Molecularly imprinted polymers with synthetic dummy templates for the preparation of capsaicin and dihydrocapsaicin from chili peppers

In this work, dummy molecularly imprinted polymers with high selectivity and affinity to capsaicin and dihydrocapsaicin are designed using N‐vanillylnonanamide as a dummy template. The performance of dummy molecularly imprinted polymers and nonimprinted polymers was evaluated using adsorption isotherms, adsorption kinetics, and selective recognition capacity. Dummy molecularly imprinted polymers were found to exhibit good site accessibility, taking just 20 min to achieve adsorption equilibrium; they were also highly selective toward capsaicin and dihydrocapsaicin. We successfully used dummy molecularly imprinted polymers as a specific sorbent for selectively enriching capsaicin and dihydrocapsaicin from chili pepper samples. In a scaled‐up experiment, the selective recovery of capsaicinoids was calculated to be 77.8% using solid‐phase extraction. To the best of our knowledge, this is the first example of the use of N‐vanillylnonanamide as a dummy template in molecularly imprinted polymers to simultaneously enrich capsaicin and dihydrocapsaicin.     

Molybdenum-catalyzed reduction of molecular dinitrogen into ammonia under ambient reaction conditions

Synthesis of transition metal–dinitrogen complexes and stoichiometric transformations of their coordinated dinitrogen into ammonia and hydrazine have so far been well investigated in order to achieve a novel nitrogen fixation under ambient conditions. As an extension of our study, the dimolybdenum–dinitrogen complex bearing PNP pincer ligands has been found to work as an effective catalyst for the formation of ammonia from dinitrogen, where 52 equiv of ammonia are produced based on the catalyst (26 equiv of ammonia are produced based on the molybdenum atom of the catalyst). This is the most effective catalytic reaction system for the formation of ammonia from molecular dinitrogen catalyzed by transition metal–dinitrogen complexes as catalysts under ambient reaction conditions. Herein, we describe recent results concerning the catalytic reaction, including the proposed reaction pathway.     

Understanding Molecular Dynamics with Stochastic Processes via Real or Virtual Dynamics

Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation[J. Chem. Phys. 147 , 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended "middle" scheme[J. Chem. Phys. 147 , 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation is proposed for understanding efficient stochastic thermostatting processes with molecular dynamics.     

Tetracyclines as a potential antiviral therapy against Crimean Congo hemorrhagic fever virus: Docking and molecular dynamic studies

Crimean-Congo Hemorrhagic Fever Virus (CCHFV) is one of the deadliest human diseases with mortality rate near 50%. Special attention should be paid to this virus since there is no approved treatment for it. On the other hand, the recent outbreak of Ebola virus which is a member of hemorrhagic fever viruses shows this group of viruses can be extremely dangerous. Previous studies have indicated that nucleoprotein of CCHFV, a pivotal protein in virus replication, is an appropriate target for antiviral drug development. The aim of this study is finding inhibitor(s) of this protein. Herein, a virtual screening procedure employing docking followed by molecular dynamic was used to identify small molecule inhibitors of the nucleoprotein from FDA-approved drugs. Regarding CCHFV, using in-silico method is a safe way to achieve its inhibitor(s) since this virus is categorized as a World Health Organization (WHO) biosafety level 4 pathogen and therefore investigation in general laboratories is restricted. In conclusion, considering docking and molecular dynamic results alongside with bioavailability of FDA-approved drugs, doxycycline and minocycline are proposed as potential inhibitors of CCHFV nucleoprotein. There is hope, this study encourage other research groups for in-vitro and in-vivo studies about the efficacy of those two medicines in CCHFV treatment.     

Disruption of redox catalytic functions of peroxiredoxin-thioredoxin complex in Mycobacterium tuberculosis H37Rv using small interface binding molecules

Mycobacterium tuberculosis has distinctive ability to detoxify various microbicidal superoxides and hydroperoxides via a redox catalytic cycle involving thiol reductants of peroxiredoxin (Prx) and thioredoxin (Trx) systems which has conferred on it resistance against oxidative killing and survivability within host. We have used computational approach to disrupt catalytic functions of Prx-Trx complex which can possibly render the pathogen vulnerable to oxidative killing in the host. Using protein–protein docking method, we have successfully constructed the Prx-Trx complex. Statistics of interface region revealed contact area of each monomer less than 1500 Å² and enriched in polar amino acids indicating transient interaction between Prx and Trx. We have identified ZINC40139449 as a potent interface binding molecule through virtual screening of drug-like compounds from ZINC database. Molecular dynamics (MD) simulation studies showed differences in structural properties of Prx-Trx complex both in apo and ligand bound states with regard to root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs). Interestingly, we found stability of two conserved catalytic residues Cys61 and Cys174 of Prx and conserved catalytic motif, WCXXC of Trx upon binding of ZINC40139449. The time dependent displacement study reveals that the compound is quite stable in the interface binding region till 30 ns of MD simulation. The structural properties were further validated by principal component analysis (PCA). We report ZINC40139449 as promising lead which can be further evaluated by in vitro or in vivo enzyme inhibition assays.     

A Gibbs sampling method to determine biomarkers for asthma

PurposeTo identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling.MethodsThe molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0.6. Moreover, the differentially expressed genes (DEGs) and their correlated genes were screened and merged, called as co-expressed genes. Pathways enrichment analysis was implemented for the co-expressed genes.ResultsBased on the gene set more than 5, overall 396 MFs were determined. After Gibbs sampling, 5 differentially expressed MF were acquired according to alfa.pi > 0.6. Moreover, the genes in these 5 differentially expressed MF were merged, and 110 DEGs were identified. Subsequently, 338 co-expressed genes were gained. Based on the P value < 0.01, the co-expressed genes were significantly enriched in 6 pathways. Among these, ubiquitin mediated proteolysis contained the maximum numbers of 35 co-expressed genes, and cell cycle were enriched by the second largest number of 11 co-expressed genes, respectively.ConclusionsThe identified pathways such as ubiquitin mediated proteolysis and cell cycle might play important roles in the development of asthma and may be useful for developing the credible therapeutic approaches for diagnosis and treatment of asthma in future.     

Virtual screening of B-Raf kinase inhibitors: A combination of pharmacophore modelling,molecular docking, 3D-QSAR model and binding free energy calculation studies

B-Raf kinase has been identified as an important target in recent cancer treatment. In order to discover structurally diverse and novel B-Raf inhibitors (BRIs), a virtual screening of BRIs against ZINC database was performed by using a combination of pharmacophore modelling, molecular docking, 3D-QSAR model and binding free energy (ΔG_bind) calculation studies in this work. After the virtual screening, six promising hit compounds were obtained, which were then tested for inhibitory activities of A375 cell lines. In the result, five hit compounds show good biological activities (IC₅₀ < 50 μM). The present method of virtual screening can be applied to find structurally diverse inhibitors, and the obtained five structurally diverse compounds are expected to develop novel BRIs.     

Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.     

Synthesis of 5-{[(1Hbenzo[d]imidazol-2-yl)sulfonyl]methyl}-3-phenyl-4,5-dihydroisoxazole derivatives,invitro antibacterial and antioxidant studies along with their insilico analyses

Synthesis of a series of novel sulfone derivatives 6(a-u) possessing benzimidazoles and isoxazoline rings tailored in a single molecule 5(a-u) was done by reactions using 5-(bromomethyl)-3-phenyl-4,5-dihydroisoxazoles 3(a-u) and 5-{[(1H-benzo[d]imidazol-2-yl)thio]methyl}-3-phenyl-4,5-dihydroisoxazoles 4(a-u) molecules. The chemical structures of all the newly synthesized compounds were established by IR, ¹HNMR, ¹³CNMR and LCMS spectral data. The biological characteristics of the novel sulfone compounds, such as their antioxidant and antibacterial activity, were evaluated. Among the synthesized sulfones derivatives, compounds 6 g, 6b, and 6e demonstrated outstanding antibacterial activity while compounds 6b, 6c, 6i, 6j, and 6 k demonstrated higher antioxidant activity. Further insilico absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies of synthesized sulfones were studied which exhibited excellent intestinal absorption which is more than 80 %, and relatively moderate toxicity. Molecular docking studies confirmed the antibacterial and antioxidant potential which is comparable with the standard.     

Study on gas adsorption and desorption characteristics on water injection coal

To study the desorption mechanism of methane in coal by H₂O injection and establish the Wiser molecular structure model of bituminous coal, the Grand Canonical Monte Carlo method was used to study the desorption behavior of CH₄ in coal with different amounts of H₂O injection at molecular scale. The results showed that at 293 K, the maximum adsorption capacity of H₂O was about 16 mmol/g, and that of CH₄ was about 8 mmol/g, which was about twice that of CH₄. This indicates that H₂O has a stronger adsorption capacity than CH₄. For methane-bearing coal, when the amount of water injected is 100, the average relative concentration of CH₄ is 0.5446, and the average relative concentration of CH₄ decreases by 33.77% compared to the water content of 20. Under the same time conditions, the root mean square displacement and diffusion coefficient of CH₄ decrease with the increase of H₂O injection quantity. With the increase of H₂O injection, the motion velocity of CH₄ in vacuum layer decreased. When water was injected, methane was trapped in the coal by water. The more H₂O injected, the more methane trapped in the coal, and the less methane desorption. This research lays a theoretical foundation for further research involving coal-water interaction.