Molecular docking studies of phytochemicals from Phyllanthus niruri against Hepatitis B DNA Polymerase

Antibiotic impregnation and nanocoating of external ventricular drainage catheters for antibacterial applications: Evaluation of in vitro studies and molecular docking

The most suitable method to treat hydrocephalus disease is to insert a shunt catheter that drains the cerebral spinal fluid (CSF); however, shunt implantation is often associated with various bacterial infections. In this study, antibiotic-loaded nanospheres were prepared using the solvent evaporation technique and coated on an antibiotic-impregnated shunt surface to promote shunt antibacterial properties. Clindamycin (CDM) and rifampicin (RIF) were in combination loaded in a single nanosphere, whereas trimethoprim (TMP) was loaded individually in triblock copolymers [(d,l-lactide-random-ε-caprolactone)-block-poly(ethylene glycol)-block-(d,l-lactide-random-ε-caprolactone)] (PLEC). The drug-loading content, encapsulation efficiency, yield, size, and zeta potential of the antibiotic-loaded nanospheres were measured. The results showed that the drug-loading content of clindamycin- and rifampicin-loaded nanospheres (CDM/RIF-NPs) was approximately 3% and 8%, respectively, at a drug to polymer ratio of 1:2. In addition, trimethoprim-loaded nanospheres (TMP-NPs) showed nearly 7% drug loading at equal drug and polymer ratios. The amount of drug release was determined before and after the coating of nanospheres on the shunt surface. In addition, in silico molecular docking studies indicated the good chemical interaction of these antibiotics with PLEC, and the results were consistent with those of impregnation studies. Antibacterial tests of coated external ventricular drainage showed antibacterial activity for up to 21 days.

Prediction of adsorption capacity and biodegradability of polybrominated diphenyl ethers in soil

Polybrominated diphenyl ethers (PBDEs) are widely used brominated flame retardants with strong toxicity concerns. Understanding the behaviors of PBDEs in soil is essential to evaluate their environmental impact. However, the limited, incoherent, and inaccurate data has challenged predicting the adsorption capacity and biodegradability of all 209 PBDE congeners in the soil. Moreover, there are minimal studies regarding the interactions between adsorption and biodegradation behaviors of PBDEs in the soil. Herein, in this study, we adopted quantitative structure-property relationship (QSAR) modeling to predict the adsorption behavior of 209 PBDE congeners by estimating their organic carbon-water partition coefficient (K_OC) values. In addition, the biodegradability of commonly occurring PBDE congeners was evaluated by analyzing their affinity to extracellular enzymes responsible for biodegradation using molecular docking. The results highlight that the degree of bromination plays a significant role in both the absorption and biodegradation of PBDEs in the soil due to compound stability and molecular geometry. Our findings help to advance the knowledge on PBDE behaviors in the soil and facilitate PBDE remediation associated with a soil environment.

An insight into the potent medicinal plant Phyllanthus amarus Schum. and Thonn

Phyllanthus amarus Schum. and Thonn., a globally distributed herb is known for its several therapeutic potentials. P. amarus has a long history of use in the traditional system of medicine for over 2000 years owing to its wide array of secondary metabolites that confer significant medicinal attributes. Research on various aspects including ethnobotany, phytochemistry to bioactivity, or pharmacological studies has been conducted over the past several decades on this potent herb. P. amarus extracts have shown a broad range of pharmacological activities like hepatoprotective, antioxidant, antiviral, antimicrobial, antidiabetic, anti-inflammatory, anticancer, antimalarial, nephroprotective, diuretic, and several other properties. The present review compiles and covers literature and research of several groups across past decades to date and focuses on how the therapeutic significance of this plant can be further explored for future research either as herbal formulations, alternative medicine, or in the pharmaceutical industry.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13237-022-00409-z.

Druggability for COVID-19: in silico discovery of potential drug compounds against nucleocapsid (N) protein of SARS-CoV-2

The coronavirus disease 2019 is a contagious disease and had caused havoc throughout the world by creating widespread mortality and morbidity. The unavailability of vaccines and proper antiviral drugs encourages the researchers to identify potential antiviral drugs to be used against the virus. The presence of RNA binding domain in the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be a potential drug target, which serves multiple critical functions during the viral life cycle, especially the viral replication. Since vaccine development might take some time, the identification of a drug compound targeting viral replication might offer a solution for treatment. The study analyzed the phylogenetic relationship of N protein sequence divergence with other 49 coronavirus species and also identified the conserved regions according to protein families through conserved domain search. Good structural binding affinities of a few natural and/or synthetic phytocompounds or drugs against N protein were determined using the molecular docking approaches. The analyzed compounds presented the higher numbers of hydrogen bonds of selected chemicals supporting the drug-ability of these compounds. Among them, the established antiviral drug glycyrrhizic acid and the phytochemical theaflavin can be considered as possible drug compounds against target N protein of SARS-CoV-2 as they showed lower binding affinities. The findings of this study might lead to the development of a drug for the SARS-Cov-2 mediated disease and offer solution to treatment of SARS-CoV-2 infection.

Druggability for COVID-19: in silico discovery of potential drug compounds against nucleocapsid (N) protein of SARS-CoV-2

The coronavirus disease 2019 is a contagious disease and had caused havoc throughout the world by creating widespread mortality and morbidity. The unavailability of vaccines and proper antiviral drugs encourages the researchers to identify potential antiviral drugs to be used against the virus. The presence of RNA binding domain in the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be a potential drug target, which serves multiple critical functions during the viral life cycle, especially the viral replication. Since vaccine development might take some time, the identification of a drug compound targeting viral replication might offer a solution for treatment. The study analyzed the phylogenetic relationship of N protein sequence divergence with other 49 coronavirus species and also identified the conserved regions according to protein families through conserved domain search. Good structural binding affinities of a few natural and/or synthetic phytocompounds or drugs against N protein were determined using the molecular docking approaches. The analyzed compounds presented the higher numbers of hydrogen bonds of selected chemicals supporting the drug-ability of these compounds. Among them, the established antiviral drug glycyrrhizic acid and the phytochemical theaflavin can be considered as possible drug compounds against target N protein of SARS-CoV-2 as they showed lower binding affinities. The findings of this study might lead to the development of a drug for the SARS-Cov-2 mediated disease and offer solution to treatment of SARS-CoV-2 infection.

Efficacy of a Chinese herbal formula on hepatitis B e antigen-positive chronic hepatitis B patients

BACKGROUND

No guideline recommends antiviral therapy for hepatitis B e antigen (HBeAg)-positive chronic hepatitis B patients with persistently normal alanine aminotransferase levels and a high hepatitis B virus (HBV) DNA viral load.

AIM

To evaluate the feasibility and safety of a Chinese herbal formula as a therapeutic option for chronic HBV infection.

METHODS

In total, 395 patients (30–65 years old) with confirmed HBeAg-positive chronic hepatitis B infection and persistently normal alanine aminotransferase were randomized to receive either Chinese herbal formula or placebo for 96 wk. Endpoints to evaluate therapeutic efficacy included: (1) HBV DNA levels decreased to less than 4 log10 IU/mL at weeks 48 and 96; and (2) HBeAg clearance and seroconversion rates at weeks 48 and 96.

RESULTS

HBV DNA levels ≤ 4 log10 IU/mL were 10.05% at week 48 and 18.59% at week 96 in the treatment group. The HBeAg clearance and conversion rates were 8.54% and 8.04% at week 48 and 16.08% and 14.57% at week 96, respectively. However, HBV DNA levels ≤ 4 log10 IU/mL were 2.55% and 2.55% at weeks 48 and 96, respectively, and the HBeAg clearance rates were 3.06% and 5.61% at weeks 48 and 96, respectively, in the control group. The quantitative hepatitis B surface antigen and HBeAg levels at baseline and changes during the treatment period as well as the alanine aminotransferase elevation at weeks 12 and 24 were strong predictors of HBeAg clearance.

CONCLUSION

High rates of HBV DNA reduction, HBeAg clearance and seroconversion could be achieved with Chinese herbal formula treatments, and the treatments were relatively safe for HBeAg-positive chronic hepatitis B-infected patients with persistently normal alanine aminotransferase. The ability of the compound to modulate host immune function probably contributed to this effect.

Molecular modeling and in vitro study on pyrocatechol as potential pharmacophore of CD151 inhibitor

CD151 has been recognized as a prognostic marker, the therapeutic target of breast cancers, but less explored for small molecule inhibitors due to lack of a validated model. The 3-D structure of CD151 large extracellular loop (LEL) was modeled using the LOMETS server and validated by the Ramachandran plot. The validated structure was employed for molecular docking and structure-based pharmacophore analysis. Druglikeness was evaluated by the ADMET description protocol. Antiproliferative activity was evaluated by MTT, BrdU incorporation, flow cytometry, and cell death ELISA^PLUS assay. This study predicted the best model for CD151-LEL with 94.1% residues in favored regions and Z score -2.79 kcal/mol using the threading method. The web-based receptor cavity method identified one functional target site, which was suitable for the binding of aromatic and heterocyclic compounds. Molecular docking study identified pyrocatechol (PCL) and 5-fluorouracil (FU) as potential leads of CD151-LEL. The pharmacophore model identified interaction points of modeled CD151-LEL with PCL and FU. Also, the analysis of ADMET properties revealed the drug-likeness of PCL and FU. The viability of MDA-MB 231 cells was significantly reduced with PCL and FU but less affected MCF-12A, normal healthy breast epithelial cell line. With 50% toxic concentration, both PCL and FU significantly inhibited 82.46 and 87.12% proliferation, respectively, of MDA-MB 231 cells by altering morphology and inducing G1 cell cycle arrest and apoptosis. In addition, PCL and FU inhibited the CD151 expression by 4.5-and 4.8-folds, respectively. This study suggests the further assessment of pyrocatechol as a potential lead of CD151 in breast cancer at the molecular level.

UPLC-HRMS and NMR applied in the evaluation of solid-phase extraction methods as a rational strategy of dereplication of Phyllanthus spp. aiming at the discovery of cytotoxic metabolites

The classical approach to drug discovery from natural products (NP's) requires strenuous and complex purification steps for the isolation and structural elucidation. Modern strategies as dereplication aim to accelerate the identification of known compounds present in a crude or partially purified extract. In this work, we investigated the influence of the solid-phase extraction (Oasis, Plexa, and Agilent C18 cartridges with and without organic modifiers) chemical profile obtained by UPLC-QTOF-MS and NMR and cytotoxicities of aqueous extracts from Phyllanthus niruri and P. amarus. Our results showed differences between the SPE cartridges and the mass recovered. P. niruri showed higher mass recovery than P. amarus indicating a higher amount of secondary metabolites. The UPLC-QTOF-MS analysis revealed that P. niruri crude extract presents higher contents of phenolic compounds than P. amarus. According to NMR analysis, P. niruri contained more tyrosine, corilagin, and glycosidic residues while P. amarus, presented higher content of ellagic acid. The different stationary phases, as well as mobile phases for exploratory SPE, enabled the exploitation of the different chemical functionalities within the Phyllanthus species. The SPE (MeOH:H₂O 70:30 with C18 cartridges) samples showed greater in vitro cytotoxicity than the crude extracts, with IC₅₀ ranging from 8.01 to 94.92 μg mL^-1 against the tumor lines tested. The solid phase extraction allowed the concentration of molecules with desirable physicochemical characteristics, which might increase the hit of therapeutically useful substances.

Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations

The aminotransferase from Bacillus circulans (BtrR), which is involved in the biosynthesis of butirosin, catalyzes the pyridoxal phosphate (PLP)-dependent transamination reaction to convert valienone to β-valienamine (a new β-glycosidase inhibitor for the treatment of lysosomal storage diseases) with an optical purity enantiomeric excess value. To explore the stereoselective mechanism of valienamine generated by BtrR, multiple molecular dynamics (MD) simulations were performed for the BtrR/PLP/valienamine and BtrR/PLP/β-valienamine complexes. The theoretical results showed that β-valienamine could make BtrR more stable and dense than valienamine. β-valienamine could increase the hydrogen bond probability and decrease the binding free energy between coenzyme PLP and BtrR by regulating the protein structure of BtrR, which was conducive to the catalytic reaction. β-valienamine maintained the formation of cation-p interactions between basic and aromatic amino acids in BtrR, thus enhancing its stability and catalytic activity. In addition, CAVER 3.0 analysis revealed that β-valienamine could make the tunnel of BtrR wider and straight, which was propitious to the removal of products from BtrR. Steered MD simulation results showed that valienamine interacted with more residues in the tunnel during dissociation compared with β-valienamine, resulting in the need for a stronger force to be acquired from BtrR. Taken together, BtrR was more inclined to catalyze the substrates to form β-valienamine, either from the point of view of the catalytic reaction or product removal.

Phyllanthus niruri versus Placebo for Chronic Hepatitis B Virus Infection: A Randomized Controlled Trial

BACKGROUND

This study aimed to investigate the efficacy and safety of a 12-month treatment with Phyllanthus niruri in subjects with chronic hepatitis B virus (HBV) infection.

PATIENTS AND METHODS

A placebo-controlled, parallel-group double-blind trial was performed. Clinical assessments took place at baseline and at 1, 3, 9, and 12 months after the treatment start and 6 months after treatment end.

RESULTS

In the first 2 years, 50 eligible subjects with chronic HBV accepted to participate. Of those, 47 completed all the study-related visits (6% drop-out rate): 24 of the 26 (92%) allocated to the Phyllanthus group and 23 of the 24 (96%) allocated to the placebo group completed the study. No statistically significant differences in viral load were found between the intervention and placebo groups after 12 months and no subjects showed HBsAg clearance. With regards to safety, there were no changes in renal function parameters in both groups after 12 months and no serious adverse events occurred due to the treatment. The study was stopped at the end of the second year because there was no apparent benefit of the treatment.

CONCLUSION

This study does not support the use of Phyllanthus niruri for the treatment of chronic hepatitis B.

Frangulosid as a novel hepatitis B virus DNA polymerase inhibitor: a virtual screening study

Hepatitis B virus (HBV) infects more than 400 million humans Worldwide. Currently, development of new anti-HBV agents is focused on inhibiting of HBV DNA polymerase activity. The natural components of medicinal plant have a broad spectrum of biological activities with therapeutic properties which can be exploited in various steps of drug discovery. Currently, in silico analyses have been introduced as alternative or supplements methods for drug discovery. This study was planned to in silico screening novel HBV DNA polymerase inhibitor(s) from R. palmatum, R. coreanus and S. officinalis. For this purpose, a set of dominant phytochemicals from mentioned plants were retrieved from PubChem database and primary screening was performed with molecular docking method using iGemdock 2.1 software. SwissADME and MedChem Designer 3.0 were used to calculate the drug-likeness parameters of the ligands. Furthermore, the genotoxicity of the studied ligands was predicted using Toxtree 2.6.6 software. Final analysis of screened compounds was done using Autodock 4 software. Result confirmed that Frangulosid and Lindleyin acid have most and least efficacy in HBV DNA polymerase inhibition with the inhibition constant of 2.97 and 53.83 µM, respectively. Results also showed that, the amino acids, involved in interaction, were different for each compound. In this regards, results revealed that the main amino acids residues of the receptor, involved in interaction with Quercetin-3-glucuronide, Frangulosid and Lindleyin separately, located in 420-424, 606-615 and 512-542 spectra, respectively. In conclusion, Frangulosid can be considered as a good candidate for more investigation of its anti-HBV activity.

Succinate production positively correlates with the affinity of the global transcription factor Cra for its effector FBP in Escherichia coli

BACKGROUND

Effector binding is important for transcription factors, affecting both the pattern and function of transcriptional regulation to alter cell phenotype. Our previous work suggested that the affinity of the global transcription factor catabolite repressor/activator (Cra) for its effector fructose-1,6-bisphosphate (FBP) may contribute to succinate biosynthesis. To support this hypothesis, single-point and three-point mutations were proposed through the semi-rational design of Cra to improve its affinity for FBP.

RESULTS

For the first time, a positive correlation between succinate production and the affinity of Cra for FBP was revealed in Escherichia coli. Using the best-fit regression function, a cubic equation was used to examine and describe the relationship between succinate production and the affinity of Cra for FBP, demonstrating a significant positive correlation between the two factors (coefficient of determination R² = 0.894, P = 0.000 < 0.01). The optimal mutant strain was Tang1683, which provided the lowest mutation energy of -4.78 kcal/mol and the highest succinate concentration of 92.7 g/L, which was 34% higher than that obtained using an empty vector control. The parameters for the interaction between Cra and DNA showed that Cra bound to the promoter regions of pck and aceB to activate the corresponding genes. Normally, Cra-regulated operons under positive control are deactivated in the presence of FBP. Therefore, theoretically, the enhanced affinity of Cra for FBP will inhibit the activation of pck and aceB. However, the activation of genes involved in CO₂ fixation and the glyoxylate pathway was further improved by the Cra mutant, ultimately contributing to succinate biosynthesis.

CONCLUSIONS

Enhanced binding of Cra to FBP or active site mutations may eliminate the repressive effect caused by FBP, thus leading to increased activation of genes associated with succinate biosynthesis in the Cra mutant. This work demonstrates an important transcriptional regulation strategy in the metabolic engineering of succinate production and provides useful information for better understanding of the regulatory mechanisms of transcription factors.

Bioguided Fraction and Isolation of the Antitumor Components from Phyllanthus niruri L

Phyllanthus niruri L., a well-known medicinal plant, has been used as a folk antitumor remedy in the worldwide scale. However, the antitumor components in P. niruri have not been reported. In order to verify the antitumor components of P. niruri and the plants which have the high content of these components, we isolated the antitumor components with bioguided fraction and isolation, by different chromatographic methods from the ethyl acetate fraction of P. niruri., and identified them as ethyl brevifolincarboxylate and corilagin by ¹H-NMR, ¹³C-NMR, 2D-NMR, and mass spectrometric analyses. Cell cytotoxicity assays showed that corilagin has broad-spectrum antitumor activity, a better antitumor potential, and lower toxicity in normal cells. Besides, the coefficient of drug interaction (CDI) of 10 μM corilagin and 20 μM cDDP reached up to 0.77, which means corilagin can promote the antitumor activity of cDDP. Furthermore, by the extensive screening among 10 species of plants reported to contain corilagin, we found that Dimocarpus longan Lour. has the maximum content of corilagin. In conclusion, corilagin is the major active antitumor composition in P. niruri. L. on HCC cells and has high content in D. longan.