scholarly journals Cruzain Inhibition by Terpenoids: A Molecular Docking Analysis

2008 ◽  
Vol 3 (6) ◽  
pp. 1934578X0800300 ◽  
Author(s):  
Ifedayo V. Ogungbe ◽  
William N. Setzer
Keyword(s):  
Molecular Docking ◽  
Active Site ◽  
Binding Energies ◽  
Hydrophobic Pocket ◽  
Docking Analysis ◽  
Protein Target ◽  
Hydrophobic Compounds ◽  
Sesquiterpene Hydrocarbons ◽  
Inhibitory Activities ◽  
Molecular Docking Analysis

A molecular docking analysis has been carried out using monoterpene and sesquiterpene hydrocarbons and triterpenoids that have shown enzyme inhibitory activity as ligands for the cysteine protease cruzain. The binding energies of the docked ligands roughly correlate with their inhibitory activities. The orientations of the docked ligands are consistent with a mechanism whereby these hydrophobic compounds dock into a hydrophobic pocket near the active site, thereby blocking binding of the protein target to the protease.

scholarly journals Molecular Docking Analysis of Chloroquine and Hydroxychloroquine and Design of Anti-SARS-CoV2 Protease Inhibitor

2020 ◽  
Vol 14 (10) ◽  
pp. 52
Author(s):  
Usman Abdulfatai ◽  
Adamu Uzairu ◽  
Gideon Adamu Shallangwa ◽  
Sani Uba
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Binding Energy ◽  
Binding Site ◽  
Docking Simulation ◽  
Binding Energies ◽  
Drug Candidate ◽  
Molecular Docking Study ◽  
Docking Analysis ◽  
Molecular Docking Analysis

In this present investigation, simulated molecular docking study of chloroquine and hydroxychloroquine compounds were investigated on the SARS-CoV2 enzyme to determine the types of amino acids responsible for the biochemical reaction at the binding site. A structure-based docking design technique was explored in designing a novel derivative of chloroquine for the treatment and management of new COVID 19 disease. To achieve this, the molecular docking simulation method was used to investigate the level of chloroquine and hydroxychloroquine (Drugs presently under clinical trial) interactions on SARS-CoV2 enzyme (a causative agent of COVID 19 disease). Chloroquine and hydroxychloroquine which has been debated as drugs for the management of COVID 19 were subjected to molecular docking analysis, and the binding energies generated were found to be -6.1 kcal/mol and -6.8 kcal/mol respectively. Moreover, novel 2-((4-((7-chloroquinolin-4 yl) amino)pentyl)((methylamino)methyl)amino) ethan-1-ol as an anti-SARS-CoV2 protease was designed through the structural modification of hydroxychloroquine. The binding energy of this drug candidate was found to be -6.9 kcal/mol. This novel drug was found to formed hydrogen and conventional interactions with the binding site of SARS-CoV2 protease through amino acids such as Glutamic acid (GLU166), Glycine (GLY143), Phenylalanine (PHE140), Asparagine (ASN142), Histidine (HIS163), His (HIS172, HIS41, HIS163), Leucine (LEU41, LEU27), Glycine (GLY143), Glutamine (GLN189), Methionine (MET49, MET165), Serine (SER 46), Cysteine (CYS145) and Threonine (THR25). With this binding energy, this new drug candidate could bind better to the human SARS-CoV2 protease’ binding site. This research provides a clue for other scientists on various ways of designing and identify the types of amino acids that may be responsible for biochemical action on SARS-CoV2 protease.

scholarly journals Inhibitory Effect of Eight Secondary Metabolites from Conventional Medicinal Plants on COVID_19 Virus Protease by Molecular Docking Analysis

2020 ◽  
Author(s):  
Narges Mohammadi ◽  
Neda Shaghaghi
Keyword(s):  
Molecular Docking ◽  
Major Part ◽  
Data Bank ◽  
Inhibitory Effect ◽  
Docking Analysis ◽  
Molegro Virtual Docker ◽  
High Affinity ◽  
Inhibitory Activities ◽  
Molecular Docking Analysis ◽  
Effectiveness Function

<p>Due to the reported high ability of virulence of COVID_19 in recent months, several studies have been conducted to discover and introduce COVID_19 antiviral drugs. The results of numerous studies have shown that protease inhibitors , which make up the major part of plant derivatives can therefore be very effective in controlling virus-induced infection. The aim of this research is the bioinformatical study of COVID_19 inhibition by Secendary Metabolite of medicinal herbs. This is a descriptive-analytic study. In the present study , the structure of Secendary Metabolite and COVID_19 protease was received from the databases such as PubChem and Protein Data Bank (PDB). After that, Molecular Docking was performed by MVD(molegro virtual docker) software.The results are identified to have inhibitory activities against novel COVID-19 protease. Of these compounds, Curcumin has a stronger bond and high affinity with protease. Finally, with due attention to the high effectiveness function of plant compounds, we can conclude that these compounds may be considered as effectire COVID_19 antiprotease drugs.</p>

scholarly journals Antioxidant and α-Glucosidase Inhibitory Activities of Fisetin

2018 ◽  
Vol 13 (11) ◽  
pp. 1934578X1801301 ◽  
Author(s):  
Yike Yue ◽  
Yongsheng Chen ◽  
Sheng Geng ◽  
Guizhao Liang ◽  
Benguo Liu
Keyword(s):  
Antioxidant Activity ◽  
Molecular Docking ◽  
Medicinal Plants ◽  
Hydrogen Bonds ◽  
Competitive Inhibition ◽  
Radical Scavenging ◽  
Docking Analysis ◽  
Inhibitory Activities ◽  
Molecular Docking Analysis

Fisetin is a flavonoid widespread in vegetables, fruits and medicinal plants. The in vitro antioxidant and α-glucosidase inhibitory activities of fisetin were systemically investigated in this study. The DPPH and ABTS radical scavenging performance of fisetin was higher than that of BHA. In the ORAC and PSC assays, fisetin also exhibited strong antioxidant activity. The α-glucosidase inhibitory activity of fisetin (IC50, 9.38±0.35 μg/mL) was significantly superior to that of acarbose (IC50, 1.07±0.15 mg/mL). Its inhibition type was determined to be a mixed competitive and non-competitive inhibition mode. Molecular docking analysis suggested it could exert the α-glucosidase inhibitory role by forming hydrogen bonds with the TRP391, ASP392, ARG428 and ASP568 residues of α-glucosidase.

scholarly journals Analysis of the Molecular Interactions between Cytochromes P450 3A4 and 1A2 and Aflatoxins: A Docking Study

2019 ◽  
Vol 9 (12) ◽  
pp. 2467 ◽  
Author(s):  
Isui Abril García-Montoya ◽  
Norma Rosario Flores-Holguín ◽  
Linda-Lucila Landeros-Martínez ◽  
Mónica Alvarado-González ◽  
Quintín Rascón-Cruz ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Amino Acids ◽  
Molecular Docking ◽  
Charge Transfer ◽  
Active Site ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Cytochromes P450 ◽  
Docking Analysis ◽  
Molecular Docking Analysis

Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 were analyzed using density functional theory. Different methodologies—B3LYP/6-311G(d,p) and M06-2X/6-311G(d,p)—were applied for geometrical calculations. Chemical reactivity parameters were used in the calculation of charge transfer values during the interaction between protein and ligand. The binding energy, the electrostatic interactions, and the amino acids of the active site were determined by molecular docking analysis between AF and cytochromes P450 (3A4 and 1A2), employing different PDB files (CYP3A4:1TQN, 2V0M, 4NY4 and 1W0E, and CYP1A2:2HI4). Molecular docking analysis indicated that the central rings of the AF are involved in the interaction with the HEM group of the active site. The differences in the molecular structure of the AF affect their position regarding the HEM group. The resulting configurations presented considerable variation in the amino acids and the position of the coupling. The charge transfer values showed that there is oxidative damage inside the active site and that the HEM group is responsible for the main charge transferences.

scholarly journals Bioactive Aporphine Alkaloids from the Roots of Artabotrys spinosus: Cholinesterase Inhibitory Activity and Molecular Docking Studies

2018 ◽  
Vol 13 (10) ◽  
pp. 1934578X1801301
Author(s):  
Jirapast Sichaem ◽  
Santi Tip-pyang ◽  
Kiattisak Lugsanangarm
Keyword(s):  
Molecular Docking ◽  
Inhibitory Activity ◽  
Mixed Mode ◽  
Docking Studies ◽  
Experimental Results ◽  
Docking Analysis ◽  
Molecular Docking Studies ◽  
Cholinesterase Inhibitory Activity ◽  
Inhibitory Activities ◽  
Molecular Docking Analysis

Six aporphine alkaloids (1–6) were isolated from Artabotrys spinosus roots based on bioassay-guided fraction and chromatographic methods. All isolated alkaloids were evaluated for their cholinesterase (ChEs) inhibitory activities, in which compounds 4 and 6 exhibited the highest activity toward butyrylcholinesterase (BChE) and acetylcholinesterase (AChE), respectively. The Lineweaver-Burk plots suggested that 4 and 6 were mixed mode inhibitors toward BChE and AChE enzymes, respectively. In addition, the experimental results were also confirmed by molecular docking analysis. This information can help in designing a new inhibitor in the class of aporphine alkaloids in against Alzheimer's disease.

scholarly journals Molecular docking analysis of antimicrobial peptides with the CXCL1 protein target for colorectal cancer

2021 ◽  
Vol 17 (3) ◽  
pp. 369-376
Author(s):  
Praveen Kumar Kumar ◽  
◽  
Shanmughavel Piramanayagam ◽  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Drug Discovery ◽  
Antimicrobial Peptides ◽  
Target Protein ◽  
Drug Resistant ◽  
Docking Analysis ◽  
Protein Target ◽  
Molecular Docking Analysis

Antimicrobial peptides (AMPs) play a prominent role in drug discovery due to the rapid increase in drug resistant infections. Hence, we report the molecular docking analysis of antimicrobial peptides MREEKKERKRD and MVQGAKRGGRLHRV with the target protein CXCL1 in the context of colorectal cancer for further consideration in drug discovery.

scholarly journals Inhibitory Effect of Eight Secondary Metabolites from Conventional Medicinal Plants on COVID_19 Virus Protease by Molecular Docking Analysis

2020 ◽  
Author(s):  
Narges Mohammadi ◽  
Neda Shaghaghi
Keyword(s):  
Molecular Docking ◽  
Major Part ◽  
Data Bank ◽  
Inhibitory Effect ◽  
Docking Analysis ◽  
Molegro Virtual Docker ◽  
High Affinity ◽  
Inhibitory Activities ◽  
Molecular Docking Analysis ◽  
Effectiveness Function

<p>Due to the reported high ability of virulence of COVID_19 in recent months, several studies have been conducted to discover and introduce COVID_19 antiviral drugs. The results of numerous studies have shown that protease inhibitors , which make up the major part of plant derivatives can therefore be very effective in controlling virus-induced infection. The aim of this research is the bioinformatical study of COVID_19 inhibition by Secendary Metabolite of medicinal herbs. This is a descriptive-analytic study. In the present study , the structure of Secendary Metabolite and COVID_19 protease was received from the databases such as PubChem and Protein Data Bank (PDB). After that, Molecular Docking was performed by MVD(molegro virtual docker) software.The results are identified to have inhibitory activities against novel COVID-19 protease. Of these compounds, Curcumin has a stronger bond and high affinity with protease. Finally, with due attention to the high effectiveness function of plant compounds, we can conclude that these compounds may be considered as effectire COVID_19 antiprotease drugs.</p>

scholarly journals Chemical Composition, Antioxidant and Enzyme Inhibitory Activities of Onosma bourgaei and Onosma trachytricha and in Silico Molecular Docking Analysis of Dominant Compounds

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2981
Author(s):  
Erman Salih Istifli
Keyword(s):  
Molecular Docking ◽  
Chemical Composition ◽  
In Silico ◽  
Digestive Enzymes ◽  
Binding Affinities ◽  
Docking Analysis ◽  
Docking Simulations ◽  
Inhibitory Activities ◽  
In Silico Molecular Docking ◽  
Molecular Docking Analysis

The aim of this study was to investigate the chemical composition, antioxidant and enzyme inhibitory activities of methanol (MeOH) extracts from Onosma bourgaei (Boiss.) and O. trachytricha (Boiss.). In addition, the interactions between phytochemicals found in extracts in high amounts and the target enzymes in question were revealed at the molecular scale by performing in silico molecular docking simulations. While the total amount of flavonoid compounds was higher in O. bourgaei, O. trachytricha was richer in phenolics. Chromatographic analysis showed that the major compounds of the extracts were luteolin 7-glucoside, apigenin 7-glucoside and rosmarinic acid. With the exception of the ferrous ion chelating assay, O. trachytricha exhibited higher antioxidant activity than O. bourgaei. O. bourgaei exhibited also slightly higher activity on digestive enzymes. The inhibitory activities of the Onosma species on tyrosinase were almost equal. In addition, the inhibitory activities of the extracts on acetylcholinesterase (AChE) were stronger than the activity on butyrylcholinesterase (BChE). Molecular docking simulations revealed that luteolin 7-glucoside and apigenin 7-glucoside have particularly strong binding affinities against ChEs, tyrosinase, α-amylase and α-glucosidase when compared with co-crystallized inhibitors. Therefore, it was concluded that the compounds in question could act as effective inhibitors on cholinesterases, tyrosinase and digestive enzymes.

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