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 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.

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 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 Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rareEGFRmutations

2019 ◽  
Vol 116 (20) ◽  
pp. 10025-10030 ◽  
Author(s):  
Shinnosuke Ikemura ◽  
Hiroyuki Yasuda ◽  
Shingo Matsumoto ◽  
Mayumi Kamada ◽  
Junko Hamamoto ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Kinase Inhibitors ◽  
Dynamics Simulation ◽  
Cell Lung Carcinoma ◽  
Variants Of Unknown Significance ◽  
Mutational Hotspots

Next generation sequencing (NGS)-based tumor profiling identified an overwhelming number of uncharacterized somatic mutations, also known as variants of unknown significance (VUS). The therapeutic significance ofEGFRmutations outside mutational hotspots, consisting of >50 types, in nonsmall cell lung carcinoma (NSCLC) is largely unknown. In fact, our pan-nation screening of NSCLC without hotspotEGFRmutations (n= 3,779) revealed that the majority (>90%) of cases with rareEGFRmutations, accounting for 5.5% of the cohort subjects, did not receive EGFR-tyrosine kinase inhibitors (TKIs) as a first-line treatment. To tackle this problem, we applied a molecular dynamics simulation-based model to predict the sensitivity of rare EGFR mutants to EGFR-TKIs. The model successfully predicted the diverse in vitro and in vivo sensitivities of exon 20 insertion mutants, including a singleton, to osimertinib, a third-generation EGFR-TKI (R2= 0.72,P= 0.0037). Additionally, our model showed a higher consistency with experimentally obtained sensitivity data than other prediction approaches, indicating its robustness in analyzing complex cancer mutations. Thus, the in silico prediction model will be a powerful tool in precision medicine for NSCLC patients carrying rareEGFRmutations in the clinical setting. Here, we propose an insight to overcome mutation diversity in lung cancer.

Exploring the Molecular Mechanisms of 17β-HSD5-induced Carcinogenicity of Catha Edulis via Molecular Modeling Approach.

2020 ◽  
Vol 16 ◽  
Author(s):  
Maria Saeed ◽  
Sajda Ashraf ◽  
Rashad Alsanosi ◽  
Hassan A. Alhazmi ◽  
Mohammed AlBratty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Dynamics Simulation ◽  
Catha Edulis ◽  
Khat Chewing ◽  
First Time

Background: The tradition of khat chewing has been deep-rooted in the African and Arabian Peninsula for centuries. Due to its amphetamine-like psycho-stimulant or euphoric effect, Khat has been used by millions in Somalia, Ethiopia, Saudi Arabia and Yemen. The long-term use of Khat can induce tremendous health outcomes, which may be serious and irreversible. Objective: Prolong use of Khat constituents has been associated with different types of cancers such as prostatic, breast and ovarian cancer. However, it has been very difficult to identify the molecular targets involved in Khat carcinogenesis that interact with the Khat constituents by in vitro/in vivo experimental tools. Method: In silico tools to predict potential targets involved in the carcinogenesis of Khat. Pass on-line prediction server was used for the prediction of a potential molecular target for Khat constituents. Molecular Dynamics simulation and MMGBSA calculation of the predicted target. Results: Molecular Dynamics simulation and MM-GBSA calculation. Results revealed that among Khat constituents βSitosterol showed high binding affinity towards 17β-HSD5. On the other hand, this study highlights for the first time, some new interactions, which were observed in the case of cathine, cathinone and nerol during the simulation. Conclusion: In silico molecular dynamic simulation tools were used for the first time to investigate the molecular mechanism of widely used leaves of psychoactive Khat (Catha edulis) constituent, which is used extensively all over the world. The present study provides deep insight to understand the effect of Khat constituents involve in the impairment of reproductive system and its binding to 17β-HSD5. ADMET profiling also suggested that few Khat constituents do not fulfill the requirements of Lipinski rule of five i.e. poor absorption and blood-brain barrier impermeability.

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