C-methyl flavonoid from the leaves of Cleistocalyx conspersipunctatus: α-glucosidase inhibitory,molecular docking simulation and biosynthetic pathway

We extracted one new C-methyl flavonoid, farrerol 7-O-β-d-(6-O-galloyl)glucopyranoside (1), along with 11 known flavonoids, from the Cleistocalyx (C.) conspersipunctatus leaves. Elucidation of these flavonoid structures was accomplished through spectroscopic investigation and electronic circular dichroism (ECD) computation. Compared to corosolic acid (IC₅₀: 15.5 ± 0.9 μM), an established inhibitor, the compound 1 (IC₅₀: 6.9 ± 1.2 μM) was found more active in suppressing α-glucosidase. These findings imply the potential of compound 1 as a valid α-glucosidase inhibitor, which also offer evidence for future animal experiments and clinical trials. Besides, molecular docking was employed to explore the probable mechanism for α-glucosidase–compound 1 interaction. The biosynthetic pathway of these flavonoids in C. conspersipunctatus were proposed.     

Influence of the particle size on the antibacterial activity of green synthesized zinc oxide nanoparticles using Dysphania ambrosioides extract,supported by molecular docking analysis

Bacteria-associated infections have increased in recent years due to treatment resistance developed by these microorganisms. Due to the high antibacterial capacity associated with their nanometric size, nanoparticles, such as zinc oxide (ZnO), have proven to be an alternative for general medical procedures. One of the methodologies to synthesize them is green synthesis, where the most commonly used resources are plant species. Using Dysphania ambrosioides extract at various synthesis temperatures (200, 400, 600, and 800 °C), zinc oxide nanoparticles (ZnO-NPs) with average sizes ranging from 7 to 130 nm, quasi-spherical shapes, and hexagonal prism shapes were synthesized. Larger sizes were obtained by increasing the synthesis temperature. The ZnO crystalline phase was confirmed by X-ray diffraction and transmission electron microscopy. The sizes and shapes were observed by field emission scanning electron microscopy. The Zn-O bond vibration was identified by Fourier transform infrared spectroscopy. Thermogravimetry showed the stability of ZnO-NPs. The antibacterial evaluations, disk diffusion test, and minimum bactericidal concentration, demonstrated the influence of particle size. The smaller the nanoparticle size, the higher the inhibition for all pathogenic strains: Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Pseudomonas aeruginosa, and dental pathogens: Streptococcus mutans, Streptococcus sanguinis, Porphyromonas gingivalis, and Prevotella intermedia. The molecular docking study showed a favorable interaction between ZnO-NPs and some proteins in Gram-positive and Gram-negative bacteria, such as TagF in Staphylococcus epidermidis and AcrAB-TolC in Escherichia coli, which led to proposing them as possible targets of nanoparticles.     

The novel 4-hydroxyphenylpyruvate dioxygenase inhibitors in vivo and in silico approach: 3D-QSAR analysis,molecular docking,bioassay and molecular dynamics

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only an important target enzyme for the treatment of type I tyrosinemia, but also a new target for design bleaching herbicides, and it plays key role in the biosynthesis of tocopherol and plastoquinone. Thirty-six known active pyridine derivatives were collected, and comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models based on common skeleton were constructed to obtain novel HPPD herbicides with higher activity. Two new HPPD inhibitors were rationally designed and synthesized according to the CoMFA and CoMSIA models and verified by enzyme activity, biological assays, and molecular docking. The promising compound W1 ((E)-5-(3-(4-bromophenyl)acryloyl)-6-hydroxy-2,3-dihydropyridin-4(1H)-one) showed better AtHPPD inhibitory activity, and the bioassay results revealed that some weeds showed bleaching symptoms. The good binding stability of W1 and protein was confirmed by molecular dynamics simulation in 100 ns. These results would be highly useful in the progress of new HPPD inhibitors discovery.     

In silico and in vivo study of adulticidal activity from Ayapana triplinervis essential oils nano-emulsion against Aedes aegypti

Nanoinsecticides of plant origin have advantages in the resistance of Aedes aegypti, vectors of infectious diseases. The objective of this study was to evaluate the insecticidal potential of Ayapana triplinervis essential oil nano-emulsions using in silico and in vivo assays in an Aedes aegypti model. Molecular docking showed that minority compounds present in the morphotype A essential oil have a more significant binding affinity to inhibit acetylcholinesterase and juvenile hormone receptors. Aedes aegypti adults were susceptible to A. triplinervis at 150 µg.mL-1 in a diagnostic time of 15 min for morphotype A essential oil nano-emulsion and 45 min for morphotype B essential oil nano-emulsion. The evaluation of toxicity in Swiss albino mice indicated that the nano-emulsions had low acute dermal toxicity and presented LD₅₀ greater than 2000 mg.Kg^?1. Thus, it is possible to conclude that nano-emulsions have the potential to be used in the chemical control of A. aegypti.     

Phytochemical profiling,in vitro biological activities,and in-silico molecular docking studies of Typha domingensis

A comparative study between methanolic extract and n-hexane fraction of Typha domingensis (Typhaceae) was conducted for the evaluation of phytochemical potential, in vitro biological activities, and in-silico molecular docking studies. The phytochemical composition was estimated by total phenolic and total flavonoid contents, and by GC–MS analysis. Several biological activities were performed such as antioxidant assays (ABTS, FRAP, DPPH, & CUPRAC), enzyme inhibition activity (Tyrosinase, Acetylcholinesterase & Butyrylcholinesterase), thrombolytic activity, and antimicrobial activity (antibacterial & antiviral) to evaluate the medicinal importance of Typha domingensis. The results of the comparative study showed that methanolic extract has more total phenolic and total flavonoid contents (95.72 ± 5.76 mg GAE/g, 131.66 ± 7.92 mg QE/g, respectively) as compared to n-hexane fraction which confirms its maximum antioxidant potential (ABTS 114.31 ± 8.17, FRAP 116.84 ± 3.01, DPPH 283.54 ± 7.3 & CUPRAC 284.16 ± 6.5 mg TE/g). In the case of in vitro enzyme inhibition study and thrombolytic activity, better results were observed for methanolic extract. Almost similar antimicrobial patterns were observed for both methanolic extract and n-hexane fraction of Typha domingensis. The major bioactive phytochemicals identified by GC–MS were further analyzed for in-silico molecular docking studies to determine the binding affinity between ligands and the enzymes. The docking study indicated that most of the bioactive compounds showed a better binding affinity with enzymes as compared to the standard compounds (kojic acid & galantamine). The results of this study recommended that Typha domingensis has promising pharmaceutical importance and it should be further analyzed for the isolation of bioactive phytochemicals which may be useful for the treatment of several diseases.     

Evaluation of in vitro,in silico antidiabetic and antioxidant potential of bioactivity based isolated “Pakistanine” from Berberis baluchistanica

Bioassay based fractionation of methanolic extract of Berberis baluchistanica (Berberidaceae), used traditionally for internal injuries, led to the isolation of known compounds (1–4). The structure of these compounds was elucidated by different spectroscopic analysis and available literature data. Antidiabetic and antioxidant potentials of B. baluchistanica fractions and isolated compounds were evaluated using in vitro alpha- amylase and DPPH assays. The isolated compounds were identified as obamegine (1), pakistanine (2), 8-oxyberberine (3) and baluchistine (4). Obamegine was reported from many other species of this genus but it is first time isolated from B. baluchistanica in present study. Moreover, in vitro pakistanine (2) was found as bioactive lead molecule for hypoglycemic (IC₅₀:40.26 µg/ml) and antioxidant (IC₅₀:14.15 µg/ml) activities compared to acarbose (IC₅₀:33.68 µg/ml) and ascorbic acid (IC₅₀:0.41 µg/ml). To the best of our knowledge, no previous data were available for these biological activities. Additionally, in silico antidiabetic and antioxidant activity of pakistanine against two proteins, α-amylase (-9.7 kcal/mol) and tyrosinase (-8.7 kcal/mol) are reported here for the first time. The molecular docking binding interactions authenticate and support the above-mentioned activities and are helpful in predicting the mechanism of action of pakistanine (2).     

Atomistic De-novo Inhibitor Generation-Guided Drug Repurposing for SARS-CoV-2 Spike Protein with Free-Energy Validation by Well-Tempered Metadynamics

Computational drug design is increasingly becoming important with new and unforeseen diseases like COVID-19. In this study, we present a new computational de novo drug design and repurposing method and applied it to find plausible drug candidates for the receptor binding domain (RBD) of SARS-CoV-2 (COVID-19). Our study comprises three steps: atom-by-atom generation of new molecules around a receptor, structural similarity mapping to existing approved and investigational drugs, and validation of their binding strengths to the viral spike proteins based on rigorous all-atom, explicit-water well-tempered metadynamics free energy calculations. By choosing the receptor binding domain of the viral spike protein, we showed that some of our new molecules and some of the repurposable drugs have stronger binding to RBD than hACE2. To validate our approach, we also calculated the free energy of hACE2 and RBD, and found it to be in an excellent agreement with experiments. These pool of drugs will allow strategic repurposing against COVID-19 for a particular prevailing conditions.     

Identification of 3-Methoxycarpachromene and Masticadienonic Acid as New Target Inhibitors against Trypanothione Reductase from Leishmania Infantum Using Molecular Docking and ADMET Prediction

Polyphenolic and Terpenoids are potent natural antiparasitic compounds. This study aimed to identify new drug against Leishmania parasites, leishmaniasis’s causal agent. A new in silico analysis was accomplished using molecular docking, with the Autodock vina program, to find the binding affinity of two important phytochemical compounds, Masticadienonic acid and the 3-Methoxycarpachromene, towards the trypanothione reductase as target drugs, responsible for the defense mechanism against oxidative stress and virulence of these parasites. There were exciting and new positive results: the molecular docking results show as elective binding profile for ligands inside the active site of this crucial enzyme. The ADMET study suggests that the 3-Methoxycarpachromene has the highest probability of human intestinal absorption. Through this work, 3-Methoxycarpachromene and Masticadienonic acid are shown to be potentially significant in drug discovery, especially in treating leishmaniasis. Hence, drug development should be completed with promising results.     

Identification,Characterization and Antihypertensive Effect In Vivo of a Novel ACE-Inhibitory Heptapeptide from Defatted Areca Nut Kernel Globulin Hydrolysates

The areca (Areca catechu L.) nut kernel (ANK) is a good potential protein source for its high protein content of 9.89–14.62 g/100 g and a high yield of around 300,000 tons per year in China. However, utilization of the areca nut kernel is limited. To expand the usage of ANK in pharmaceutical or foods industries, areca nut kernel globulin was extracted and angiotensin-I converting enzyme (ACE) inhibition peptides were prepared and identified using gel chromatography, reversed phase HPLC separation, UPLC-ESI-MS/MS analysis and in silico screening. Finally, a novel ACE-inhibitory heptapeptide (Ala–Pro–Lys–Ile–Glu–Glu–Val) was identified and chemically synthesized. The combination pattern between APKIEEV and ACE, and the inhibition kinetics, antihypertensive effect and endothlein-1 inhibition activity of APKIEEV were studied. The results of the molecular docking demonstrated that APKIEEV could bind to four active sites (not the key active sites) of ACE via short hydrogen bonds and demonstrated high ACE-inhibitory activity (IC₅₀: 550.41 μmol/L). Moreover, APKIEEV exhibited a significantly lowering effect on both the systolic blood pressure and diastolic blood pressure of spontaneously hypertensive rats, and had considerable suppression ability on intracellular endothelin-1. These results highlight the potential usage of APKIEEV as ingredients of antihypertensive drugs or functional foods.     

Prediction of African Swine Fever Virus Inhibitors by Molecular Docking-Driven Machine Learning Models

African swine fever virus (ASFV) causes a highly contagious and severe hemorrhagic viral disease with high mortality in domestic pigs of all ages. Although the virus is harmless to humans, the ongoing ASFV epidemic could have severe economic consequences for global food security. Recent studies have found a few antiviral agents that can inhibit ASFV infections. However, currently, there are no vaccines or antiviral drugs. Hence, there is an urgent need to identify new drugs to treat ASFV. Based on the structural information data on the targets of ASFV, we used molecular docking and machine learning models to identify novel antiviral agents. We confirmed that compounds with high affinity present in the region of interest belonged to subsets in the chemical space using principal component analysis and k-means clustering in molecular docking studies of FDA-approved drugs. These methods predicted pentagastrin as a potential antiviral drug against ASFVs. Finally, it was also observed that the compound had an inhibitory effect on AsfvPolX activity. Results from the present study suggest that molecular docking and machine learning models can play an important role in identifying potential antiviral drugs against ASFVs.