In silico assessment of the binding of reported bioactive compounds from Phaseolus vulgaris L. (Fabaceae) towards the wild-type and mutant estrogen receptor-alpha

Background@#Breast cancer is one of the leading causes of deaths in women worldwide, affecting nearly 7.8 million people. In 2020 in the Philippines, there were around 150,000 Filipinos who were newly diagnosed with the disease. The complex pathogenesis of breast cancer in addition to the emergence of resistance to therapy makes the treatment very challenging. Compounds that can antagonize the effects of estradiol towards ER-α, especially the mutant Y537S type are sought for. @*Objectives@#The focus of this study was the in-silico assessment of the reported secondary metabolites from Phaseolus vulgaris L. (fam. Fabaceae) towards the wild-type and mutant ER-α. Bioisosteric replacement was conducted to generate analogs that can possibly have a comparable binding affinity as estradiol towards estrogen receptors alpha. @*Results@#Majority of the secondary metabolites present in Phaseolus vulgaris L. belong to the group of phytoestrogens, phytosterols, and plant hormones. These groups of compounds exhibited favorable binding energies toward the wild-type and mutant (Y537S) estrogen receptors alpha. Moreover, they bind to the same ligand binding pocket as estradiol, involving similar interactions and amino acid residues. @*Conclusion@#Compounds from Phaseolus vulgaris L. can potentially target ER-α. Four gibberellin A19 analogs were generated that exhibited favorable binding towards the wild- and mutant- ER-α and may be further optimized to obtain a promisin gcompound against breast cancer.

Selective Separation and Preconcentration of Caffeine from Natural and Pharmaceutical Products using New Polyurethane Foams

Abstract Two polyurethane foam-based sorbents (PUF) were synthesized by imprinting and grafting techniques and examined for selective separation and preconcentration of caffeine (CAF) in some pharmaceutical products and in black tea. Molecularly imprinted PUF was synthesized based on hydrogen-bonding interactions between CAF and alizarin yellow G (AYG) and subsequent polymerization into PUF. The static experiments indicated optimum sorption conditions at pH=6.5 and 5.5 for imprinted PUF (AY-IPUF) and grafted PUF (AY-GPUF), respectively. In the online experiments, the suitable preconcentration time was found to be 40 and 20s for (AY-IPUF) and (AY-GPUF), respectively, at a flow rate of 1.75 mL.min-1. Desorption of CAF has been affected by passing 500 µL of 0.05, 0.01 mol.L−1 HCl eluent onto (AY-IPUF) and (AY-GPUF), respectively. The online methods have provided satisfactory enrichment factors of 8.4 and 10.5 for (AY-IPUF) and (AY-GPUF), respectively. The time consumed for preconcentartion, elution and determination steps was 1.48 and 1.05 min, thus, the throughput was 42 and 57 h-1, for (AY-IPUF) and (AY-GPUF), respectively. The developed sorbents were studied for the determination of CAF in pharmaceutical samples which will be helpful to minimize caffeinism. Finally, in silico bioactivity, ADMET and drug-likeness predictive computational studies of caffeine were also carried out

In silico screening of Allium cepa phytochemicals for their binding abilities to SARS and SARS-CoV-2 3C-like protease and COVID-19 human receptor ACE-2

@# Corona virus SARS-CoV-2-induced viral disease (COVID-19) is a zoonotic disease that was initially transmitted from animals to humans. The virus surfaced towards the end of December 2019 in Wuhan, China where earlier SARS (Severe Acute Respiratory Syndrome) had also surfaced in 2003. Unlike SARS, SARS-CoV-2 (a close relative of the SARS virus) created a pandemic, and as of February 24 2021, caused 112,778,672 infections and 2,499,252 deaths world-wide. Despite the best efforts of scientists, no drugs against COVID-19 are yet in sight; five vaccines have received emergency approval in various countries, but it would be a difficult task to vaccinate twice the world population of 8 billion. The objective of the present study was to evaluate through in silico screening a number of phytochemicals in Allium cepa (onion) regarding their ability to bind to the main protease of COVID-19 known as the 3C-like protease or 3CLpro, (PDB ID: 6LU7), 3CLpro of SARS (PDB ID: 3M3V), and human angiotensin converting enzyme-2 (ACE-2), [PDB ID: 1R42], which functions as a receptor for entry of the virus into humans. Molecular docking (blind docking, that is docking not only against any target pocket) were done with the help of AutoDockVina. It was observed that of the twenty-two phytochemicals screened, twelve showed good binding affinities to the main protease of SARS-CoV-2. Surprisingly, the compounds also demonstrated good binding affinities to ACE-2. It is therefore very likely that the binding affinities shown by these compounds against both 3CLpro and ACE-2 merit further study for their potential use as therapeutic agents.

Application of in silico screening technology in the medical research of natural products / 国际药学研究杂志

Natural products have always been one of the important sources of new chemical drugs. In recent years, with the continuous increase in the number of natural products reported, the separation and enrichment of new natural compounds have become more and more difficult, and the traditional high throughput screening methods have been unable to meet the needs of new drug development. Given its high efficiency and low cost, in silico(virtual)screening technology has gradually become indispensable in the research and development of new natural products. In this article, we introduce and compare the advantages and disadvantages of four in silico screening methods, collect and sort out the application cases of the virtual screening technology in the research of new natural products in recent years to provide a reference for researchers.

Validation of computationally predicted substrates for laccase

Present study reports the validation (oxidation) of computationally predicted oxidation of xenobiotic contaminants by commercially available pure laccase from Trametes versicolor. Selected contaminants were predicted as potential targets for laccase oxidation by using in-silico docking tool. The oxidation by laccase was measured by change in absorbance at specific λ max of each compound. Sinapic acid and tyrosine were taken as positive and negative controls, respectively. Oxidation was observed in m-chlorophenol, 2,4 di-chlorophenol, 2,4,6 tri-chlorophenol, captan, atrazine and thiodicarb, except malathion, which showed no activity. It could be speculated that the predicted substrates showing oxidation shared homology at structural and chemical level with positive control compounds. In case of malathion, structural non-homology with sinapic acid could be attributed to its inactivity towards laccase that required further structural analysis. Thus, a remediation tool proposing an advanced remediation approach combining the application of theoretical in-silico method and subsequent experimental validation using pure laccase could be proposed. As number and type of xenobiotics increase, the unfeasibility to screen them experimentally for bioremediation also rise. This approach would be useful to reduce the time and cost required in other screening methods.