scholarly journals Molecular Dynamics Simulation of the E.coli FtsZ

2018 ◽  
Author(s):  
Vidyalakshmi C Muthukumar
Keyword(s):  
Molecular Dynamics ◽  
Crystal Structures ◽  
Dynamics Simulation ◽  
Small Shift ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Central Helix ◽  
Ftsz Assembly

AbstractPrevious molecular dynamics studies of the FtsZ protein revealed that the protein has high intrinsic flexibility which the crystal structures were unable to reveal. The initial configuration in these studies was based on the available crystal structure data and therefore, the effect of the C-terminal Intrinsically Disordered Region (IDR) of FtsZ could not be observed in these previous studies. Recent investigations have revealed that the C-terminal IDR is crucial for FtsZ assembly in vitro and Z ring formation in vivo. Therefore, in this study, we simulate FtsZ with the IDR.Simulations of the FtsZ monomer in different nucleotide bound forms (without nucleotide, GTP, GDP) were performed. In the conformations of FtsZ monomer with GTP, GTP binds variably with the protein. Such variable interaction with the monomer has not been observed in any previous simulation studies of FtsZ and not observed in crystal structures. The central helix bends towards the C-terminal domain in the GTP bound form, thus making way for polymerization. Nucleotide dependent small shift/rotation of the C-terminal domain was observed in average structures.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

scholarly journals Exploring Aurone Derivatives as Potential Human Pancreatic Lipase Inhibitors through Molecular Docking and Molecular Dynamics Simulations

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4657
Author(s):  
Phuong Thuy Viet Nguyen ◽  
Han Ai Huynh ◽  
Dat Van Truong ◽  
Thanh-Dao Tran ◽  
Cam-Van Thi Vo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Pancreatic Lipase ◽  
Inhibitory Activity ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Catalytic Active Site ◽  
Dynamics Simulations

Inhibition of human pancreatic lipase, a crucial enzyme in dietary fat digestion and absorption, is a potent therapeutic approach for obesity treatment. In this study, human pancreatic lipase inhibitory activity of aurone derivatives was explored by molecular modeling approaches. The target protein was human pancreatic lipase (PDB ID: 1LPB). The 3D structures of 82 published bioactive aurone derivatives were docked successfully into the protein catalytic active site, using AutoDock Vina 1.5.7.rc1. Of them, 62 compounds interacted with the key residues of catalytic trial Ser152-Asp176-His263. The top hit compound (A14), with a docking score of −10.6 kcal⋅mol−1, was subsequently submitted to molecular dynamics simulations, using GROMACS 2018.01. Molecular dynamics simulation results showed that A14 formed a stable complex with 1LPB protein via hydrogen bonds with important residues in regulating enzyme activity (Ser152 and Phe77). Compound A14 showed high potency for further studies, such as the synthesis, in vitro and in vivo tests for pancreatic lipase inhibitory activity.

scholarly journals In silico identification of novel chemical compounds with anti-TB potential for the inhibition of InhA and EthR from Mycobacterium tuberculosis

2020 ◽  
Author(s):  
Sajal Kumar Halder ◽  
Fatiha Elma
Keyword(s):  
Molecular Dynamics ◽  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Chemical Compounds ◽  
Dynamics Simulation ◽  
Health Concern ◽  
Radius Of Gyration

ABSTRACTTuberculosis (TB) continuously pose a major public health concern around the globe, with a mounting death toll of approximately 1.4 million in 2019. The reduced bioavailability, increased toxicity and resistance of several first-line and second-line anti-TB drugs such as isoniazid, ethionamide have necessitated the search for new medications. In this research, we have identified several novel chemical compounds with anti-TB properties using various computational tools like molecular docking analysis, drug-likeness evaluation, ADMET profiling, P450 site of metabolism prediction and molecular dynamics simulation study. This study involves fifty drug-like compounds with antibacterial activity that inhibit InhA and EthR involved in the synthesis of one of the major lipid components, mycolic acid, which is crucial for the viability of Mycobacterium tuberculosis. Among these fifty compounds, 3-[3-(4-Fluorophenyl)-1,2,4-oxadiazol-5-yl]-N-(2-methylphenyl) piperidine-1-carboxamide (C22) and 5-(4-Ethyl-phenyl)-2-(1H-tetrazol-5-ylmethyl)-2H-tetrazole (C29) were found to pass the two-step molecular docking, P450 site of metabolism prediction and pharmacokinetics filtering analysis successfully. Their binding stability for target proteins have been evaluated through RMSD, RMSF, Radius of gyration analysis from 10 ns Molecular Dynamics Simulation (MDS) run. Our identified drugs could be a capable therapeutic for Tuberculosis drug discovery, having said that more in vitro and in vivo testing is required to justify their potential as novel drug and mode of action.

scholarly journals Molecular docking and molecular dynamics simulation study of inositol phosphorylceramide synthase – inhibitor complex in leishmaniasis: Insight into the structure based drug design

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1610 ◽  
Author(s):  
Vineetha Mandlik ◽  
Shailza Singh
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Simulation ◽  
Sphingolipid Metabolism ◽  
Drug Candidate ◽  
Binding Modes ◽  
Structure Based Drug Design ◽  
Starting Point ◽  
Synthase Inhibitor

Inositol phosphorylceramide synthase (IPCS) has emerged as an important, interesting and attractive target in the sphingolipid metabolism of Leishmania. IPCS catalyzes the conversion of ceramide to IPC which forms the most predominant sphingolipid in Leishmania. IPCS has no mammalian equivalent and also plays an important role in maintaining the infectivity and viability of the parasite. The present study explores the possibility of targeting IPCS; development of suitable inhibitors for the same would serve as a treatment strategy for the infectious disease leishmaniasis. Five coumarin derivatives were developed as inhibitors of IPCS protein. Molecular dynamics simulations of the complexes of IPCS with these inhibitors were performed which provided insights into the binding modes of the inhibitors. In vitro screening of the top three compounds has resulted in the identification of one of the compounds (compound 3) which shows little cytotoxic effects. This compound therefore represents a good starting point for further in vivo experimentation and could possibly serve as an important drug candidate for the treatment of leishmaniasis.

Heparin-reduced graphene oxide nanocomposites for curcumin delivery: in vitro, in vivo and molecular dynamics simulation study

2019 ◽  
Vol 7 (3) ◽  
pp. 1011-1027 ◽  
Author(s):  
Xiaoqun Shi ◽  
Yang Wang ◽  
Haiyan Sun ◽  
Yujuan Chen ◽  
Xingzhen Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphene Oxide ◽  
Molecular Dynamics Simulation ◽  
Reduced Graphene Oxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Reduced Graphene

We fabricated novel rGO-based nanocomposites and analyzed their interaction with drug and proteins via a molecular dynamics study.

scholarly journals Molecular Dynamics simulation of the E.coli FtsZ dimer

2018 ◽  
Author(s):  
Vidyalakshmi C Muthukumar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Homology Modelling ◽  
Initial Configuration ◽  
Dynamics Simulation ◽  
Initial Structure ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Intrinsically Disordered Region

AbstractFtsZ dimer was studied to gain insights into FtsZ protofilament formation. In a previous simulation study of the M.janaschii dimer it was found that the monomer-monomer contacts in the GDP bound dimer is lower which results in the high curvature of the GDP bound protofilaments. In this study, we have simulated the E.coli FtsZ dimer. The initial structure was obtained from our previous study in which we had simulated the E.coli FtsZ monomer with its C-terminal IDR (Intrinsically Disordered region) built by homology modelling. The M.janaschii FtsZ dimer subunit contacts were used in the initial configuration. Simulations of the dimer were performed with GTP, GDP and ATP. We observed that the C-terminal domain rotates considerably during dimerization. We also observed the different dynamics of the GTP, GDP and ATP bound dimers due to which assembly into straight protofilaments is favoured only in the presence of GTP.

scholarly journals An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Pankaj Jain ◽  
Amit Joshi ◽  
Nahid Akhtar ◽  
Sunil Krishnan ◽  
Vikas Kaushik
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Docking ◽  
In Silico ◽  
Cell Epitope ◽  
Cost Effective ◽  
Dynamics Simulation ◽  
Cloning And Expression

Abstract Background Canine circovirus is a deadly pathogen of dogs and causes vasculitis and hemorrhagic enteritis. It causes lethal gastroenteritis in pigs, fox, and dogs. Canine circovirus genome contains two main (and opposite) transcription units which encode two open reading frames (ORFs), a replicase-associated protein (Rep) and the capsid (Cap) protein. The replicase protein and capsid protein consist of 303 amino acids and 270 amino acids respectively. Several immuno-informatics methods such as epitope screening, molecular docking, and molecular-dynamics simulations were used to craft peptide-based vaccine construct against canine circovirus. Results The vaccine construct was designed by joining the selected epitopes with adjuvants by suitable linker. The cloning and expression of the vaccine construct was also performed using in silico methods. Screening of epitopes was conducted by NetMHC server that uses ANN (Artificial neural networking) algorithm. These methods are fast and cost-effective for screening epitopes that can interact with dog leukocyte antigens (DLA) and initiate an immune response. Overall, 5 epitopes, YQHLPPFRF, YIRAKWINW, ALYRRLTLI, HLQGFVNLK, and GTMNFVARR, were selected and used to design a vaccine construct. The molecular docking and molecular dynamics simulation studies show that these epitopes can bind with DLA molecules with stability. The codon adaptation and in silico cloning studies show that the vaccine can be expressed by Escherichia coli K12 strain. Conclusion The results suggest that the vaccine construct can be useful in preventing the dogs from canine circovirus infections. However, the results need further validation by performing other in vitro and in vivo experiments.

scholarly journals Immunoinformatics and molecular dynamics approaches: Next generation vaccine design against West Nile virus

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253393
Author(s):  
Md Tahsin Khan ◽  
Rahatul Islam ◽  
Tarhima Jahan Jerin ◽  
Araf Mahmud ◽  
Sahara Khatun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
West Nile Virus ◽  
Dynamics Simulation ◽  
West Nile ◽  
Strong Immune Response ◽  
Generation Vaccine ◽  
Life Threatening ◽  
Microbial System

West Nile Virus (WNV) is a life threatening flavivirus that causes significant morbidity and mortality worldwide. No preventive therapeutics including vaccines against WNV are available for human use. In this study, immunoinformatics approach was performed to design a multi epitope-based subunit vaccine against this deadly pathogen. Human (HLA) and Mice (H-2) allele specific potential T-cell and B-cell epitopes were shortlisted through a stringent procedure. Molecular docking showed selected epitopes that have stronger binding affinity with human TLR-4. Molecular dynamics simulation confirmed the stable nature of the docked complex. Furthermore, in silico cloning analysis ensures efficient expression of desired gene in the microbial system. Interestingly, previous studies showed that two of our selected epitopes have strong immune response against WNV. Therefore, selected epitopes could be strong vaccine candidates to prevent WNV infections in human. However, further in vitro and in vivo investigations could be strengthening the validation of the vaccine candidate against WNV.

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