scholarly journals Vitex negundo L. Essential Oil: Odorant Binding Protein Efficiency Using Molecular Docking Approach and Studies of the Mosquito Repellent

Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1061
Author(s):  
Bamidele Joseph Okoli ◽  
Zakari Ladan ◽  
Fanyana Mtunzi ◽  
Yayock Chigari Hosea
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Hydrophobic Interactions ◽  
Malaria Prevention ◽  
Effective Vaccine ◽  
Compositional Variation ◽  
Vitex Negundo ◽  
Toxicity Profile ◽  
Α Helix ◽  
Odorant Binding

(1) Background: Malaria fever affects millions of people yearly in Africa and Asia’s tropical and subtropical areas. Because there is no effective vaccine, malaria prevention is solely dependent on avoiding human-vector interaction. (2) Aim: This study examines the interaction between the constituents of Vitex negundo essential oil and Anopheles gambiae Odorant Binding Proteins (OBP) as well as the compositional variation, repellent efficacy, and toxicity profile. (3) Methods: The oils were subjected to GC-MS and mosquito behavioral analysis. OBP–ligand interactions, Anopheles species authentication, and the toxicity profile were determined by molecular docking, PCR assay and in silico ADME/tox tool. Docking protocol validation was achieved by redocking the co-crystallized ligands into the protein binding pocket and root mean square deviation (RMSD) calculation. (4) Results: The oil yields and compositions are climate–soil dependent with ≈71.39% monoterpenes and ≈16.32% sesquiterpene. Optimal repellency is achieved at 15 min at ED50 0.08–0.48% v/v while the RMSD was estimated to be within 0.24–1.35 Å. Strong affinities were demonstrated by α-pinene (−6.4 kcal/mol), citronellal (−5.5 kcal/mol), linalool (−5.4 kcal/mol), and myrcene (−5.8 kcal/mol) for OBP1, OBP7, OBP4, and OBP; respectively. The hydrophobic interactions involve Leu17 (α-helix 1), Cys35 (α-helix 2), ALA52 (α-helix 3), Leu73, Leu76 (α-helix 4), Ala88, Met91, Lys93, Trp114 (α-helix 5), Phe123 (α-helix 6), and Leu124 (α-helix 7) receptors within the binding cavities, and may cause blocking of the olfactory receptors resulting in disorientation. (5) Conclusion: The ligand efficiency metrics, ADME/tox and repellency screening are within the threshold values; hence, α-pinene, linalool, and myrcene are safe and fit-to-use in the development of a green and novel repellent.

scholarly journals Molecular docking and pharmacokinetic screening of eucalyptol (1,8 cineole) from eucalyptus essential oil against SARS-CoV-2

2020 ◽  
Vol 12 (3) ◽  
pp. 536-545
Author(s):  
Arun D. SHARMA ◽  
Inderjeet KAUR
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
In Silico Analysis ◽  
Active Site Residues ◽  
Virus Family

SARS-CoV-2 (COVID-19), member of corona virus family, is a positive single stranded RNA virus. Due to lack of drugs it is spreading its tentacles across the world. Being associated with cough, fever, and respiratory distress, this disease caused more than 15% mortality worldwide. Mpro/3CLpro has recently been regarded as a suitable target for drug design due to its vital role in virus replication. The current study focused on the inhibitory activity of eucalyptol (1,8 cineole), an essential oil component from eucalyptus oil, against Mpro/3CLprofrom SARS-CoV-2. Till date there is no work is undertaken on in-silico analysis of this compound against Mpro/3CLproof SARS-CoV-2. Molecular docking studies were conducted by using 1-click dock tool and Patchdock analysis. In-silico absorption, distribution, metabolism, excretion and toxicity (ADMET) profile were also studied. The calculated parameters such as docking score indicated effective binding of eucalyptol to COVID-19 Mpro protein. Active site prediction revealed the involvement of active site residues in ligand binding. Interactions results indicated that, Mpro/3CLpro/eucalyptol complexes forms hydrophobic interactions. ADMET studies provided guidelines and mechanistic scope for identification of potent anti-COVID 19 drug. Therefore, eucalyptol may represent potential herbal treatment to act as COVID-19 Mpro/3CLproinhibitor, a finding which must be validated in vivo.

scholarly journals Molecular docking analysis and evaluation of the antibacterial and antioxidant activities of the constituents of Ocimum cufodontii

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Muhdin Aliye ◽  
Aman Dekebo ◽  
Hailemichael Tesso ◽  
Teshome Abdo ◽  
Rajalakshmanan Eswaramoorthy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Hydrophobic Interactions ◽  
Antioxidant Activities ◽  
Reducing Power ◽  
Principal Component ◽  
Inhibition Zone ◽  
Hexane Extract ◽  
Docking Analysis ◽  
Molecular Docking Analysis

AbstractOcimum cufodontii ((Lanza) A.J.Paton) has been traditionally used in Ethiopia against bacteria. The extracts of the leaves and roots of O. cufodontii after silica gel column chromatography furnished compounds 1–5, compounds 3 and 4 are new natural products. The oil from the hydro-distillation of the leaves, after analyzed with GC–MS, has led to the identification of β-caryophyllene as a principal component, suggesting the essential oil as medicine and spices to enhance the taste of food. The constituents of O. cufodontii were assessed for their antibacterial activity against E. coli, K. pneumonia, S. typhymurium and S. aureus. The best activity was displayed against S. aureus by the hexane extract of the roots, compound 4, and the essential oil with an inhibition zone of 17, 15, and 19 mm, respectively. Molecular docking analysis revealed that compound 1 has better docking efficiency and forms hydrophobic interactions with five amino acids (ARG192, PHE196, GLU185, GLU193, and LYS189). This suggests that the compounds may act as potential inhibitors of DNA gyrase. The constituents were also assessed for their antioxidant activities using DPPH, ferric thicyanate and ferric reducing power assay. The hexane extracts of the roots inhibited the DPPH radical and peroxide formation by 90.5 and 83%, respectively, suggesting the potential of the extract as an antioxidant. Furthermore, the hexane extract of the roots of O. cufodontii exhibited the maximum reducing power compared with the EtOAc and methanol extracts. Hence, the activity displayed herein indicated as the plant has great potential as a remedy for diseases caused by bacteria and radicals.

scholarly journals Eucalyptol (1,8 cineole) from Eucalyptus Essential Oil a Potential Inhibitor of COVID 19 Corona Virus Infection by Molecular Docking Studies

2020 ◽  
Author(s):  
Arun Dev Sharma ◽  
inderjeet kaur
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
Docking Studies ◽  
Active Site Residues ◽  
Virus Family ◽  
Molecular Docking Studies ◽  
Corona Virus

Background: COVID-19, a member of corona virus family is spreading its tentacles across the world due to lack of drugs at present. Associated with its infection are cough, fever and respiratory problems causes more than 15% mortality worldwide. It is caused by a positive, single stranded RNA virus from the enveloped coronaviruse family. However, the main viral proteinase (Mpro/3CLpro) has recently been regarded as a suitable target for drug design against SARS infection due to its vital role in polyproteins processing necessary for coronavirus reproduction.Objectives: The present in silico study was designed to evaluate the effect of Eucalyptol (1,8 cineole), a essential oil component from eucalyptus oil, on Mpro by docking study.Methods: In the present study, molecular docking studies were conducted by using 1-click dock and swiss dock tools. Protein interaction mode was calculated by Protein Interactions Calculator.Results: The calculated parameters such as RMSD, binding energy, and binding site similarity indicated effective binding of eucalyptol to COVID-19 proteinase. Active site prediction further validated the role of active site residues in ligand binding. PIC results indicated that, Mpro/eucalyptol complexes forms hydrophobic interactions, hydrogen bond interactions and strong ionic interactions.Conclusions: Therefore, eucalyptol may represent potential treatment potential to act as COVID-19 Mpro inhibitor. However, further research is necessary to investigate their potential medicinal use.

scholarly journals STUDY ON THE CHEMICAL CONSTITUENTS OF THE ESSENTIAL OIL FROM NYCTANTHES ARBOR-TRISTIS AND ITS MOLECULAR DOCKING STUDIES

2019 ◽  
pp. 195-199
Author(s):  
KARTHICK V ◽  
VENKATAREDDY G ◽  
DHARANI J ◽  
RAVI S
Keyword(s):  
Molecular Docking ◽  
Chemical Composition ◽  
Essential Oil ◽  
Hydrophobic Interactions ◽  
Chemical Constituents ◽  
Docking Studies ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Molecular Docking Studies ◽  
Bacterial Proteins

Objectives: The objectives of this study were to determine the chemical composition of the essential oil obtained from the flowers of Nyctanthes arbor-tristis (NAT) and to carryout molecular docking studies against three bacterial proteins to study the mechanism of the antibacterial activity. Methods: The essential oil was obtained from the flowers of NAT by hydrodistillation and the chemical composition was determined by gas chromatography–mass spectrometry analysis. Docking study was carried out for 14 compounds identified from NAT against three bacterial proteins 1UAG, 3TYE, and 3UDI. Results: Fourteen compounds were identified in the essential oil. 1-octanol (74.81%) is the predominant compound followed by phytol (6.80%), bis (2-ethylhexyl) phthalate (5.88%), and eucarvone (4.23%). Many compounds are similar to that of the essential oil from jasmine. Among the 14 compounds identified, 7,9-di-tert-butyl-1-oxaspiro (4,5) deca-6,9-diene-2,8-dione interacted well with 1UAG and 3TYE and showed binding scores of −8.9 and −7.2 K Cal/mol, respectively, involving hydrophilic and hydrophobic interactions. With the protein 3UDI, the compound eucarvone exhibited a binding score of −7.1 K Cal/mol. Conclusion: The similarities between the essential oil constituents of flowers the two plants NAT and jasmine. Therefore, it could be concluded that NAT flowers of Coimbatore are a good source of fragrance for cosmetic industry and as an antibacterial agent.

Development of nanoemulsion from Vitex negundo L. essential oil and their efficacy of antioxidant, antimicrobial and larvicidal activities (Aedes aegypti L.)

2017 ◽  
Vol 24 (17) ◽  
pp. 15125-15133 ◽  
Author(s):  
Sundararajan Balasubramani ◽  
Thamaraiselvi Rajendhiran ◽  
Anil Kumar Moola ◽  
Ranjitha Kumari Bollipo Diana
Keyword(s):  
Essential Oil ◽  
Aedes Aegypti ◽  
Vitex Negundo ◽  
Larvicidal Activities

Structure, stability and folding of the α-helix

2001 ◽  
Vol 68 ◽  
pp. 95-110 ◽  
Author(s):  
Andrew J. Doig ◽  
Charles D. Andrew ◽  
Duncan A. E. Cochran ◽  
Eleri Hughes ◽  
Simon Penel ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrophobic Interactions ◽  
Data Bank ◽  
Site Directed Mutagenesis ◽  
Model Systems ◽  
Side Chain ◽  
Structure Stability ◽  
Helical Peptides ◽  
Vast Number ◽  
Α Helix

Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

scholarly journals (De)stabilization of Alpha-Synuclein Fibrillary Aggregation by Charged and Uncharged Surfactants

2021 ◽  
Vol 22 (22) ◽  
pp. 12509
Author(s):  
Joana Angélica Loureiro ◽  
Stéphanie Andrade ◽  
Lies Goderis ◽  
Ruben Gomez-Gutierrez ◽  
Claudio Soto ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Hydrophobic Interactions ◽  
Neurodegenerative Disorder ◽  
Sodium Dodecyl ◽  
Lewy Bodies ◽  
Alpha Synuclein ◽  
Cetyltrimethylammonium Chloride ◽  
Α Helix ◽  
Β Sheet

Parkinson’s disease (PD) is the second most common neurodegenerative disorder. An important hallmark of PD involves the pathological aggregation of proteins in structures known as Lewy bodies. The major component of these proteinaceous inclusions is alpha (α)-synuclein. In different conditions, α-synuclein can assume conformations rich in either α-helix or β-sheets. The mechanisms of α-synuclein misfolding, aggregation, and fibrillation remain unknown, but it is thought that β-sheet conformation of α-synuclein is responsible for its associated toxic mechanisms. To gain fundamental insights into the process of α-synuclein misfolding and aggregation, the secondary structure of this protein in the presence of charged and non-charged surfactant solutions was characterized. The selected surfactants were (anionic) sodium dodecyl sulphate (SDS), (cationic) cetyltrimethylammonium chloride (CTAC), and (uncharged) octyl β-D-glucopyranoside (OG). The effect of surfactants in α-synuclein misfolding was assessed by ultra-structural analyses, in vitro aggregation assays, and secondary structure analyses. The α-synuclein aggregation in the presence of negatively charged SDS suggests that SDS-monomer complexes stimulate the aggregation process. A reduction in the electrostatic repulsion between N- and C-terminal and in the hydrophobic interactions between the NAC (non-amyloid beta component) region and the C-terminal seems to be important to undergo aggregation. Fourier transform infrared spectroscopy (FTIR) measurements show that β-sheet structures comprise the assembly of the fibrils.

scholarly journals Inhibitory Effects of Cortex Dictamni Aqueous Extract on Dipeptidyl Peptidase I and Chymase Activities and the Screening of Active Ingredients in Cortex Dictamni Based on Molecular Docking Technique

2020 ◽  
Vol 12 (1) ◽  
pp. 19
Author(s):  
Qi Wang ◽  
Tao Wei ◽  
Xiaoying Zhou
Keyword(s):  
Molecular Docking ◽  
Aqueous Extract ◽  
Hydrophobic Interactions ◽  
Cell Model ◽  
Docking Simulation ◽  
Dipeptidyl Peptidase ◽  
Stable Complex ◽  
Molecular Docking Study ◽  
Natural Inhibitor ◽  
Anti Inflammatory

Dipeptidyl peptidase I (DPPI) and chymase, the granulo-proteases produced and released by mast cells, are important targets of anti-inflammatory drug research and development. Cortex Dictamni is a definite nature drug with anti-inflammatory activity, but the mechanism is unclear and effects of Cortex Dictamni on DPPI and chymase are unknown. This study focuses on effects of Cortex Dictamni aqueous extract (CDAE) on DPPI and chymase activities using cell model, bio-molecular interactions and the Molecular docking study by Discovery Studio (DS) analysis. The results showed that CDAE could significantly inhibit DPPI and chymase activities in vitro and in living rat spleen lymphocytes. Molecular docking simulation demonstrated that Troxerutin, the one of the active compounds of Cortex Dictamni, formed a hydrogen bond with amino acid ILE429 and a strong hydrophobic interaction with TYR64 CYS234 PRO279 ALA382 of DPPI. These interactions allow Troxerutin to form a stable complex with the DPPI, implicating that Troxerutin might be a potential natural inhibitor of DPPI. Dictamnoside M, another active compound of Cortex Dictamni formed hydrogen bonds and hydrophobic interactions within the binding pocket of chymase domain and form a stable complex with the chymase. Dictamnoside M maybe a potential natural inhibitor of chymase. This study suggested a new nature inhibitor Cortex Dictamni and its active components with the anti-inflammatory effects.

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