scholarly journals Investigation of potential antiviral natural products with an effect on HPV18 E6 protein by molecular docking method

2021 ◽  
Vol 11 (11) ◽  
pp. 586
Author(s):  
Mehdi Fazeli ◽  
Hosna Sarvazad ◽  
Nasrin Rahnejat ◽  
Rezvan Rostampour ◽  
Mahtab Ghanbari Rad ◽  
...  
Keyword(s):  
Molecular Docking ◽  
3D Structure ◽  
Target Protein ◽  
Pharmacokinetic Parameters ◽  
Therapeutic Effects ◽  
Docking Method ◽  
Hpv18 E6 ◽  
E6 Protein ◽  
Plant Compounds ◽  
Molecular Docking Method

Background: Infection with the Human Papillomavirus (HPV) causes cellular dysplasia, which leads to cervical cancers in women and penile or rectal cancers in men.        Objective: This in silico study identified the plant compounds with potential therapeutic effects against HPV 18 oncogenic virus using the molecular docking method.   Methods: The three-dimensional (3D) structure of HPV18 E6 protein, as the target protein, and the 3D structure of plant compounds with potential therapeutic effect against viruses, as ligands, was obtained from the protein databases (RCSB) and PubChem, respectively. Both structures of ligands and target protein were subjected to AutoDock tools-1.5.6, ver.4 separately. The structure with the most negative affinity was docked to reconsider its connection location. The results were analyzed more based on pharmacodynamic and pharmacokinetic parameters.     Results: The docking of HPV18 E6 protein with 19 selected ligands resulted in four compounds, curcumin, silymarin, saikosaponin c, and lactupicrin, showing the best docking scores; they had better binding free energies with HPV E6 protein. Among four compounds against HPV18 E6, silymarin and curcumin were less dangerous than other compounds due to the lack of inhibition of the human Ether-à-go-go-Related Gene (hERG). Of these two compounds, silymarin had lower oral absorption, lactopicrin had less skin absorption, lactopicrin is the substrate of P-gp, and saikosaponin c crosses the blood-brain barrier.   Conclusion: Among potential antiviral plants against HPV18E6, four compounds were found to be effective. According to these findings, it is recommended that in vitro and in vivo examinations be conducted to determine the effectiveness of these compounds against HPV18  Keywords: Biological products, Antiviral agents, HPV18, Molecular docking, Computational biology, E6 protein

scholarly journals AKTIVITAS DARI KUERSETIN SEBAGAI AGEN PENCERAH KULIT SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 207
Author(s):  
K. D. Adnyani ◽  
L. W. E. Lestari ◽  
H. Prabowo ◽  
P. A. I. A. Siaka ◽  
N. P. L. Laksmiani
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Target Protein ◽  
Related Protein ◽  
Skin Whitening ◽  
Whitening Agent ◽  
Docking Method ◽  
Tyrosinase Related Protein ◽  
Molecular Docking Method

Increasing melanogenesis process causes excessive melanin synthesis resulting in darkening of the skin color. The melanogenesis process requires mealnogenesis enzymes, one of which is tyrosinase-related protein 1. One of the flavonoid compounds that has the potential as a skin lightening agent is quercetin. The antioxidant activity of quercetin plays a very important role in antimelanogenesis. This study aims to determine the affinity and molecular mechanism of quercetin on the target protein tyrosinase-related protein 1 using in silico molecular docking method. Molecular docking is carried out through stages including optimization of the structure of quercetin compounds, preparation of the target protein tyrosinase-related protein 1, validation of the molecular docking method, and docking of quercetin on the tyrosinase-related protein 1. Docking of quercetin with tyrosinase-related protein 1 produces binding energy values of -7.81 kcal/mol, while docking of native ligand with tyrosinase-related protein 1 produces binding energy values of -5.39 kcal/mol. Quercetin has a strong affinity for tyrosinase-related protein 1 which is indicated by the binding energy from the docking results. Quercetin has activity as a skin whitening agent with in silico test with molecular mechanisms through inhibition of the activity of tyrosinase-related protein 1 enzyme.  Keywords: skin whitening agent, in silico, quercetin, tyrosinase-related protein 1

scholarly journals STUDI POTENSI SIANIDIN DAN PEONIDIN DARI UBI JALAR UNGU (ipomoea batatas L.) SEBAGAI AGEN DEPIGMENTASI SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 34
Author(s):  
N. P.L. Laksmiani ◽  
I G.P. Putra ◽  
I P.W. I P. W. Nugraha ◽  
I W. Suwartawan ◽  
N. K.S. Ani
Keyword(s):  
Molecular Docking ◽  
Sweet Potato ◽  
In Silico ◽  
Target Protein ◽  
Program Optimization ◽  
Test Compound ◽  
Docking Method ◽  
Purple Sweet Potato ◽  
Native Ligand ◽  
Molecular Docking Method

Hyperpigmentation is caused by enhancement of melanin production that causes skin darkening. Purple sweet potato is one of the plants that is potentially developed as skin depigmentation agent because it contains anthocyanin. The most common types of anthocyanins in purple sweet potato are cyanidin and peonidin which are in vitro proven to be used as skin lightening. The objective of this study is to determine the potential of cyanidin and peonidin as skin depigmentation agent against target protein D-Dopachrome taumerase  through in silico molecular docking method. The research steps include the preparation of target protein using Chimera 1.10.1 program, optimization of cyanidine and peonidin 3D structures using Hyperchem 8 program, validation of molecular docking method, and docking of cyanidine and peonidine on target protein using Autodock 4.2 program. The bond energy between cyanidin and peonidin with the target protein D-Dopachrome taumerase are -7.75 kcal / mol and -8.38 kcal / mol. The cyanidin and peonidin bond values ??are smaller than the native ligand, suggesting that the bond between the test compound (cyanidin and peonidin) with the target protein are stronger and more stable than the native ligand, so that the affinity of the test compound was greater than the native ligand. This suggests that the cyanidin and peonidin compounds in purple sweet potato have potential as a depigmentation agent by inhibiting D-Dopachrome taumerase protein.

Computational drug repurposing study of antiviral drugs against main protease, RNA polymerase, and spike proteins of SARS-CoV-2 using molecular docking method

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Alireza Jalalvand ◽  
Somayeh Behjat Khatouni ◽  
Zahra Bahri Najafi ◽  
Foroozan Fatahinia ◽  
Narges Ismailzadeh ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
3D Structure ◽  
Drug Repurposing ◽  
Antiviral Drugs ◽  
Effective Drug ◽  
Main Protease ◽  
Docking Method ◽  
Inhibitory Potential ◽  
Molecular Docking Method

Abstract Objectives The new Coronavirus (SARS-CoV-2) created a pandemic in the world in late 2019 and early 2020. Unfortunately, despite the increasing prevalence of the disease, there is no effective drug for the treatment. A computational drug repurposing study would be an appropriate and rapid way to provide an effective drug in the treatment of the coronavirus disease of 2019 (COVID-19) pandemic. In this study, the inhibitory potential of more than 50 antiviral drugs on three important proteins of SARS-CoV-2, was investigated using the molecular docking method. Methods By literature review, three important proteins, including main protease, RNA-dependent RNA polymerase (RdRp), and spike, were selected as the drug targets. The three-dimensional (3D) structure of protease, spike, and RdRp proteins was obtained from the Protein Data Bank. Proteins were energy minimized. More than 50 antiviral drugs were considered as candidates for protein inhibition, and their 3D structure was obtained from Drug Bank. Molecular docking settings were defined using Autodock 4.2 software and the algorithm was executed. Results Based on the estimated binding energy of docking and hydrogen bond analysis and the position of drug binding, five drugs including, indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, had the highest inhibitory potential for all three proteins. Conclusions According to the results, among the mentioned drugs, saquinavir and lopinavir showed the highest inhibitory potential for all three proteins compared to the other drugs. This study suggests that saquinavir and lopinavir could be included in the laboratory phase studies as a two-drug treatment for SARS-CoV-2 inhibition.

scholarly journals Bhringraj Derived Phytochemicals against Pneumonia

2020 ◽  
pp. 93-96
Author(s):  
Debajani Tripathy ◽  
Chandana Adhikari ◽  
Mukundjee Pandey ◽  
Dipankar Bhattacharayay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Glutamic Acid ◽  
Interaction Energy ◽  
Plant Extract ◽  
Klebsiella Pneumonia ◽  
Discovery Studio ◽  
Docking Method ◽  
Dehydrogenase Enzyme ◽  
Molecular Docking Method

Phytochemicals from Bhringaraj plant extract are traditionally used to cure Pneumonia. It is caused by Klebsiella pneumonia. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that glutamic acid can effectively deactivate the dehydrogenase enzyme, thereby interrupting the life cycle of the organism.

scholarly journals Trigonella foenum-graecum Derived Phytochemicals against Tuberculosis

2020 ◽  
pp. 121-124
Author(s):  
Bidyashree Tripathy ◽  
Elina Sahoo ◽  
Sidhartha Ray ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Interaction Energy ◽  
Dihydrofolate Reductase ◽  
Plant Extract ◽  
Discovery Studio ◽  
Trigonella Foenum Graecum ◽  
Docking Method ◽  
Molecular Docking Method

Phytochemicals from Trigonella foenum-graecum plant extract are traditionally used to cure Tuberculosis. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that this plant extract can effectively deactivate the dihydrofolate reductase enzyme thereby interrupting the life cycle of the organism.

scholarly journals Michelia champaca L. Derived Phytochemicals against Peptidase Do of Bordetella pertussis Causing Cough

2020 ◽  
pp. 133-135
Author(s):  
Sanjeeb Kumar Dash ◽  
Sidhartha Ray ◽  
Smruti Ranjan Behera ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Interaction Energy ◽  
Plant Extract ◽  
Bordetella Pertussis ◽  
Discovery Studio ◽  
Docking Method ◽  
Michelia Champaca ◽  
Molecular Docking Method

Phytochemicals from Michelia champaca L. plant extract are traditionally used to cure cough.  Cough can be caused by many reasons. Caugh can be caused by the infection of Bordetella pertussis. The objective of the study is to identify the phytochemical of Michelia champaca capable of curing cough. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that magnoflorine can effectively deactivate the peptidase Do enzyme which will interrupt the life cycle of the microorganism and inhibit the multiplication.

scholarly journals Capsicum anum L. Derived Phytochemicals against Haemophilus influenzae Causing Bronchitis

2020 ◽  
pp. 100-103
Author(s):  
Debadatta Nayak ◽  
Debesh Kumar Hota ◽  
Tophani Sahu ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Haemophilus Influenzae ◽  
Interaction Energy ◽  
Plant Extract ◽  
Haemophilus Influenza ◽  
Discovery Studio ◽  
Docking Method ◽  
Coa Hydrolase ◽  
Molecular Docking Method

Phytochemicals from Capsicum anum L. plant extract are traditionally used to cure bronchitis. Bronchitis is caused by Haemophilus influenzae. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that myrcetin and quercetin can effectively deactivate the Palmitoyl-CoA hydrolase enzyme thereby interrupting the life cycle of Haemophilus influenza.

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