovani: Considering the RNAi-mediated gene control. Front Genet 2024; 14:1329339. [PMID: 38390455 PMCID: PMC10883313 DOI: 10.3389/fgene.2023.1329339] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/12/2023] [Indexed: 02/24/2024] Open
Abstract
Leishmaniasis, a parasitic disease caused by different species of the protozoa parasite Leishmania, is a neglected tropical human disease that is endemic in about a hundred countries worldwide. According to the World Health Organization (WHO), the annual incidence of cutaneous leishmaniasis (CL) is estimated to be 0.7-1.2 million cases globally, whereas the annual incidence of visceral leishmaniasis is estimated to be 0.2-0.4 million cases. In many eukaryotic organisms, including human beings and protozoan parasites, centrin genes encode proteins that play essential roles within the centrosome or basal body. Human microRNAs (miRNAs) have been linked to several infectious and non-infectious diseases associated with pathogen-host interactions, and they play the emphatic roles as gene expression regulators. In this study, we used the MirTarget bioinformatics tool, which is a machine learning-based approach implemented in miRDB, to predict the target of human miRNAs in Leishmania donovani centrin genes. For cross-validation, we utilized additional prediction algorithms, namely, RNA22 and RNAhybrid, targeting all five centrin isotypes. The centrin-3 (LDBPK_342160) and putative centrin-5 (NC_018236.1) genes in L. donovani were targeted by eight and twelve human miRNAs, respectively, among 2,635 known miRNAs (miRBase). hsa-miR-5193 consistently targeted both genes. Using TargetScan, TarBase, miRecords, and miRTarBase, we identified miRNA targets and off-targets in human homologs of centrin, inflammation, and immune-responsive genes. Significant targets were screened based on GO terminologies and KEGG pathway-enrichment analysis (Log10 p-value >0.0001). In silico tools that predict the biological roles of human miRNAs as primary gene regulators in pathogen-host interactions help unravel the regulatory patterns of these miRNAs, particularly in the early stages of inflammatory responses. It is also noted that these miRNAs played an important role in the late phase of adaptive immune response, inclusively their impacts on the immune system's response to L. donovani.
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Affiliation(s)
- Manei M Aljedaie
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Pravej Alam
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Cysewski P, Przybyłek M, Jeliński T. Predicting sulfanilamide solubility in the binary mixtures using a reference solvent approach. Polim Med 2024; 54:0-0. [PMID: 38315072 DOI: 10.17219/pim/178284] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Solubility is a fundamental physicochemical property of active pharmaceutical ingredients. The optimization of a dissolution medium aims not only to increase solubility and other aspects are to be included such as environmental impact, toxicity degree, availability, and costs. Obtaining comprehensive solubility characteristics of chemical compounds is a non-trivial and demanding process. Therefore, support from theoretical approaches is of practical importance. OBJECTIVES This study aims to examine the accuracy of the reference solubility approach in the case of sulfanilamide dissolution in a variety of binary solvents. This pharmaceutically active substance has been extensively studied, and a substantial amount of solubility data is available. Unfortunately, using this set of data directly for theoretical modeling is impeded by noticeable inconsistencies in the published solubility data. Hence, this aspect is addressed by data curation using theoretical and experimental confirmations. MATERIAL AND METHODS In the experimental part of our study, the popular shake-flask method combined with ultraviolet (UV) spectrophotometric measurements was applied for solubility determination. The computational phase utilized the conductor-like screening model for real solvents (COSMO-RS) approach. RESULTS The analysis of the results of solubility calculations for sulfonamide in binary solvents revealed abnormally high error values for acetone-ethyl acetate mixtures, which were further confirmed with experimental measurements. Additional confirmation was obtained by extending the solubility measurements to a series of homologous acetate esters. CONCLUSIONS Our study addresses the crucial issue of coherence of solubility data used for many theoretical inquiries, including parameter fitting of semi-empirical models, in-depth thermodynamic interpretations and application of machine learning protocols. The effectiveness of the proposed methodology for dataset curation was demonstrated for sulfanilamide solubility in binary mixtures. This approach enabled not only the formulation of a consistent dataset of sulfanilamide solubility binary solvent mixtures, but also its implementation as a qualitative tool guiding rationale solvent selection for experimental solubility screening.
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Affiliation(s)
- Piotr Cysewski
- Department of Physical Chemistry, Faculty of Pharmacy, Ludwik Rydgier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Poland
| | - Maciej Przybyłek
- Department of Physical Chemistry, Faculty of Pharmacy, Ludwik Rydgier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Poland
| | - Tomasz Jeliński
- Department of Physical Chemistry, Faculty of Pharmacy, Ludwik Rydgier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Poland
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Ooida J, Kiyohara N, Noguchi H, Oguchi Y, Nagane K, Sakaguchi T, Aoyama G, Shige F, Chapman JV, Asami M, Kofoed KF, Pham MHC, Suzuki K. An In Silico Model for Predicting the Efficacy of Edge-to-Edge Repair for Mitral Regurgitation. J Biomech Eng 2024; 146:021004. [PMID: 37978048 DOI: 10.1115/1.4064055] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
In recent years, transcatheter edge-to-edge repair (TEER) has been widely adopted as an effective treatment for mitral regurgitation (MR). The aim of this study is to develop a personalized in silico model to predict the effect of edge-to-edge repair in advance to the procedure for each individual patient. For this purpose, we propose a combination of a valve deformation model for computing the mitral valve (MV) orifice area (MVOA) and a lumped parameter model for the hemodynamics, specifically mitral regurgitation volume (RVol). Although we cannot obtain detailed information on the three-dimensional flow field near the mitral valve, we can rapidly simulate the important medical parameters for the clinical decision support. In the present method, we construct the patient-specific pre-operative models by using the parameter optimization and then simulate the postoperative state by applying the additional clipping condition. The computed preclip MVOAs show good agreement with the clinical measurements, and the correlation coefficient takes 0.998. In addition, the MR grade in terms of RVol also has good correlation with the grade by ground truth MVOA. Finally, we try to investigate the applicability for the predicting the postclip state. The simulated valve shapes clearly show the well-known double orifice and the improvement of the MVOA, compared with the preclip state. Similarly, we confirmed the improved reverse flow and MR grade in terms of RVol. A total computational time is approximately 8 h by using general-purpose PC. These results obviously indicate that the present in silico model has good capability for the assessment of edge-to-edge repair.
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Affiliation(s)
- Junichi Ooida
- Canon Inc., 3-30-2 Shimomaruko, Ota-ku, Tokyo 146-8501, Japan
| | - Naoki Kiyohara
- Canon Inc., 3-30-2 Shimomaruko, Ota-ku, Tokyo 146-8501, Japan
| | | | - Yuichiro Oguchi
- Canon Inc., 3-30-2 Shimomaruko, Ota-ku, Tokyo 146-8501, Japan
| | - Kohei Nagane
- Canon Inc., 3-30-2 Shimomaruko, Ota-ku, Tokyo 146-8501, Japan
| | - Takuya Sakaguchi
- Canon Medical Systems Corporation, 1385 Shimoishigami, Ohtawara, Tochigi 324-8550, Japan
| | - Gakuto Aoyama
- Canon Medical Systems Corporation, 1385 Shimoishigami, Ohtawara, Tochigi 324-8550, Japan
| | - Fumimasa Shige
- Canon Medical Systems Corporation, 1385 Shimoishigami, Ohtawara, Tochigi 324-8550, Japan
| | - James V Chapman
- Canon Medical Informatics, Inc., 5850 Opus Parkway, Suite 300, Minnetonka, MN 55343
| | - Masahiko Asami
- Division of Cardiology, Mitsui Memorial Hospital, 1 Kandaizumi-cho, Chiyoda-ku, Tokyo 101-8643, Japan
| | - Klaus Fuglsang Kofoed
- Department of Cardiology and Radiology, Rigshospitalet & University of Copenhagen, Blegdamsvej 9, København 2100, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, Rigshospitalet & University of Copenhagen, Blegdamsvej 9, København 2100, Denmark
| | - Michael Huy Cuong Pham
- Department of Cardiology and Radiology, Rigshospitalet & University of Copenhagen, Blegdamsvej 9, København 2100, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, Rigshospitalet & University of Copenhagen, Blegdamsvej 9, København 2100, Denmark
| | - Koshiro Suzuki
- Canon Inc., 3-30-2 Shimomaruko, Ota-ku, Tokyo 146-8501, Japan
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Finlayson L, McMillan L, Suveges S, Steele D, Eftimie R, Trucu D, Brown CTA, Eadie E, Hossain-Ibrahim K, Wood K. Simulating photodynamic therapy for the treatment of glioblastoma using Monte Carlo radiative transport. J Biomed Opt 2024; 29:025001. [PMID: 38322729 PMCID: PMC10846422 DOI: 10.1117/1.jbo.29.2.025001] [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] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024]
Abstract
Significance Glioblastoma (GBM) is a rare but deadly form of brain tumor with a low median survival rate of 14.6 months, due to its resistance to treatment. An independent simulation of the INtraoperative photoDYnamic therapy for GliOblastoma (INDYGO) trial, a clinical trial aiming to treat the GBM resection cavity with photodynamic therapy (PDT) via a laser coupled balloon device, is demonstrated. Aim To develop a framework providing increased understanding for the PDT treatment, its parameters, and their impact on the clinical outcome. Approach We use Monte Carlo radiative transport techniques within a computational brain model containing a GBM to simulate light path and PDT effects. Treatment parameters (laser power, photosensitizer concentration, and irradiation time) are considered, as well as PDT's impact on brain tissue temperature. Results The simulation suggests that 39% of post-resection GBM cells are killed at the end of treatment when using the standard INDYGO trial protocol (light fluence = 200 J / cm 2 at balloon wall) and assuming an initial photosensitizer concentration of 5 μ M . Increases in treatment time and light power (light fluence = 400 J / cm 2 at balloon wall) result in further cell kill but increase brain cell temperature, which potentially affects treatment safety. Increasing the p hotosensitizer concentration produces the most significant increase in cell kill, with 61% of GBM cells killed when doubling concentration to 10 μ M and keeping the treatment time and power the same. According to these simulations, the standard trial protocol is reasonably well optimized with improvements in cell kill difficult to achieve without potentially dangerous increases in temperature. To improve treatment outcome, focus should be placed on improving the photosensitizer. Conclusions With further development and optimization, the simulation could have potential clinical benefit and be used to help plan and optimize intraoperative PDT treatment for GBM.
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Affiliation(s)
- Louise Finlayson
- SUPA, University of St Andrews, School of Physics and Astronomy, St Andrews, United Kingdom
| | - Lewis McMillan
- SUPA, University of St Andrews, School of Physics and Astronomy, St Andrews, United Kingdom
| | - Szabolcs Suveges
- University of Dundee, Division of Mathematics, Dundee, United Kingdom
| | - Douglas Steele
- University of Dundee, Medical School, Division Imaging Science and Technology, Dundee, United Kingdom
| | - Raluca Eftimie
- Université de Bourgogne Franche-Comté, Laboratoire Mathématiques de Besançon, Besançon, France
| | - Dumitru Trucu
- University of Dundee, Division of Mathematics, Dundee, United Kingdom
| | | | - Ewan Eadie
- Ninewells Hospital, Photobiology Unit, Dundee, United Kingdom
| | - Kismet Hossain-Ibrahim
- University of Dundee, School of Medicine, Division Cellular and Molecular Medicine, Dundee, United Kingdom
- Ninewells Hospital and Medical School, Department of Neurosurgery, Dundee, United Kingdom
| | - Kenneth Wood
- SUPA, University of St Andrews, School of Physics and Astronomy, St Andrews, United Kingdom
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Kumar R, Jayaraman M, Ramadas K, Chandrasekaran A. Computational identification and analysis of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the human POR gene: a structural and functional impact. J Biomol Struct Dyn 2024; 42:1518-1532. [PMID: 37173831 DOI: 10.1080/07391102.2023.2211674] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/02/2023] [Indexed: 05/15/2023]
Abstract
Cytochrome P450 oxidoreductase (POR) protein is essential for steroidogenesis, and POR gene mutations are frequently associated with P450 Oxidoreductase Deficiency (PORD), a disorder of hormone production. To our knowledge, no previous attempt has been made to identify and analyze the deleterious/pathogenic non-synonymous single nucleotide polymorphisms (nsSNPs) in the human POR gene through an extensive computational approach. Computational algorithms and tools were employed to identify, characterize, and validate the pathogenic SNPs associated with certain diseases. To begin with, all the high-confidence SNPs were collected, and their structural and functional impacts on the protein structures were explored. The results of various in silico analyses affirm that the A287P and R457H variants of POR could destabilize the interactions between the amino acids and the hydrogen bond networks, resulting in functional deviations of POR. The literature study further confirms that the pathogenic mutations (A287P and R457H) are associated with the onset of PORD. Molecular dynamics simulations (MDS) and essential dynamics (ED) studies characterized the structural consequences of prioritized deleterious mutations, representing the structural destabilization that might disrupt POR biological function. The identified deleterious mutations at the cofactor's binding domains might interfere with the essential interactions between the protein and cofactors, thus inhibiting POR catalytic activity. The consolidated insights from the computational analyses can be used to predict potential deleterious mutants and understand the disease's pathological basis and the molecular mechanism of drug metabolism for the application of personalized medication. HIGHLIGHTSNADPH cytochrome P450 oxidoreductase (POR) mutations are associated with a broad spectrum of human diseasesIdentified and analyzed the most deleterious nsSNPs of POR through the sequence and structure-based prediction toolsInvestigated the structural and functional impacts of the most significant mutations (A287P and R457H) associated with PORDMolecular dynamics and PCA-based FEL analysis were utilized to probe the mutation-induced structural alterations in PORCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajalakshmi Kumar
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pillayarkuppam, Puducherry, India
| | - Manikandan Jayaraman
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Krishna Ramadas
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Adithan Chandrasekaran
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pillayarkuppam, Puducherry, India
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Tognolini M, Lodola A, Giorgio C. Drug discovery: In silico dry data can bypass biological wet data? Br J Pharmacol 2024; 181:340-344. [PMID: 37872106 DOI: 10.1111/bph.16266] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
The recent and extraordinary increase in computer power, along with the availability of efficient algorithms based on artificial intelligence, has prompted a large number of inexperienced scientists to challenge the complex and yet competitive world of drug discovery, by pretending to identify new hits through the sole use of computer aided drug design (CADD). Does the golden era of dry data run the risk of overshadowing the importance of wet data and, in doing so, forget that in silico and biological data need each other in successful preclinical drug discovery programmes?
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Affiliation(s)
| | - Alessio Lodola
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Carmine Giorgio
- Department of Food and Drug, University of Parma, Parma, Italy
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Sabarathinam S, Rajappan Chandra SK, Satheesh S. Network pharmacology based pharmacokinetic assessment and evaluation of the therapeutic potential of catechin derivatives as a potential myostatin inhibitor: A special view on Sarcopenic Obesity. Nat Prod Res 2024; 38:856-860. [PMID: 36941755 DOI: 10.1080/14786419.2023.2191197] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/08/2023] [Indexed: 03/23/2023]
Abstract
Sarcopenic obesity has become a significant age-related metabolic problem. Catechins are flavanol, derivatives which poses a strong antioxidant activity. The major components of catechin derivatives. were identified through our physicochemical and pharmacokinetic parameters estimation. Therefore, in this study, network pharmacology was used to explore the multiple targets related to Sarcopenia, Metabolic syndrome, and obesity. The targets were identified from network analysis. The catechin derivatives were screened using Lipinski's rule of five, Veber scale, Egan scale, and Muegge scale. From this drugglikness property catechin and Epicatechin was selected which were docked towards the myostatin inhibition PDB ID: 3HH2. Furthermore, the computational docking method on Catechin and Epicatechin with the stronger interaction towards myostatin inhibition receptor with the binding energy of -6.90 kcal/mol. and -7.0 kcal/mol from autodock software, respectively, for catechin and Epicatechin. Higher binding energy confirms the pharmacotherapeutic activity of Catechin and Epicatechin toward the myostatin inhibitor target.
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Affiliation(s)
- Sarvesh Sabarathinam
- Interdisciplinary Institute of Indian System of Medicine (IIISM) SRM Institute of Science & Technology, Kattankulathur-603203, Chengalpattu, Tamil Nadu, India
| | - Satish Kumar Rajappan Chandra
- Interdisciplinary Institute of Indian System of Medicine (IIISM) SRM Institute of Science & Technology, Kattankulathur-603203, Chengalpattu, Tamil Nadu, India
| | - Sanjana Satheesh
- Department of Biotechnology, Birla Institute of Technology and Science, Dubai Campus, Dubai International Academic City, Dubai, P.O. Box 345055, United Arab Emirates
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Razafindrakoto ZR, Tombozara N, Ramanitrahasimbola D, Andrianjara C, Zhao M, Marchioni E, Rakotondramanana DA, Julien David D. In silico ADMET and anti-inflammatory profiles of the stigmast-4-en-3-one and isolation of isovanillin as the antioxidant principle of Imperata cylindrica (L.) P. Beauv. Nat Prod Res 2024:1-8. [PMID: 38293732 DOI: 10.1080/14786419.2024.2305649] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Imperata cylindrica (L.) P. Beauv. is an invasive species widely used in treatment of several diseases associated with pain and inflammation in different countries including Madagascar. This work aims to report the isolation of the antioxidant, analgesic and anti-nflammatory compounds from the methanol extract of I. cylindrica. The bio-guided method was used to isolate its bioactive compounds by combining chromatographic methods, writhing test in mice and antioxidant assays. Stigmast-4-en-3-one was isolated as one among the compounds responsible for the analgesic and anti-inflammatory properties and isovanillin as one among the antioxidant compounds from the extract. Stigmast-4-en-3-one showed a good oral pharmacokinetic profile and good binding affinities with some pro-inflammatory targets. It did not show any mutagenic effect, nor a carcinogenic one and had a low risk to be a cardiotoxic agent. All of our results provide scientific justification for its traditional medicinal use in the management of pain and inflammatory related diseases.
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Affiliation(s)
| | | | - David Ramanitrahasimbola
- Institut Malgache de Recherches Appliquées (IMRA), Antananarivo, Madagascar
- Département, Pharmacie, Faculté de Médecine, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - Minjie Zhao
- Chimie Analytique des Molécules Bioactives et Pharmacognosie (CAMBAP), Institut Pluridisciplinaire Hubert Curien (IPHC), CNRS-UMR 7178, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Eric Marchioni
- Chimie Analytique des Molécules Bioactives et Pharmacognosie (CAMBAP), Institut Pluridisciplinaire Hubert Curien (IPHC), CNRS-UMR 7178, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | | | - Diane Julien David
- Chimie Analytique des Molécules Bioactives et Pharmacognosie (CAMBAP), Institut Pluridisciplinaire Hubert Curien (IPHC), CNRS-UMR 7178, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
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Golchha NC, Abdulhameed Odhar H, Nighojkar A, Nighojkar S. Molecular docking, dynamics and in vitro analysis of multi-target inhibitors for Clostridioides difficile. Bioinformation 2024; 20:39-48. [PMID: 38352908 PMCID: PMC10859948 DOI: 10.6026/973206300200039] [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: 01/01/2024] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
The opportunistic pathogen, Clostridioides difficile owes its extreme pathogenicity for its ability to develop antibiotic resistance and recurrent infections. The current antibiotics used for the treatment are showing declining sensitivity and rising antibiotic resistance. Therefore, it is of interest to develop the anti-clostridial drugs to overcome these issues. Hence, we have explored ZINC library to find the suitable lead compounds against five target proteins of C. difficile. Multistep virtual screening is performed to find the suitable compounds that are checked for their stability using molecular dynamics and are validated in vitro against C. difficile. In our study, five compounds viz., ZINC64969876, ZINC13641164, ZINC13691348, ZINC5554596 and ZINC3894278 that inhibit HisC, Spo0A, PdcA, DAHP synthase and cyclic-di GMP proteins, respectively have been identified. Further, these compounds were tested in vitro against four different isolates of C. difficile and all of them were found to inhibit the pathogen. However, to use these compounds as anti-clostridial drugs, further testing needs to be done. The selected compounds from our study are reported for the first time as antimicrobial agents against C. difficile.
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Affiliation(s)
- Nikita Chordia Golchha
- School of Biotechnology, Devi Ahilya University, Takshashila Campus, Khandwa Road, INDORE-452001, India
| | | | - Anand Nighojkar
- Maharaja Ranjit Singh College of Professional Sciences, Hemkunt Campus, Khandwa Road, Indore, 452001, India
| | - Sadhana Nighojkar
- Mata Gujri College of Professional Studies, A.B. Road, Indore, 452001, India
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Collins SP, Mailloux B, Kulkarni S, Gagné M, Long AS, Barton-Maclaren TS. Development and application of consensus in silico models for advancing high-throughput toxicological predictions. Front Pharmacol 2024; 15:1307905. [PMID: 38333007 PMCID: PMC10850302 DOI: 10.3389/fphar.2024.1307905] [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: 10/05/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Abstract
Computational toxicology models have been successfully implemented to prioritize and screen chemicals. There are numerous in silico (quantitative) structure-activity relationship ([Q]SAR) models for the prediction of a range of human-relevant toxicological endpoints, but for a given endpoint and chemical, not all predictions are identical due to differences in their training sets, algorithms, and methodology. This poses an issue for high-throughput screening of a large chemical inventory as it necessitates several models to cover diverse chemistries but will then generate data conflicts. To address this challenge, we developed a consensus modeling strategy to combine predictions obtained from different existing in silico (Q)SAR models into a single predictive value while also expanding chemical space coverage. This study developed consensus models for nine toxicological endpoints relating to estrogen receptor (ER) and androgen receptor (AR) interactions (i.e., binding, agonism, and antagonism) and genotoxicity (i.e., bacterial mutation, in vitro chromosomal aberration, and in vivo micronucleus). Consensus models were created by combining different (Q)SAR models using various weighting schemes. As a multi-objective optimization problem, there is no single best consensus model, and therefore, Pareto fronts were determined for each endpoint to identify the consensus models that optimize the multiple-criterion decisions simultaneously. Accordingly, this work presents sets of solutions for each endpoint that contain the optimal combination, regardless of the trade-off, with the results demonstrating that the consensus models improved both the predictive power and chemical space coverage. These solutions were further analyzed to find trends between the best consensus models and their components. Here, we demonstrate the development of a flexible and adaptable approach for in silico consensus modeling and its application across nine toxicological endpoints related to ER activity, AR activity, and genotoxicity. These consensus models are developed to be integrated into a larger multi-tier NAM-based framework to prioritize chemicals for further investigation and support the transition to a non-animal approach to risk assessment in Canada.
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Affiliation(s)
- Sean P. Collins
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
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Hassan A, Rijo P, Abuamara TMM, Ali Lashin LS, Kamar SA, Bangay G, Al-Sawahli MM, Fouad MK, Zoair MA, Abdalrhman TI, Elebeedy D, Ibrahim IA, Mohamed AF, Abd El Maksoud AI. Synergistic Differential DNA Demethylation Activity of Danshensu ( Salvia miltiorrhiza) Associated with Different Probiotics in Nonalcoholic Fatty Liver Disease. Biomedicines 2024; 12:279. [PMID: 38397881 PMCID: PMC10886676 DOI: 10.3390/biomedicines12020279] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a major hepatic disorder occurring in non-alcohol-drinking individuals. Salvianic acid A or Danshensu (DSS, 3-(3, 4-dihydroxyphenyl)-(2R)-lactic acid), derived from the root of Danshen (Salvia miltiorrhiza), has demonstrated heart and liver protective properties. In this work, we investigated the antioxidant activity and hepatoprotective activity of Danshensu alone and in combination with different agents, such as probiotic bacteria (Lactobacillus casei and Lactobacillus acidophilus), against several assays. The inhibition mechanism of the methylation gene biomarkers, such as DNMT-1, MS, STAT-3, and TET-1, against DSS was evaluated by molecular docking and RT-PCR techniques. The physicochemical and pharmacokinetic ADMET properties of DSS were determined by SwissADME and pkCSM. The results indicated that all lipid blood test profiles, including cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C), were reduced after the oral administration of Danshensu combined with probiotics (L. casei and L. acidophilus) that demonstrated good, efficient free radical scavenging activity, measured using anti-oxidant assays. ADMET and drug-likeness properties certify that the DSS could be utilized as a feasible drug since DSS showed satisfactory physicochemical and pharmacokinetic ADMET properties.
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Affiliation(s)
- Amr Hassan
- Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt
| | - Patrícia Rijo
- CBIOS—Lusófona University’s Research Center for Biosciences and Health Technologies, 1749-024 Lisbon, Portugal;
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Tamer M. M. Abuamara
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Histology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt
| | - Lashin Saad Ali Lashin
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Medical Physiology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Sherif A. Kamar
- Department of Basic Medical Science, Faculty of Dentistry, Al-Ahliyya Amman University, Amman 19111, Jordan; (T.M.M.A.); (L.S.A.L.); (S.A.K.)
- Department of Anatomy and Embryology, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Gabrielle Bangay
- CBIOS—Lusófona University’s Research Center for Biosciences and Health Technologies, 1749-024 Lisbon, Portugal;
- Universidad de Alcalá de Henares. Facultad de Farmacia, Departamento de Ciencias Biomédicas (Área de Farmacología; Nuevos agentes antitumorales, Acción tóxica sobre células leucémicas), Ctra. Madrid-Barcelona km. 33,600, 28805 Alcalá de Henares, Madrid, España
| | - Majid Mohammed Al-Sawahli
- Department of Pharmaceutics, College of Pharmacy, The Islamic University, Najaf 54001, Iraq;
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Kafr Elsheikh University, Kafr Elsheikh 33516, Egypt
| | - Marina K. Fouad
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
| | - Mohammad A. Zoair
- Department of Physiology, Faculty of Medicine, Al-Azhar University, Cairo 11884, Egypt;
| | - Tamer I. Abdalrhman
- Department of Histology, Faculty of Medicine, Al-Azhar University, Assiut 71524, Egypt;
| | - Dalia Elebeedy
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
| | - Ibrahim A. Ibrahim
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt;
| | - Aly F. Mohamed
- Holding Company for Vaccine and Sera Production (VACSERA), Giza 22311, Egypt;
| | - Ahmed I. Abd El Maksoud
- College of Biotechnology, Misr University of Science and Technology, Giza 12573, Egypt; (M.K.F.); (D.E.); (A.I.A.E.M.)
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat 32897, Egypt
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Rathod S, Dey S, Choudhari P, Mahuli D, Rochlani S, Dhavale R, Chaudhari S, Tamboli Y, Kilbile J, Rajakumara E. High-throughput computational screening for identification of potential hits against bacterial Acriflavine resistance protein B (AcrB) efflux pump. J Biomol Struct Dyn 2024:1-17. [PMID: 38264919 DOI: 10.1080/07391102.2024.2302936] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Antibiotic resistance is a pressing global health challenge, driven in part by the remarkable efflux capabilities of efflux pump in AcrB (Acriflavine Resistance Protein B) protein in Gram-negative bacteria. In this study, a multi-approached computational screening strategy encompassing molecular docking, In silico absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis, druglikeness assessment, molecular dynamics simulations and density functional theory studies was employed to identify novel hits capable of acting against AcrB-mediated antibiotic resistance. Ligand library was acquired from the COCONUT database. Performed computational analyses unveiled four promising hit molecules (CNP0298667, CNP0399927, CNP0321542 and CNP0269513). Notably, CNP0298667 exhibited the highest negative binding affinity of -11.5 kcal/mol, indicating a possibility of strong potential to disrupt AcrB function. Importantly, all four hits met stringent druglikeness criteria and demonstrated favorable in silico ADMET profiles, underscoring their potential for further development. MD simulations over 100 ns revealed that the CNP0321542-4DX5 and CNP0269513-4DX5 complexes formed robust and stable interactions with the AcrB efflux pump. The identified hits represent a promising starting point for the design and optimization of novel therapeutics aimed at combating AcrB-mediated antibiotic resistance in Gram-negative bacteria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sreenath Dey
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Sangareddy, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Sneha Rochlani
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, India
| | - Somdatta Chaudhari
- Department of Pharmaceutical Chemistry, Progressive Education Society's Modern College of Pharmacy, Nigdi, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Jaydeo Kilbile
- University Department of Basic and Applied Sciences (Chemistry), MGM University, Aurangabad, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Sangareddy, India
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50
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Simanjuntak MV, Jauhar MM, Syaifie PH, Arda AG, Mardliyati E, Shalannanda W, Hermanto BR, Anshori I. Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches. Bioinform Biol Insights 2024; 18:11779322231224187. [PMID: 38274992 PMCID: PMC10809879 DOI: 10.1177/11779322231224187] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Breast cancer is the most commonly diagnosed cancer globally, with the highest incidence of breast cancer occurring in Asian countries including Indonesia. Among the types of breast cancer, the estrogen receptor (ER)-positive subtype which is prominent with estrogen receptor alpha (ERα) and heat shock protein 90 (HSP90) overexpression genes becomes the most prevalent than the others, approximately 75% of all breast cancer cases. ERα and HSP90 play a role in breast cancer activities including breast tumor growth, invasion, and metastasis mechanism. Propolis, a natural bee product, has been explored for its anticancer activity. However, there is lack of studies that evaluated the potential inhibitor from propolis compounds to the ERα and HSP90 proteins. Therefore, this article focuses on examining the correlation between ERα and HSP90's role in breast cancer and investigating the potential of 93 unique propolis compositions in inhibiting these genes in breast cancer using in silico approaches. This study revealed the positive correlation between ERα and HSP90 genes in breast cancer disease development. Furthermore, we also found novel potential bioactive compounds of propolis against breast cancer through binding with ERα and HSP90; they were 3',4',7-trihydroxyisoflavone and baicalein-7-O-β-D glucopyranoside, respectively. Further research on these compounds is needed to elucidate deeper mechanisms and activity in the real biological system to develop new breast cancer drug treatments.
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Affiliation(s)
- Masriana Vivi Simanjuntak
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Muhammad Miftah Jauhar
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Biomedical Engineering, The Graduate School of Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Adzani Gaisani Arda
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wervyan Shalannanda
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Beni Rio Hermanto
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Isa Anshori
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
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