Pose scoring by NMR

Recently, we have developed a fast approach to calculate NMR chemical shifts using the divide and conquer method at the semiempirical level. To demonstrate the utility of this approach for characterizing protein-ligand interactions, we used the deviation of calculated chemical shift perturbations from experiment to determine the orientation of a ligand (GPI-1046) in the binding pocket of the FK506 binding protein (FKBP12). Moreover, we were able to select the native state of the ligand from a collection of decoy poses. A key hydrogen bond between O1 and HN in Ile56 was also identified. Our results suggest that ligand-induced chemical shift perturbations can be used to refine protein/ligand structures.     

Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction

Pairwise decomposition of the interaction energy between molecules is shown to be a powerful tool that can increase our understanding of macromolecular recognition processes. Herein we calculate the pairwise decomposition of the interaction energy between the protein human carbonic anhydrase II (HCAII) and the fluorine-substituted ligand N-(4-sulfamylbenzoyl)benzylamine (SBB) using semiempirical quantum mechanics based methods. We dissect the interaction between the ligand and the protein by dividing the ligand and the protein into subsystems to understand the structure-activity relationships as a result of fluorine substitution. In particular, the off-diagonal elements of the Fock matrix that is composed of the interaction between the ionic core and the valence electrons and the exchange energy between the subsystems or atoms of interest is examined in detail. Our analysis reveals that the fluorine-substituted benzylamine group of SBB does not directly affect the binding energy. Rather, we find that the strength of the interaction between Thr199 of HCAII and the sulfamylbenzoyl group of SBB affects the binding affinity between the protein and the ligand. These observations underline the importance of the sulfonamide group in binding affinity as shown by previous experiments (Maren, T. H.; Wiley: C. E. J. Med. Chem. 1968, 11, 228-232). Moreover, our calculations qualitatively agree with the structural aspects of these protein-ligand complexes as determined by X-ray crystallography.     

A facile one‐pot synthesis of novel substituted 1,2,3,4‐tetrahydropyrimidine,part 2: Synthesis of 1‐(aralkyl/aryl)‐3‐(alkyl/aralkyl/aryl)‐5‐aroyl‐1,2,3,4‐tetrahydropyrimidines

1‐(Aralkyl/aryl)‐3‐(alkyyaralkyl)‐5‐aroyl‐1,2,3,4‐tetrahydropyrimidines ( 2a‐c ) have been synthesized by dethiomethylation of 5‐aroyl‐6‐methylthio‐1,2,3,4‐tetrahydropyrimidines ( 1a‐c ). An alternative one‐pot synthetic strategy has been developed for the title compounds 2a‐t by the reaction of enaminones 3 with pri mary amine and formaldehyde in refluxing methanol in good yields.     

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Summary An efficient and economical GC method for rapid determination of FAMEs in rapeseed-mustard is described. The seeds were transmethylated with acetylchloride, using microwave heating and separation achieved on a 3 m column packed with a mixture of 2% SP-2300 and 3% SP-2310 on Chromosorb ‘W’. The method is compared with the conventional heating method and extended efficiently for half-seed analysis. The fatty acid composition of the FAMEs mixtures prepared by both methods was similar with highly significant correlation coefficients (P<0.001).     

Ageratum conyzoides L. and Its Secondary Metabolites in the Management of Different Fungal Pathogens

Ageratum conyzoides L. (Family—Asteraceae) is an annual aromatic invasive herb, mainly distributed over the tropical and subtropical regions of the world. It owns a reputed history of indigenous remedial uses, including as a wound dressing, an antimicrobial, and mouthwash as well as in treatment of dysentery, diarrhea, skin diseases, etc. In this review, the core idea is to present the antifungal potential of the selected medicinal plant and its secondary metabolites against different fungal pathogens. Additionally, toxicological studies (safety profile) conducted on the amazing plant A. conyzoides L. are discussed for the possible clinical development of this medicinal herb. Articles available from 2000 to 2020 were reviewed in detail to exhibit recent appraisals of the antifungal properties of A. conyzoides. Efforts were aimed at delivering evidences for the medicinal application of A. conyzoides by using globally recognized scientific search engines and databases so that an efficient approach for filling the lacunae in the research and development of antifungal drugs can be adopted. After analyzing the literature, it can be reported that the selected medicinal plant effectively suppressed the growth of numerous fungal species, such as Aspergillus, Alternaria, Candida, Fusarium, Phytophthora, and Pythium, owing to the presence of various secondary metabolites, particularly chromenes, terpenoids, flavonoids and coumarins. The possible mechanism of action of different secondary metabolites of the plant against fungal pathogens is also discussed briefly. However, it was found that only a few studies have been performed to demonstrate the plant’s dosage and safety profile in humans. Considered all together, A. conyzoides extract and its constituents may act as a promising biosource for the development of effective antifungal formulations for clinical use. However, in order to establish safety and efficacy, additional scientific research is required to explore chronic toxicological effects of ageratum, to determine the probability of interactions when used with different herbs, and to identify safe dosage. The particulars presented here not only bridge this gap but also furnish future research strategies for the investigators in microbiology, ethno-pharmacology, and drug discovery.     

Applications of Fruit Polyphenols and Their Functionalized Nanoparticles Against Foodborne Bacteria: A Mini Review

The ingestion of contaminated water and food is known to cause food illness. Moreover, on assessing the patients suffering from foodborne disease has revealed the role of microbes in such diseases. Concerning which different methods have been developed for protecting food from microbes, the treatment of food with chemicals has been reported to exhibit an unwanted organoleptic effect while also affecting the nutritional value of food. Owing to these challenges, the demand for natural food preservatives has substantially increased. Therefore, the interest of researchers and food industries has shifted towards fruit polyphenols as potent inhibitors of foodborne bacteria. Recently, numerous fruit polyphenols have been acclaimed for their ability to avert toxin production and biofilm formation. Furthermore, various studies have recommended using fruit polyphenols solely or in combination with chemical disinfectants and food preservatives. Currently, different nanoparticles have been synthesized using fruit polyphenols to curb the growth of pathogenic microbes. Hence, this review intends to summarize the current knowledge about fruit polyphenols as antibacterial agents against foodborne pathogens. Additionally, the application of different fruit extracts in synthesizing functionalized nanoparticles has also been discussed.     

Furostane‐Type Steroidal Saponins from the Roots of Chlorophytum borivilianum

Four new furostanol steroid saponins, borivilianosides A–D ( 1 – 4 , resp.), corresponding to (3β,5α,22R,25R)‐26‐(β‐D ‐glucopyranosyloxy)‐22‐hydroxyfurostan‐3‐yl O‐β‐D ‐xylopyranosyl‐(1→3)‐O‐β‐D ‐glucopyranosyl‐(1→4)‐O‐[α‐L ‐rhamnopyranosyl‐(1→2)]‐β‐D ‐galactopyranoside ( 1 ), (3β,5α,22R,25R)‐ 26‐(β‐D ‐glucopyranosyloxy)‐22‐methoxyfurostan‐3‐yl O‐β‐D ‐xylopyranosyl‐(1→3)‐O‐β‐D ‐glucopyranosyl‐(1→4)‐O‐[α‐L ‐rhamnopyranosyl‐(1→2)]‐β‐D ‐galactopyranoside ( 2 ), (3β,5α,22R,25R)‐26‐(β‐D ‐glucopyranosyloxy)‐22‐methoxyfurostan‐3‐yl O‐β‐D ‐xylopyranosyl‐(1→3)‐O‐[β‐D ‐glucopyranosyl‐(1→2)]‐O‐β‐D ‐glucopyranosyl‐(1→4)‐β‐D ‐galactopyranoside ( 3 ), and (3β,5α,25R)‐26‐(β‐D ‐glucopyranosyloxy)furost‐20(22)‐en‐3‐yl O‐β‐D ‐xylopyranosyl‐(1→3)‐O‐[β‐D ‐glucopyranosyl‐(1→2)]‐O‐β‐D ‐glucopyranosyl‐(1→4)‐β‐D ‐galactopyranoside ( 4 ), together with the known tribuluside A and (3β,5α,22R,25R)‐26‐(β‐D ‐glucopyranosyloxy)‐22‐methoxyfurostan‐3‐yl O‐β‐D ‐xylopyranosyl‐(1→2)‐O‐[β‐D ‐xylopyranosyl‐(1→3)]‐O‐β‐D ‐glucopyranosyl‐(1→4)‐O‐[α‐L ‐rhamnopyranosyl‐(1→2)]‐β‐D ‐galactopyranoside were isolated from the dried roots of Chlorophytum borivilianum Sant and Fern . Their structures were elucidated by 2D ‐NMR analyses (COSY, TOCSY, NOESY, HSQC, and HMBC) and mass spectrometry.     

Nanofibril self-assembly of an arylene ethynylene macrocycle

Nanofibril structures have been fabricated from an arylene ethynylene macrocycle (AEM), which consists of a square frame corner-joined by four carbazole moieties. The fabrication was performed through a gelating process by cooling a warm, homogeneous solution in cyclohexane at high temperature (e.g., 100 degrees C) to room temperature. During the gelation, the molecules become organized, with optimal pi-pi stacking in cooperation with the side-chain association. The favorable pi-pi stacking facilitates the 1D growth of molecular assembly.     

Horse radish peroxidase immobilized polyaniline for hydrogen peroxide sensor

Horse radish peroxidase (HRP) has been electrochemically entrapped into perchlorate (ClO) doped polyaniline (PANI) film deposited onto indium‐tin‐oxide (ITO) coated glass plate. This HRP‐PANI‐ClO/ITO bioelectrode characterized using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), UV‐Visible spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) techniques has been utilized for estimation of hydrogen peroxide (H₂O₂). This H₂O₂ sensor exhibits response time of 5 s, linearity from 3 to 136 mM, sensitivity as 0.5638 µA mM^?1 cm^?2 with linear regression of 0.985. The value of the Michaelis–Menten constant (K_m) has been obtained as 1.984 mM. Copyright © 2009 John Wiley & Sons, Ltd.