scholarly journals Docking and Molecular Dynamic Simulations Study to Search Curcumin Analogue Compounds as Potential Inhibitor Against SARS-CoV-2: A Computational Approach

2021 ◽  
Vol 24 (3) ◽  
pp. 85-90
Author(s):  
Neni Frimayanti ◽  
Adel Zamri ◽  
Yum Eryanti ◽  
Noval Herfindo ◽  
Veza Azteria
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Computational Study ◽  
Binding Free Energy ◽  
Biological Activities ◽  
Positive Control ◽  
Curcumin Analog ◽  
Dynamic Simulations ◽  
Potential Inhibitor ◽  
Compounds Stability

Coronavirus is a pandemic in the world. It requires researchers and scientists to work hard to find a vaccine or drug to inhibit the development of the coronavirus. Many drugs have been used, such as remdesivir, lopinavir, and chloroquine. However, how effective is the use of these drugs for inhibiting the coronavirus’s growth? There is no research has been done. Curcumin is now known as one of the compounds that have some biological activities, and it is also can potentially be used as a CoV-2 inhibitor. The computational study, i.e., molecular docking and molecular dynamic, can help researchers to predict which compounds have the potential as an inhibitor against the CoV-2 coronavirus. In this study, lopinavir was used as a positive control. Lopinavir and 45 curcumin analog compounds were docked against the main protease protein with 6LU7 PDB ID. Based on the docking results, it was discovered that compound 1, compound 2, and compound 4 have the same binding orientation as lopinavir. Molecular dynamic simulation with the lowest binding free energy conformation was used to check these compounds’ stability. Only compound 4 was maintained to observe hydrogen bonding with Lys5 and Lys137 with a distance of 2.9 Å. The distance of hydrogen bonds and binding free energy over simulation time is essential to elucidate the potential compound’s affinity. For then, compound 4 can be used as a potential inhibitor against the CoV-2 coronavirus.

scholarly journals Structural and Energetic Affinity of Annocatacin B with ND1 Subunit of the Human Mitochondrial Respiratory Complex I as a Potential Inhibitor: An In Silico Comparison Study with the Known Inhibitor Rotenone

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1840
Author(s):  
Camilo Febres-Molina ◽  
Jorge A. Aguilar-Pineda ◽  
Pamela L. Gamero-Begazo ◽  
Haruna L. Barazorda-Ccahuana ◽  
Diego E. Valencia ◽  
...  
Keyword(s):  
Free Energy ◽  
In Silico ◽  
Complex I ◽  
Binding Free Energy ◽  
Biological Activities ◽  
Experimental Studies ◽  
Respiratory Complex ◽  
Mitochondrial Respiratory Complex ◽  
Respiratory Complex I ◽  
Mitochondrial Respiratory

ND1 subunit possesses the majority of the inhibitor binding domain of the human mitochondrial respiratory complex I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, that some metabolites from Annona muricata called acetogenins have important biological activities, such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine mitochondrial respiratory complex I by bis-tetrahydrofurans acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human mitochondrial respiratory complex I. In this work, we evaluate the in silico molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, quantum mechanical optimizations, molecular dynamics simulations and the molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known mitochondrial respiratory complex I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger binding free energy compared to the rotenone complex. Detailed analysis of the binding free energy shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of the mitochondrial respiratory complex I.

scholarly journals Unveiling the helicity switching mechanism of a rigid two-tiered stacked architecture

RSC Advances ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 1501-1508
Author(s):  
Peng Liu ◽  
Yafei Duan ◽  
Xihui Bian ◽  
Xiaoyao Tan
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Atomic Level ◽  
Free Energy Calculations ◽  
Switching Process ◽  
Molecular Dynamic Simulations ◽  
Conformational Switching ◽  
Dynamic Simulations ◽  
Energy Calculations ◽  
Switching Mechanism

The conformational switching process of a rigid two-tiered stacked architecture has been revealed at the atomic level with the aid of molecular dynamic simulations and free-energy calculations.

scholarly journals Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

RSC Advances ◽  
2018 ◽  
Vol 8 (61) ◽  
pp. 34867-34876 ◽  
Author(s):  
S. Tolosa ◽  
J. A. Sansón ◽  
A. Hidalgo
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Theoretical Study ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Cytosine Deamination ◽  
Energy Profiles ◽  
Free Energy Profiles ◽  
Hydrolytic Deamination ◽  
Smd Simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

scholarly journals Structure-Based Virtual Screening and Molecular Dynamic Simulation Studies to Identify Novel Cytochrome bc1 Inhibitors as Antimalarial Agents

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Rahul P. Gangwal ◽  
Gaurao V. Dhoke ◽  
Mangesh V. Damre ◽  
Kanchan Khandelwal ◽  
Abhay T. Sangamwar
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Van Der Waals Interactions ◽  
Electrostatic Energy ◽  
Hydrogen Bond Acceptor

Cytochrome bc1 (EC 1.10.2.2, bc1) is an essential component of the cellular respiratory chain, which catalyzes electron transfer from quinol to cytochrome c and concomitantly the translocation of protons across the membrane. It has been identified as a promising target in malaria parasites. The structure-based pharmacophore modelling and molecular dynamic simulation approach have been employed to identify novel inhibitors of cytochrome bc1. The best structure-based pharmacophore hypothesis (Hypo1) consists of one hydrogen bond acceptor (HBA), one general hydrophobic (HY), and two hydrophobic aromatic features (HYAr). Further, hydrogen interactions and hydrophobic interactions of known potent inhibitors with cytochrome bc1 were compared with Hypo1, which showed that the Hypo1 has good predictive ability. The validated Hypo1 was used to screen the chemical databases. The hits obtained were subsequently subjected to the molecular docking analysis to identify false-positive hits. Moreover, the molecular docking results were further validated by molecular dynamics simulations. Binding-free energy analysis using MM-GBSA method reveals that the van der Waals interactions and the electrostatic energy provide the basis for favorable absolute free energy of the complex. The five virtual hits were identified as possible candidates for the designing of potent cytochrome bc1 inhibitors.

scholarly journals Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations

2008 ◽  
Vol 8 (1) ◽  
pp. 25-34 ◽  
Author(s):  
Thomas M. Frimurer ◽  
Ole Hvilsted Olsen ◽  
Günther H. Peters ◽  
Morten Dahl Sørensen ◽  
Jens JØRgen Led
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Side Chain ◽  
Free Energy Perturbation ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Side Chain Conformation ◽  
Energy Perturbation ◽  
Energy Mapping ◽  
Adiabatic Energy

scholarly journals Insight on the In Silico Study and Biological Activity Assay of Chalcone-Based 1, 5-Benzothiazepines as Potential Inhibitor for Breast Cancer MCF7

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Neni Frimayanti ◽  
◽  
Marzieh Yaeghoobi ◽  
Ihsan Ikhtiarudin ◽  
Dhea Rizki Wannisyah Putri ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Free Energy ◽  
Biological Activity ◽  
Molecular Dynamic ◽  
In Silico ◽  
Binding Free Energy ◽  
Crystallographic Structure ◽  
Anticancer Activities ◽  
Adme Prediction ◽  
In Silico Study

In silico study was performed to twelve 1,5-benzothiazepine chalcone derivatives with the protein target from the crystallographic structure modeling of the enzyme tyrosine kinase. The objective of this study is to execute and to estimate the biological activity of chalcone-based 1,5-benzothiazepine derivatives as potential inhibitors for breast cancer MCF7. To get insight into potential anticancer activities, molecular docking, molecular dynamic and ADME prediction were performed. Docking results reported that compound MA9 with binding free energy of -11.2 kcal / mol can interact through hydrogen bonds with amino acids Cys788 on 1T46 protein active site. In addition, the lowest binding free energy conformation indicated its stability during molecular dynamic simulation. MA9 is also shown to have drug likeness properties based on ADME prediction. In order to evaluate the modeling outcomes, MTT assay were performed for some of the most and least promising benzologs (i.e., MA1, MA6, MA8 and MA9). As expected, compound MA9 with the best calculated anticancer properties revealed the best inhibition against MCF7cell line in vitro. Thus, this compound was chosen as the reference for the next stage in the drug design.

scholarly journals Identification of the Potential Hits for Hindering Interaction of SARS-CoV-2 Main Protease (M pro ) from the Pool of Antiviral Phytochemicals utilizing Molecular Docking and Molecular Dynamics (MD) Simulations

2021 ◽  
Author(s):  
Chirag N. Patel ◽  
Dharmesh G. Jaiswal ◽  
Siddhi P. Jani ◽  
Naman Mangukia ◽  
Robin M. Parmar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Docking ◽  
Virus Assembly ◽  
Binding Free Energy ◽  
Natural Compounds ◽  
Free Energy Calculations ◽  
Host Protein ◽  
Dynamic Simulations ◽  
Main Protease

Abstract The novel SARS-CoV-2 is an etiological factor that triggers Coronavirus disease in 2019 (COVID-19) and tends to be an imminent occurrence of a pandemic. Out of all recognized solved complexes linked to SARS-CoV, Main protease (Mpro) is considered a desirable antiviral phytochemical that play a crucial role in virus assembly and possibly non-interactive capacity to adhere to any viral host protein. In this research, SARS-CoV-2 MPro was chosen as a focus for the detection of possible inhibitors using a variety of different analytical methods such as molecular docking, ADMET analysis, dynamic simulations and binding free energy measurements. Virtual screening of known natural compounds recognized Withanoside V, Withanoside VI, Racemoside B, Racemoside A and Shatavarin IX as future inhibitors of SARS-CoV-2 MPro with stronger energy binding. Also, simulations of molecular dynamics for a 100 ns time scale showed that much of the main SARS-CoV-2 MPro interactions had been maintained in the simulation routes. Binding free energy calculations using the MM/PBSA method ranked the top five possible natural compounds that can act as effective SARS-CoV-2 MPro inhibitors.

scholarly journals Identification of antiviral phytochemicals as a potential SARS-CoV-2 main protease (Mpro) inhibitor using docking and molecular dynamics simulations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chirag N. Patel ◽  
Siddhi P. Jani ◽  
Dharmesh G. Jaiswal ◽  
Sivakumar Prasanth Kumar ◽  
Naman Mangukia ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Natural Compounds ◽  
Free Energy Calculations ◽  
Public Health Care ◽  
Dynamic Simulations ◽  
Energy Calculations ◽  
Main Protease ◽  
Binding Free Energy Calculations ◽  
Dynamics Simulations

AbstractNovel SARS-CoV-2, an etiological factor of Coronavirus disease 2019 (COVID-19), poses a great challenge to the public health care system. Among other druggable targets of SARS-Cov-2, the main protease (Mpro) is regarded as a prominent enzyme target for drug developments owing to its crucial role in virus replication and transcription. We pursued a computational investigation to identify Mpro inhibitors from a compiled library of natural compounds with proven antiviral activities using a hierarchical workflow of molecular docking, ADMET assessment, dynamic simulations and binding free-energy calculations. Five natural compounds, Withanosides V and VI, Racemosides A and B, and Shatavarin IX, obtained better binding affinity and attained stable interactions with Mpro key pocket residues. These intermolecular key interactions were also retained profoundly in the simulation trajectory of 100 ns time scale indicating tight receptor binding. Free energy calculations prioritized Withanosides V and VI as the top candidates that can act as effective SARS-CoV-2 Mpro inhibitors.

scholarly journals Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation

2020 ◽  
Author(s):  
Zhijian Xu ◽  
Cheng Peng ◽  
Yulong Shi ◽  
Zhengdan Zhu ◽  
Kaijie Mu ◽  
...  
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Homology Modelling ◽  
Binding Mode ◽  
Free Energy Calculations ◽  
Integrative Approach ◽  
Energy Calculation ◽  
Potential Inhibitor ◽  
Small Molecule Drugs ◽  
Main Protease

Abstract2019-nCov has caused more than 80 deaths as of 27 January 2020 in China, and infection cases have been reported in more than 10 countries. However, there is no approved drug to treat the disease. 2019-nCov Mpro is a potential drug target to combat the virus. We built homology models based on SARS Mpro structures, and docked 1903 small molecule drugs to the models. Based on the docking score and the 3D similarity of the binding mode to the known Mpro ligands, 4 drugs were selected for binding free energy calculations. Both MM/GBSA and SIE methods voted for nelfinavir, with the binding free energy of −24.69±0.52 kcal/mol and −9.42±0.04 kcal/mol, respectively. Therefore, we suggested that nelfinavir might be a potential inhibitor against 2019-nCov Mpro.

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