The effect of plant metabolites on coronaviruses: A comprehensive review focusing on their IC50 values and molecular docking scores

2021 ◽  
Vol 21 ◽  
Author(s):  
Parastou Farshi ◽  
Eda Ceren Kaya ◽  
Fataneh Hashempour-Baltork ◽  
Kianoush Khosravi-Darani
Keyword(s):  
Molecular Docking ◽  
Inhibitory Effect ◽  
Organosulfur Compounds ◽  
Amino Acid Residues ◽  
Plant Metabolites ◽  
Primary Metabolites ◽  
Secondary Plant Metabolites ◽  
Protein Receptors ◽  
Ic50 Values ◽  
Natural Drugs

: Coronaviruses have caused worldwide outbreaks in different periods. SARS (severe acute respiratory syndrome), was the first emerged virus from this family, followed by MERS (Middle East respiratory syndrome) and SARS-CoV-2 (2019-nCoV or COVID 19), which is newly emerged. Many studies have been conducted on the application of chemical and natural drugs for treating these coronaviruses and they are mostly focused on inhibiting the proteases of viruses or blocking their protein receptors through binding to amino acid residues. Among many substances which are introduced to have an inhibitory effect against coronaviruses through the mentioned pathways, natural components are of specific interest. Secondary and primary metabolites from plants, are considered as potential drugs to have an inhibitory effect on coronaviruses. IC50 value (the concentration in which there is 50% loss in enzyme activity), molecular docking score and binding energy are parameters to understand the ability of metabolites to inhibit the specific virus. In this study we did a review of 154 papers on the effect of plant metabolites on different coronaviruses and data of their IC50 values, molecular docking scores and inhibition percentages are collected in tables. Secondary plant metabolites such as polyphenol, alkaloids, terpenoids, organosulfur compounds, saponins and saikosaponins, lectins, essential oil, and nicotianamine, and primary metabolites such as vitamins are included in this study.

scholarly journals A Comprehensive Review on the Effect of Plant Metabolites on Coronaviruses: Focusing on Their Molecular Docking Score and IC50 Values

2020 ◽  
Author(s):  
Parastou Farshi ◽  
Eda Ceren Kaya ◽  
Fataneh Hashempour-Baltork ◽  
Kianoush Khosravi-Darani
Keyword(s):  
Molecular Docking ◽  
Organosulfur Compounds ◽  
Amino Acid Residues ◽  
Plant Metabolites ◽  
Primary Metabolites ◽  
Secondary Plant Metabolites ◽  
Docking Score ◽  
Protein Receptors ◽  
Ic50 Values ◽  
Natural Drugs

Coronaviruses such as SARS (severe acute respiratory syndrome), MERS (Middle East respiratory syndrome), and newly emerged SARS-CoV-2, also called 2019-nCoV and COVID 19, have caused worldwide outbreaks in different time periods. There are many studies about chemical and natural drugs to treat these coronaviruses by inhibiting their proteases or their protein receptors through binding to amino acid residues. Plants secondary and primary metabolites are considered as potential drugs to inhibit various types of coronaviruses. IC50 value (the concentration in which there is 50% loss in enzyme activity) and molecular docking score and binding energy are parameters to understand the metabolites ability to inhibit the specific virus. In this study we did review on more than 110 papers on plant metabolites effect on different coronaviruses. Secondary plant metabolites such as polyphenols (flavonoids, coumarins, stilbenes), alkaloids, terpenoids, organosulfur compounds saponins, saikosaponins, lectins, essential oils, nicotianamine and primary metabolites such as vitamins.

scholarly journals Impact of B-Ring Substitution and Acylation with Hydroxy Cinnamic Acids on the Inhibition of Porcine α-Amylase by Anthocyanin-3-Glycosides

Foods ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 367 ◽  
Author(s):  
Julia A. H. Kaeswurm ◽  
Lisa Könighofer ◽  
Melanie Hogg ◽  
Andreas Scharinger ◽  
Maria Buchweitz
Keyword(s):  
Inhibitory Effect ◽  
Postprandial Blood Glucose ◽  
Titration Calorimetry ◽  
Plant Metabolites ◽  
Diabetes Mellitus Type Ii ◽  
Secondary Plant Metabolites ◽  
Vis Spectroscopy ◽  
Postprandial Blood Glucose Level ◽  
The Impact ◽  
Amylase Inhibitors

An inhibitory effect on α-amylase and α-glucosidase is postulated for polyphenols. Thus, ingestion of those secondary plant metabolites might reduce postprandial blood glucose level (hyperglycemia), which is a major risk factor for diabetes mellitus type II. In addition to a previous study investigating structure−effect relationships of different phenolic structures, the effect of anthocyanins is studied in detail here, by applying an α-amylase activity assay, on the basis of the conversion of 2-chloro-4-nitrophenyl-4-O-ß-galactopyranosyl maltoside (GalG2CNP) and detection of CNP release by UV/Vis spectroscopy and isothermal titration calorimetry (ITC). All anthocyanin-3-glucosides showed a mixed inhibition with a strong competitive proportion, Kic < 134 µM and Kiu < 270 µM; however, the impact of the B-ring substitution was not statistically significant. UV/Vis detection failed to examine the inhibitory effect of acylated cyanidins isolated from black carrot (Daucus carota ssp. Sativus var. Autrorubens Alef.). However, ITC measurements reveal a much stronger inhibitory effect compared to the cyanidin-3-glucoside. Our results support the hypothesis that anthocyanins are efficient α-amylase inhibitors and an additional acylation with a cinnamic acid boosts the observed effect. Therefore, an increased consumption of vegetables containing acylated anthocyanin derivatives might help to prevent hyperglycemia.

scholarly journals The inhibitory effect of KN-93 and KN-62 as a result of CaM-directed blocking animal CaMK2 and plant CDPK activation

2020 ◽  
Vol 26 ◽  
pp. 298-304
Author(s):  
D. O. Novozhylov ◽  
P. A. Karpov ◽  
D. O. Samofalova ◽  
M. A. Popitak ◽  
Ya. B. Blume
Keyword(s):  
Molecular Docking ◽  
Calcium Binding ◽  
Higher Plants ◽  
Inhibitory Effect ◽  
Binding Domain ◽  
Point Of View ◽  
Reference Structure ◽  
Amino Acid Residues ◽  
Score Functions ◽  
Calcium Binding Domain

Aim. The goal of the study was determine whether, from a molecular point of view, inhibitors KN-93 and KN-62 are capable to disrupt the functioning of plant homologs of CaMK2 and being used as tools for the experimental study of Ca2+-dependent phosphorylation in higher plants. Methods. Selected calmodulin 1 H.sapiens reference structure and reconstructed spatial structure of calcium-binding domain of CPK1 A.thaliana. We have conducted the molecular docking of calmodulin-mediated inhibitors to CaMK2: KN-93 and KN-62 for CALM1 H. sapiens and calcium-binding domain of CPK1 A. thaliana with full ligand mobility and static amino acid residues with the use of CCDC GOLD Suite. Results. We have established the presence of spatially homologous structures within CALM1 and CPK1 that might be the binding sites for KN-93 and KN-62. Performing the molecular docking we have shown the utility of those pockets from the point of binding energy for KN-93 and KN-62. We have conducted comparative analysis basing on the results of the CCDC GOLD Suite score functions (GoldScore and ASPScore). Conclusions. It has been shown that the inhibitors of animal CaMK2 - KN93 and KN62 are capable of interacting with the site of the CaM-like domain of the plant protein kinase CPK1 homologous to the similar site of animal calmodulin, which may impair its functionality. Keywords: CaMK2, CDPK, CPK1, protein kinases, molecular docking, KN-93, KN-62. 

In vitro and in silico studies of two 1,4-naphthoquinones and their topical formulation in bigels

2021 ◽  
Vol 18 ◽  
Author(s):  
Imen Khelifi ◽  
Audrey Tourrette ◽  
Daycem Khelifi ◽  
Thomas Efferth ◽  
El Akrem Hayouni ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Water Solubility ◽  
Biological Activities ◽  
Binding Energies ◽  
Topical Formulation ◽  
Plant Metabolites ◽  
Secondary Plant Metabolites ◽  
In Silico Studies

Background: 1,4-Naphthoquinones (1,4-NQs) are secondary plant metabolites with numerous biological activities. 1,4-NQs display low water solubility and poor bioavailability. Bigels are a new technology with great potential, which are designated as drug delivery systems. Biphasic bigels consisting of solid and liquid components represent suitable formulations improving the diffusion and bioavailability of NQs into the skin. Objective: We evaluated the in silico and in vitro activity of 5,8-dihydroxy-1,4-naphthoquinone (M1) and 2,3-dichloro-5,8-dihydroxy-1,4-naphthoquinone (M2) on elastase and assessed their cytotoxicity towards COLO38 melanoma cells. The 1,4-NQs were loaded into bigels for topical application. Methods: Molecular docking was performed, and cytotoxicity was evaluated on COLO38 cells using the resazurin assay. M1 and M2 were separately incorporated into bigels consisting of hydrogel organogel with sweet almond oil as a non-polar solvent and span 65 as organogelator. Their rheological behavior and microscopic properties were characterized. The diffusion kinetics and permeation of 1,4-NQs from bigels were studied by a paddle-over-extraction cell and a “Franz cell” in vitro permeation model. Results: Molecular docking data predicted high interactions between elastase and ligands. Hydrogen bonds to LYS233 were observed for M1, M2, and phosphoramidon (positive control). The average binding energies were -8.5 and -9.7 kcal/mol for M1 and M2 and -12.6 kcal/mol for phosphoramidon. M1 and M2 inhibited the elastase activity by 58.9 and 56.6%, respectively. M1 and M2 were cytotoxic towards COLO38 cells (IC50: 2.6 and 9.8 µM) y. The M1 release from bigels was faster and more efficient than that of M2. Conclusion: M1 and M2 are promising for skin disease treatment. Biphasic organogel-hydrogel bigels are efficient and safe formulations to overcome their low bioavailability.

scholarly journals Plant resistance does not compromise parasitoid-based biocontrol of a strawberry pest

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Daniela Weber ◽  
Paul A. Egan ◽  
Anne Muola ◽  
Lars E. Ericson ◽  
Johan A. Stenberg
Keyword(s):  
Plant Resistance ◽  
Leaf Beetle ◽  
Plant Metabolites ◽  
Breeding Programs ◽  
Primary Metabolites ◽  
Secondary Plant Metabolites ◽  
Phenotypic Resistance ◽  
Primary And Secondary Metabolites ◽  
Carbohydrate Levels ◽  
Plant Nutritional Quality

AbstractPlant nutritional  quality can influence interactions between herbivores and their parasitoids. While most previous work has focused on a limited set of secondary plant metabolites, the tri-trophic effects of overall phenotypic resistance have been understudied. Furthermore, the joint effects of secondary and primary metabolites on parasitoids are almost unexplored. In this study, we compared the performance and survival of the parasitoid species Asecodes parviclava Thompson on wild woodland strawberry (Fragaria vesca L.) genotypes showing variation in resistance against the parasitoid’s host, the strawberry leaf beetle (Galerucella tenella L.). Additionally, we related the metabolic profiles of these plant genotypes to the tritrophic outcomes in order to identify primary and secondary metabolites involved in regulating plant potential to facilitate parasitism. We found that parasitoid performance was strongly affected by plant genotype, but those differences in plant resistance to the herbivore were not reflected in parasitoid survival. These findings could be explained in particular by a significant link between parasitoid survival and foliar carbohydrate levels, which appeared to be the most important compounds for parasitism success. The fact that plant quality strongly affects parasitism should be further explored and utilized in plant breeding programs for a synergistic application in sustainable pest management.

scholarly journals Symmetrical Heterocyclic Cage Skeleton: Synthesis, Urease Inhibition Activity, Kinetic Mechanistic Insight, and Molecular Docking Analyses

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 312 ◽  
Author(s):  
Muhammad Hanif ◽  
Fariha Kanwal ◽  
Muhammad Rafiq ◽  
Mubashir Hassan ◽  
Muhammad Mustaqeem ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Competitive Inhibition ◽  
Inhibitory Effect ◽  
Urease Inhibition ◽  
Inhibition Activity ◽  
Design And Synthesis ◽  
Interactive Behavior ◽  
Ic50 Values ◽  
Urease Inhibition Activity

The present study focuses on the design and synthesis of a cage-like organic skeleton containing two triazole rings jointed via imine linkage. These molecules can act as urease inhibitors. The in-vitro urease inhibition screening results showed that the combination of the two triazole skeleton in the cage-like morphology exhibited comparable urease inhibition activity to that of the reference thiourea while the metallic complexation, especially with copper, nickel, and palladium, showed excellent activity results with IC50 values of 0.94 ± 0.13, 3.71 ± 0.61, and 7.64 ± 1.21 (3a–c), and 1.20 ± 0.52, 3.93 ± 0.45, and 12.87 ± 2.11 µM (4a–c). However, the rest of compounds among the targeted series exhibited a low to moderate enzyme inhibition potential. To better understand the compounds’ underlying mechanisms of the inhibitory effect (3a and 4a) and their most active metal complexes (3b and 4b), we performed an enzymatic kinetic analysis using the Lineweaver–Burk plot in the presence of different concentrations of inhibitors to represent the non-competitive inhibition nature of the compounds, 3a, 4a, and 4b, while mixed type inhibition was represented by the compound, 3b. Moreover, molecular docking confirmed the binding interactive behavior of 3a within the active site of the target protein.

Effect of human galanin on the response of circulating catecholamines to hypoglycemia in man

1995 ◽  
Vol 133 (6) ◽  
pp. 723-728 ◽  
Author(s):  
Ettore C degli Uberti ◽  
Maria R Ambrosio ◽  
Marta Bondanelli ◽  
Giorgio Transforini ◽  
Alberto Valentini ◽  
...  
Keyword(s):  
Heart Rate ◽  
Healthy Subjects ◽  
Sympathetic Nerve Activity ◽  
Heart Rate Response ◽  
Statistical Significance ◽  
Inhibitory Effect ◽  
Amino Acid Residues ◽  
Nerve Activity ◽  
Receptor Stimulation

degli Uberti EC, Ambrosio MR, Bondanelli M, Trasforini G, Valentini A, Rossi R, Margutti A, Campo M. Effect of human galanin on the response of circulating catecholamines to hypoglycemia in man. Eur J Endocrinol 1995;133:723–8. ISSN 0804–4643 Human galanin (hGAL) is a neuropeptide with 30 amino acid residues that has been found in the peripheral and central nervous system, where it often co-exists with catecholamines. In order to clarify the possible role of hGAL in the regulation of sympathoadrenomedullary function, the effect of a 60 min infusion of hGAL (80 pmol·kg−1 · min−1) on plasma epinephrine and norepinephrine responses to insulin-induced hypoglycemia in nine healthy subjects was investigated. Human GAL administration significantly reduced both the release of basal norepinephrine and the response to insulin-induced hypoglycemia, whereas it attenuated the epinephrine response by 26%, with the hGAL-induced decrease in epinephrine release failing to achieve statistical significance. Human GAL significantly increased the heart rate in resting conditions and clearly exaggerated the heart rate response to insulin-induced hypoglycemia, whereas it had no effect on the blood pressure. We conclude that GAL receptor stimulation exerts an inhibitory effect on basal and insulin-induced hypoglycemia-stimulated release of norepinephrine. These findings provide further evidence that GAL may modulate sympathetic nerve activity in man but that it does not play an important role in the regulation of adrenal medullary function. Ettore C degli Uberti, Chair of Endocrinology, University of Ferrara, Via Savonarola 9, I-44100 Ferrara, Italy

Homology Modeling of Mus Musculus CDK5 and Molecular Docking Studies with Flavonoids

2017 ◽  
Vol 9 (6) ◽  
Author(s):  
Sowmya Suri ◽  
Rumana Waseem ◽  
Seshagiri Bandi ◽  
Sania Shaik
Keyword(s):  
Molecular Docking ◽  
3D Model ◽  
Structural Features ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Cyclin Dependent Kinase ◽  
Ligand Complex ◽  
Ligand Interaction ◽  
Molecular Docking Studies ◽  
Cyclin Dependent Kinase 5

A 3D model of Cyclin-dependent kinase 5 (CDK5) (Accession Number: Q543f6) is generated based on crystal structure of P. falciparum PFPK5-indirubin-5-sulphonate ligand complex (PDB ID: 1V0O) at 2.30 Å resolution was used as template. Protein-ligand interaction studies were performed with flavonoids to explore structural features and binding mechanism of flavonoids as CDK5 (Cyclin-dependent kinase 5) inhibitors. The modelled structure was selected on the basis of least modeler objective function. The model was validated by PROCHECK. The predicted 3D model is reliable with 93.0% of amino acid residues in core region of the Ramachandran plot. Molecular docking studies with flavonoids viz., Diosmetin, Eriodictyol, Fortuneletin, Apigenin, Ayanin, Baicalein, Chrysoeriol and Chrysosplenol-D with modelled protein indicate that Diosmetin is the best inhibitor containing docking score of -8.23 kcal/mol. Cys83, Lys89, Asp84. The compound Diosmetin shows interactions with Cys83, Lys89, and Asp84.

Synthesis and Assessment of Novel Anti-chlamydial Benzylidene Acylhydrazides Derivatives

2018 ◽  
Vol 15 (1) ◽  
pp. 31-36 ◽  
Author(s):  
Xiaofeng Bao ◽  
Ying Xue ◽  
Chao Xia ◽  
Yin Lu ◽  
Ningjing Yang ◽  
...  
Keyword(s):  
Inhibitory Effect ◽  
Dependent Manner ◽  
Iron Starvation ◽  
Hydrochloride Salt ◽  
Obligate Intracellular ◽  
Biphasic Life Cycle ◽  
Ic50 Value ◽  
Ic50 Values ◽  
Dose Dependent ◽  
Better Than

Background: Chlamydiae, characterized by a unique biphasic life cycle, are a group of Gram-negative obligate intracellular bacterial pathogens responsible for diseases in a range of hosts including humans. Benzylidene acylhydrazide CF0001 could inhibit chlamydiae independent of iron starvation and T3SS inhibition. This finding promoted us to design and synthesize more benzylidene acylhydrazides to find novel anti-chlamydial agents. Methods: The carboxylic acids 1a-1d were coupled with Boc-hydrazide inpresence of EDCI and DMAP to obtain the intermediate 2a-2d in 60-62% yields. N-Boc deprotections were performed to obtain hydrazide hydrochloride salt 3a-3d. Nextly, the hydrazides were subjected to condensation with aldehydes to obtain benzylidene acylhydrazides 4a-4g in 30-52% yields in two steps. Results: Compound 4d exhibited best inhibitory effect on the formation and growth of chlamydial inclusions. The IC50 value of compound 4d for infectious progenies was 3.55 µM, better than 7.30 µM of CF0001. Conclusion: To find novel anti-chlamydial agents, we have designed and synthesized benzylidene acylhydrazides 4a-4g. Compounds 4a, 4d, 4g showed inhibitory activity on C. muridarum with the IC50 values from 3.55-12 µM. The 3,5-dibromo-4-hydroxyl substitutes on ring B are critical to keep their anti-chlamydial activity. Compound 4d inhibited C. muridarum in a dose-dependent manner without apparent cytotoxicity.

Inhibition Profiling of Urease and Carbonic Anhydrase II by High- Throughput Screening and Molecular Docking Studies of Structurally Diverse Organic Compounds

2020 ◽  
Vol 17 ◽  
Author(s):  
Majid Ali ◽  
Syed Majid Bukhari ◽  
Asma Zaidi ◽  
Farhan A. Khan ◽  
Umer Rashid ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Carbonic Anhydrase ◽  
Metal Complexes ◽  
Organic Compounds ◽  
High Throughput ◽  
High Throughput Screening ◽  
Docking Studies ◽  
Carbonic Anhydrase Ii ◽  
Molecular Docking Studies ◽  
Ic50 Values

Background:: Structurally diverse organic compounds and available drugs were screened against urease and carbonic anhydrase II in a formulation acceptable for high-throughput screening. Objective: The study was conducted to find out potential inhibitors of urease and carbonic anhydrase II. Methods:: Quantification of the possible HITs was carried out by determining their IC50 values. Results and Discussion:: of several screened compounds including derivatives of oxadiazole, coumarins, chromane-2, 4- diones and metal complexes of cysteine-omeprazole showed promising inhibitory activities with IC50 ranging from 47 μM to 412 μM against the urease. The interactions of active compounds with active sites of enzymes were investigated through molecular docking studies which revealed that (R)-1-(4-amino-4-(5-(thiophen-2-yl)-1,3,4-oxadiazol-2-yl) butyl) guanidine possessing IC50 of 47 μM, interacts with one of the nickel metal atom of urease besides further interactions as predictable hydrogen bonds with KCX490, Asp633, His492, His407 and His409 along with Ala440 and 636. Bi-ligand metal complexes of 4-aminoantipyrine based Schiff bases showed activation of urease with AC50 ranging from 68 μM to 112 μM. Almost 21 compounds with varying functional groups including pyrimidines, oxadiazoles, imidazoles, hydrazides and tin based compounds were active carbonic anhydrase II inhibitors presenting 98 μM to 390 μM IC50 values. Several N-substituted sulfonamide derivatives were inactive against carbonic anhydrase II. Conclusion:: Among all the screened compounds, highly active inhibitor of carbonic anhydrase II was (4-(3- hydroxyphenyl)-6-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)phenyl) methanone with IC50 of 98.0 μM. This particular compound showed metallic interaction with Zn ion of carbonic anhydrase II through hydroxyl group of phenyl ring.

Sign in / Sign up

Export Citation Format

Share Document