Estimation of a stronger heparin binding locus in fibronectin domain III<sup>14</sup>using thermodynamics and molecular dynamics

Gupta, Sakshi; Tiwari, Neha; Verma, Jyoti; Waseem, Mohammad; Subbarao, Naidu; Munde, Manoj

doi:10.1039/d0ra01773f

Cited by 10 publications

(8 citation statements)

References 53 publications

(75 reference statements)

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“…The equilibrium setup of the system (protease–bromelain complex) was required and it was completed, followed by two-step ensembles NVT (constant number of particles, pressure, and temperature) and NPT (constant number of particles, pressure, and t emperature). Both ensembles provide control over temperature, pressure coupling, resulting constancy, and stabilization of the system through complete simulation [ 25 ]. GORMACS contain several packages, for protease–bromelain complex MDS analysis, we used gmx rms for Root Mean Square Deviation (RMSD) [ 26 ], gmx rmsf for Root Mean Square fluctuation (RMSF), gmx gyrate for the calculation of Radius of Gyration (Rg) [ 22 , 27 ], and gmx hbond for the calculation of numbers of hydrogen-bond formed during interaction.…”

Section: Methodsmentioning

confidence: 99%

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

et al. 2022

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Natural resources, particularly plants and microbes, are an excellent source of bioactive molecules. Bromelain, a complex enzyme mixture found in pineapples, has numerous pharmacological applications. In a search for therapeutic molecules, we conducted an in silico study on natural phyto-constituent bromelain, targeting pathogenic bacteria and viral proteases. Docking studies revealed that bromelain strongly bound to food-borne bacterial pathogens and SARS-CoV-2 virus targets, with a high binding energy of −9.37 kcal/mol. The binding interaction was mediated by the involvement of hydrogen bonds, and some hydrophobic interactions stabilized the complex and molecular dynamics. Simulation studies also indicated the stable binding between bromelain and SARS-CoV-2 protease as well as with bacterial targets which are essential for DNA and protein synthesis and are required to maintain the integrity of membranous proteins. From this in silico study, it is also concluded that bromelain could be an effective molecule to control foodborne pathogen toxicity and COVID-19. So, eating pineapple during an infection could help to interfere with the pathogen attaching and help prevent the virus from getting into the host cell. Further, research on the bromelain molecule could be helpful for the management of COVID-19 disease as well as other bacterial-mediated diseases. Thus, the antibacterial and anti-SARS-CoV-2 virus inhibitory potentials of bromelain could be helpful in the management of viral infections and subsequent bacterial infections in COVID-19 patients.

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Section: Methodsmentioning

confidence: 99%

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

et al. 2022

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“…It was followed by two-step ensembles NVT (constant number of particles, pressure, and temperature) and NPT (constant number of particles, pressure, and temperature). Both ensembles control temperature and pressure coupling resulting in constancy and system stabilization through complete simulation [ 33 ]. GROMACS has many different scripts for complexes MDS analysis and was utilized gmx rms for Root Mean Square Deviation (RMSD) [ 34 ], gmx rmsf for Root Mean Square fluctuation (RMSF), gmx gyrate for the calculation of Radius of Gyration (Rg) [ 35 ] and gmx H bond for the calculation of numbers of hydrogen-bond (H bond) formed during the interaction.…”

Section: Methodsmentioning

confidence: 99%

Bio-Computational Evaluation of Compounds of Bacopa Monnieri as a Potential Treatment for Schizophrenia

Alharbi

2022

Molecules

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Schizophrenia is a horrible mental disorder characterized by distorted perceptions of reality. Investigations have not identified a single etiology for schizophrenia, and there are multiple hypotheses based on various aspects of the disease. There is no specific treatment for schizophrenia. Hence, we have tried to investigate the updated information stored in the genetic databases related to genes that could be responsible for schizophrenia and other related neuronal disorders. After implementing combined computational methodology, such as protein-protein interaction analysis led by system biology approach, in silico docking analysis was performed to explore the 3D binding pattern of Bacopa monnieri natural compounds while interacting with STXBP1. The best-identified compound was CID:5319292 based on −10.3 kcal/mol binding energy. Further, selected complexes were dynamically evaluated by MDS methods, and the output reveals that the STXBP1-CID:5281800 complex showed the lowest RMSD value, i.e., between 0.3 and 0.4 nm. Hence, identified compounds could be used to develop and treat neuronal disorders after in vivo/in vitro testing.

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“…Equilibrium setup for the (Doxo–protease complex) system was essential and done followed by two-step ensembles NVT (constant n umber of particles, v olume, and t emperature) and NPT (constant n umber of particles, p ressure, t emperature). Both ensembles provide control over temperature, pressure coupling resulting in constancy and stabilization of the system through complete simulation (Gupta et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of doxorubicin as a potential therapeutic against SARS-CoV-2 (COVID-19) protease: a molecular docking and dynamics simulation studies

Jamal

Alharbi

Ahmad

2021

Journal of Biomolecular Structure and Dynamics

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After one year, the COVID-19 pandemic caused by SARS-CoV-2 is still the largest concern for the scientific community. Of the many recognized drug targets of SARS-CoV-2, the main protease is one of the most important target due to its function in viral replication. We conducted an in silico study with repurposing drugs of antibiotics class against virus protease and peptidase using AutoDock tool. The following significant binding energy interaction was observed with protease (PDB: 6LU7) like piperacillin –7.25; tobramycin –9.20 and doxorubicin (Doxo) –10.04 kcal/mol and with peptidase (PDB: 2GTB) piperacillin –7.08; tobramycin –8.54 and Doxo –9.89 kcal/mol. Furthermore, the interaction and stability behavior of the Doxo–protease and Doxo–peptidase complexes were analyzed for a 100-nanosecond (ns) time. Calculated RMSD values observed using molecular dynamics simulation (MDS) were found to be 0.15–0.25 nm, RMSF calculation per residues showed a value near 0.2 nm and R g values remained approximately 2.25 nm. MM-PBSA analysis of total binding energy calculation of Doxo–protease and Doxo–peptidase complexes are found to be –148.692 and –105.367 kJ/mol, respectively. Moreover, amino acid residue ASP-197 showed the lowest contribution binding energy i.e. –18.1185 kJ/mol, and amino acid residue ASP-187 showed –17.0267 kJ/mol contribution energy. Thus, significant docking interaction and stable dynamicity of Doxo–protease complex with time was suggested that Doxo could be a choice to inhibit potentially the viral proteases that could prevent the entry inside the host cell to control the COVID-19 disease. Communicated by Ramaswamy H. Sarma

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Estimation of a stronger heparin binding locus in fibronectin domain III¹⁴using thermodynamics and molecular dynamics

Abstract: Binding Thermodynamics of FHIP I and FHIP II with heparin.

Cited by 10 publications

References 53 publications

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Bio-Computational Evaluation of Compounds of Bacopa Monnieri as a Potential Treatment for Schizophrenia

Identification of doxorubicin as a potential therapeutic against SARS-CoV-2 (COVID-19) protease: a molecular docking and dynamics simulation studies

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Estimation of a stronger heparin binding locus in fibronectin domain III14using thermodynamics and molecular dynamics

Abstract: Binding Thermodynamics of FHIP I and FHIP II with heparin.

Cited by 10 publications

References 53 publications

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Bio-Computational Evaluation of Compounds of Bacopa Monnieri as a Potential Treatment for Schizophrenia

Identification of doxorubicin as a potential therapeutic against SARS-CoV-2 (COVID-19) protease: a molecular docking and dynamics simulation studies

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Estimation of a stronger heparin binding locus in fibronectin domain III¹⁴using thermodynamics and molecular dynamics