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Pitsillou E, Beh RC, Liang JJ, Tang TS, Zhou X, Siow YY, Ma Y, Hu Z, Wu Z, Hung A, Karagiannis TC. EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals. J Mol Graph Model 2023; 125:108602. [PMID: 37597309 DOI: 10.1016/j.jmgm.2023.108602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Thinh Sieu Tang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Xun Zhou
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Yun Siow
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yinghao Ma
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifang Hu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifei Wu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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2
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Archana VP, Armaković SJ, Armaković S, Celik I, Bhagyasree J, Dinesh Babu K, Rudrapal M, Divya IS, Pillai RR. Exploring the structural, photophysical and optoelectronic properties of a diaryl heptanoid curcumin derivative and identification as a SARS-CoV-2 inhibitor. J Mol Struct 2023; 1281:135110. [PMID: 36785704 PMCID: PMC9910092 DOI: 10.1016/j.molstruc.2023.135110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Developing modifiable natural products those having antiviral activities against SARS-CoV-2 is a key research area which is popular in current scenario of COVID pandemic. A diaryl heptanoid curcumin and its derivatives are already presenting promising candidates for anti-viral drug development. We have synthesized single crystals of a dimethylamino derivative of natural curcumin and structural characterization was done by single crystal XRD analysis. Using steady-state absorption and emission spectra and guided by complimentary ab initio calculations, we unraveled the solvent effects on the photophysical properties of the dimethyl amino curcumin derivative. Chemical reactivity of the compound has investigated using frontier molecular orbitals and molecular electrostatic potential surface. High stability of the curcumin derivative in water environment has evaluated by Radial Distributions Functions (RDF) calculated via Molecular Dynamics (MD) simulations. The inhibitory activity of the title compound was evaluated by in silico methods and the stability of the protein-ligand complexes were studied using Molecular Dynamics simulations and MM-PBSA analysis. With this detailed study, we hope to motivate scientific community to develop new curcumin derivatives against SARS-CoV-2 virus.
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Affiliation(s)
- Vikaraman P. Archana
- Department of Polymer Chemistry, Government College, Attingal, University of Kerala, Thiruvananthapuram, Kerala, India,Department of Chemistry, Government College for Women, University of Kerala, Vazhuthacaud, Thiruvananthapuram, Kerala, India
| | - Sanja J. Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - J.B. Bhagyasree
- Department of Polymer Chemistry, Government College, Attingal, University of Kerala, Thiruvananthapuram, Kerala, India
| | - K.V. Dinesh Babu
- Department of Chemistry, Government College for Women, University of Kerala, Vazhuthacaud, Thiruvananthapuram, Kerala, India
| | - Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology & Pharmaceutical Sciences, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur-522213, India
| | - Indira S. Divya
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
| | - Renjith Raveendran Pillai
- Department of Physics, University College, University of Kerala, Thiruvananthapuram, Kerala, India,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia,Corresponding author
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3
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Shukla R, Chandra A, Kumar A, Kandpal P, Avashthi H, Goel VK, Qamar I, Singh N, Kelvin DJ, Singh TR. Repurposing of drugs against methyltransferase as potential Zika virus therapies. Sci Rep 2023; 13:7870. [PMID: 37188743 PMCID: PMC10184974 DOI: 10.1038/s41598-023-33341-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
In recent years, the outbreak of infectious disease caused by Zika Virus (ZIKV) has posed a major threat to global public health, calling for the development of therapeutics to treat ZIKV disease. Several possible druggable targets involved in virus replication have been identified. In search of additional potential inhibitors, we screened 2895 FDA-approved compounds using Non-Structural Protein 5 (NS5) as a target utilizing virtual screening of in-silco methods. The top 28 compounds with the threshold of binding energy -7.2 kcal/mol value were selected and were cross-docked on the three-dimensional structure of NS5 using AutoDock Tools. Of the 2895 compounds screened, five compounds (Ceforanide, Squanavir, Amcinonide, Cefpiramide, and Olmesartan_Medoxomil) ranked highest based on filtering of having the least negative interactions with the NS5 and were selected for Molecular Dynamic Simulations (MDS) studies. Various parameters such as RMSD, RMSF, Rg, SASA, PCA and binding free energy were calculated to validate the binding of compounds to the target, ZIKV-NS5. The binding free energy was found to be -114.53, -182.01, -168.19, -91.16, -122.56, and -150.65 kJ mol-1 for NS5-SFG, NS5-Ceforanide, NS5-Squanavir, NS5-Amcinonide, NS5-Cefpiramide, and NS5-Ol_Me complexes respectively. The binding energy calculations suggested Cefpiramide and Olmesartan_Medoxomil (Ol_Me) as the most stable compounds for binding to NS5, indicating a strong rationale for their use as lead compounds for development of ZIKV inhibitors. As these drugs have been evaluated on pharmacokinetics and pharmacodynamics parameters only, in vitro and in vivo testing and their impact on Zika viral cell culture may suggest their clinical trials on ZIKV patients.
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Affiliation(s)
- Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anuj Kumar
- Laboratory of Immunity, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada
- European Virus Bioinformatics Center, Leutragraben 1, Jena, Germany
| | | | - Himanshu Avashthi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | - Vijay Kumar Goel
- School of Physical Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Gautam Buddh Nagar, Greater Noida, Uttar Pradesh, 201312, India.
| | - David J Kelvin
- Laboratory of Immunity, Shantou University Medical College, Shantou, China.
- Department of Microbiology and Immunology, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
- Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Faculty of Medicine, Dalhousie University, Halifax, Canada.
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
- Centre for Excellence in Healthcare Technologies and Informatics (CEHTI), Jaypee University of Information Technology (JUIT), Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Habibi A, Farhadian S, Shareghi B, Hashemi-Shahraki F. Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods. Spectrochim Acta A Mol Biomol Spectrosc 2023; 291:122264. [PMID: 36652806 DOI: 10.1016/j.saa.2022.122264] [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] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.
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Affiliation(s)
- Atefeh Habibi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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Correa JDS, Primo JDO, Balaba N, Pratsch C, Werner S, Toma HE, Anaissi FJ, Wattiez R, Zanette CM, Onderwater RCA, Bittencourt C. Copper(II) and Cobalt(II) Complexes Based on Abietate Ligands from Pinus Resin: Synthesis, Characterization and Their Antibacterial and Antiviral Activity against SARS-CoV-2. Nanomaterials (Basel) 2023; 13:1202. [PMID: 37049296 PMCID: PMC10096983 DOI: 10.3390/nano13071202] [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] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Co-abietate and Cu-abietate complexes were obtained by a low-cost and eco-friendly route. The synthesis process used Pinus elliottii resin and an aqueous solution of CuSO4/CoSO4 at a mild temperature (80 °C) without organic solvents. The obtained complexes are functional pigments for commercial architectural paints with antipathogenic activity. The pigments were characterized by Fourier-transform infrared spectroscopy (FTIR), mass spectrometry (MS), thermogravimetry (TG), near-edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and colorimetric analysis. In addition, the antibacterial efficiency was evaluated using the minimum inhibitory concentration (MIC) test, and the antiviral tests followed an adaptation of the ISO 21702:2019 guideline. Finally, virus inactivation was measured using the RT-PCR protocol using 10% (w/w) of abietate complex in commercial white paint. The Co-abietate and Cu-abietate showed inactivation of >4 log against SARS-CoV-2 and a MIC value of 4.50 µg·mL-1 against both bacteria Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). The results suggest that the obtained Co-abietate and Cu-abietate complexes could be applied as pigments in architectural paints for healthcare centers, homes, and public places.
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Affiliation(s)
- Jamille de S. Correa
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Julia de O. Primo
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Nayara Balaba
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Christoph Pratsch
- Department X-ray Microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Stephan Werner
- Department X-ray Microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Henrique E. Toma
- Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Fauze J. Anaissi
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Ruddy Wattiez
- Department of Chemistry, University of Mons, Place du Parc 23, 7000 Mons, Belgium;
| | - Cristina M. Zanette
- Department of Food Engineering, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | | | - Carla Bittencourt
- Department of Chemistry, University of Mons, Place du Parc 23, 7000 Mons, Belgium;
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Hashemi-Shahraki F, Shareghi B, Farhadian S, Yadollahi E. A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods. Spectrochim Acta A Mol Biomol Spectrosc 2023; 289:122240. [PMID: 36527971 DOI: 10.1016/j.saa.2022.122240] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.
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Affiliation(s)
- Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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Dehkordi MF, Farhadian S, Hashemi-Shahraki F, Rahmani B, Darzi S, Dehghan G. The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study. Int J Biol Macromol 2023; 235:123713. [PMID: 36801300 DOI: 10.1016/j.ijbiomac.2023.123713] [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: 09/26/2022] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.
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Affiliation(s)
- Mahvash Farajzadeh Dehkordi
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Babak Rahmani
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
| | - Sina Darzi
- Health Products Safety Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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Silva do Nascimento D, Etcheverry M, Orduz AE, Waiman CV, Zanini GP. Adsorption of cationic surfactant as a probe of the montmorillonite surface reactivity in the alginate hydrogel composites. RSC Adv 2022; 12:35469-35476. [PMID: 36540257 PMCID: PMC9742988 DOI: 10.1039/d2ra07405b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2024] Open
Abstract
Adsorption of a cationic surfactant allowed to probe the surface reactivity of montmorillonite encapsulated in a composite of alginate hydrogels (A-MMT). Dodecylbenzyldimethylammonium chloride (BAC-12) was the surfactant used for these studies. BAC-12 is part of the widely used surfactant mixture known as benzalkonium chloride. XRD showed that up to three different types of basal spacing (d 001) were present within the composite indicating that as the concentration of adsorbed BAC-12 increases, populations with different adsorption conformational arrangements are present, even unexpanded clay remains. From the SEM-EDS spectra it is observed that the clay is distributed in the whole composite. In addition, the effect of the presence of cationic and anionic biocides on BAC-12 adsorption was studied. Cationic biocides such as tetradecyllbenzyldimethylammonium chlorides (BAC-14) and paraquat (PQ) show a competitive behavior for the clay adsorption sites at BAC-12 low concentration indicating an electrostatic adsorption mechanism. However, the presence of anionic contaminants such as 2,4-D and metsulfuron methyl do not affect surfactant adsorption. In all scenarios is observed an abrupt increase of BAC-12 adsorbed amount reaching values higher than the clay CEC suggesting strong tail-tail interactions. This occurs at concentrations 10 times lower than the CMC of BAC-12 promoted by clay encapsulation in the composite. In these composites the alginate does not affect the surface reactivity of the clay, but the formation of the hydrogel allows it to be easily extracted from aqueous media which makes it an interesting material with a potential use in water remediation.
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Affiliation(s)
- Danielle Silva do Nascimento
- INQUISUR (UNS-CONICET), Departamento de Química, Universidad Nacional del Sur Av. Alem 1253 B8000CPB-Bahía Blanca Argentina
| | - Mariana Etcheverry
- INQUISUR (UNS-CONICET), Departamento de Química, Universidad Nacional del Sur Av. Alem 1253 B8000CPB-Bahía Blanca Argentina
| | - Angie E Orduz
- INQUISUR (UNS-CONICET), Departamento de Química, Universidad Nacional del Sur Av. Alem 1253 B8000CPB-Bahía Blanca Argentina
| | - Carolina V Waiman
- INQUISUR (UNS-CONICET), Departamento de Química, Universidad Nacional del Sur Av. Alem 1253 B8000CPB-Bahía Blanca Argentina
| | - Graciela P Zanini
- INQUISUR (UNS-CONICET), Departamento de Química, Universidad Nacional del Sur Av. Alem 1253 B8000CPB-Bahía Blanca Argentina
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Aramyan S, McGregor K, Sandeep S, Haczku A. SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK. Front Immunol 2022; 13:945317. [PMID: 36189278 PMCID: PMC9519185 DOI: 10.3389/fimmu.2022.945317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022] Open
Abstract
The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.
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Affiliation(s)
- Sona Aramyan
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
| | - Kirk McGregor
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
| | - Samarth Sandeep
- If and Only If (Iff) Technologies, Pleasanton, CA, United States
- *Correspondence: Samarth Sandeep, ; Angela Haczku,
| | - Angela Haczku
- University of California (UC) Davis Lung Center Pulmonary, Critical Care and Sleep Division, Department of Medicine, School of Medicine, University of California, Davis, CA, United States
- *Correspondence: Samarth Sandeep, ; Angela Haczku,
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