Ordering of C-terminal Loop and Glutaminase Domains of Glucosamine-6-Phosphate Synthase Promotes Sugar Ring Opening and Formation of the Ammonia Channel

Discovery of metal-binding proteins by thermal proteome profiling

Metal-binding proteins (MBPs) have various and important biological roles in all living species and many human diseases are intricately linked to dysfunctional MBPs. Here, we report a chemoproteomic method named 'metal extraction-triggered agitation logged by thermal proteome profiling' (METAL-TPP) to globally profile MBPs in proteomes. The method involves the extraction of metals from MBPs using chelators and monitoring the resulting protein stability changes through thermal proteome profiling. Applying METAL-TPP to the human proteome with a broad-spectrum chelator, EDTA, revealed a group of proteins with reduced thermal stability that contained both previously known MBPs and currently unannotated MBP candidates. Biochemical characterization of one potential target, glutamine-fructose-6-phosphate transaminase 2 (GFPT2), showed that zinc bound the protein, inhibited its enzymatic activity and modulated the hexosamine biosynthesis pathway. METAL-TPP profiling with another chelator, TPEN, uncovered additional MBPs in proteomes. Collectively, this study developed a robust tool for proteomic discovery of MBPs and provides a rich resource for functional studies of metals in cell biology.

Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase

How motions in enzymes might be linked to catalytic function is of considerable general interest. Recent advances in X-ray crystallography and cryogenic electron microscopy offer the promise of elucidating functionally relevant motions in proteins that are not easily amenable to study by other biophysical methods. Here we use 3D variability analysis (3DVA) on cryo-EM maps for wild type (WT) human asparagine synthetase (ASNS) and the R142I ASNS variant to identify conformational changes in the Arg-142 side chain, which mediates the formation of a catalytically relevant intramolecular tunnel. Our 3DVA results for WT ASNS are consistent with independent molecular dynamics (MD) simulations on a model generated from the X-ray structure of human ASNS. Moreover, MD simulations of computational models for the ASNS/β-aspartyl-AMP/MgPPi and R142I/β-aspartyl-AMP/MgPPi ternary complexes, suggest that the structural integrity of the tunnel is impaired in the R142I variant when β-aspartyl-AMP is present in the synthetase active site. The kinetic properties of the R142I ASNS variant support the proposed function of Arg-142. These studies illustrate the power of cryo-EM to identify localized motions and dissect the conformational landscape of large proteins. When combined with MD simulations, 3DVA is a powerful approach to understanding how conformational dynamics might regulate function in multi-domain enzymes possessing multiple active sites.

Synthesis, characterization, computational studies and in vitro antiparasitic activity of novel flavanoidal-1,2,4,5-tetrazinane-6'-thione

Keeping in view the growing resistance of conventional antiparasitic drugs, this study aimed to synthesize a series of six noble flavanoidal tetrazinane-6'-thione derivatives by employing a facile one pot reaction pathway. Structural characterizations of synthesized compounds were performed by using IR, 1HNMR, 13CNMR and LC-MS spectra. Molecular docking study showed that one of the newly synthesized compounds strongly bind with the amino residues of BSA with two hydrogen bonding interactions. Physiological properties, pharmacokinetic properties (ADME) and toxicity of all synthesized compounds was carried out using Molinspiration and pkCSM softwares. DFT calculations were performed for all synthesized compounds using B3LYP method to obtain various molecular properties. Using a previously established model for parasitic infections, Clinostomum complanatum we showed that the newly synthesized compounds have a very potent parasitic activity. To elucidate the possible mechanisms, we tested the exposed parasites and observed a perturbation in lipid peroxidation and the antioxidant enzyme superoxide dismutase. Implications of this are discussed in the light of development of these molecules as antiparasitic drugs. HIGHLIGHTSSix noble flavanoidal-1,2,4,5-tetrazinane-6'-thiones (7-12) were synthesized using flavanone derivatives and thiocarbohydrazide in acetic acid as a reagent in ethanol employing one-pot synthesis.Structural characterization of synthesized compounds was done using IR, 1HNMR, 13CNMR and LC-MS spectra.Physicochemical analysis determined that all synthesized compounds are efficiently absorbed and have good permeability.In silico ADME and Toxic properties were determined for all synthesized compounds.In vitro antiparasitic activity was performed for all synthesized compounds against Clinostomum complanatum.Molecular Docking studies demonstrated the binding interaction with BSA enzyme through hydrogen bonding.Density functional theory (DFT) have been performed to estimate the various molecular properties of the synthesized compounds.Communicated by Ramaswamy H. Sarma.

Essential Oil Derived from Underutilized Plants Cymbopogon khasianus Poses Diverse Biological Activities against "Aspergillosis" and "Mucormycosis"

Palmrosa essential oil (PEO) from Cymbopogon khasianus, is used as complementary and traditional medicine worldwide. The present study aimed at compositional profiling of PEO and molecular docking of PEO bioactive compound geraniol against fungal enzymes chitin synthase (CS), UDP-glycosyltransferase (UDPG) and glucosamine-6-phosphate synthase (GPS), as apposite sites for drug designing against "Aspergillosis" and "Mucormycosis" and in vitro confirmation. Compositional profile of PEO was completed by GC-FID analysis. For molecular docking, Patch-dock tool was conducted. Ligand-enzyme 3D interactions were also calculated. ADMET properties (absorption, distribution, metabolism, excretion and toxicity) were also calculated. GC-FID discovered the occurrence of geraniol as a major component in PEO, thus nominated for docking analysis. Docking analysis specified active binding of geraniol to GPS, CS and UDPG fungal enzymes. Wet-lab authentication was achieved by three fungal strains Aspergillus niger, A. oryzae and Mucor sp. Docking studies revealed that ligand geraniol exhibited intercations with GPS, CS and UDPG fungal enzymes by H-bond and hydrophobic interactions. Geraniol obeyed LIPINSKY rule, and exhibited adequate bioactivity. Wet lab results indicated that PEO was able to inhibit fungal growth against "Aspergillosis" and "Mucormycosis".

The Hexosamine Biosynthesis Pathway: Regulation and Function

The hexosamine biosynthesis pathway (HBP) produces uridine diphosphate-N-acetyl glucosamine, UDP-GlcNAc, which is a key metabolite that is used for N- or O-linked glycosylation, a co- or post-translational modification, respectively, that modulates protein activity and expression. The production of hexosamines can occur via de novo or salvage mechanisms that are catalyzed by metabolic enzymes. Nutrients including glutamine, glucose, acetyl-CoA, and UTP are utilized by the HBP. Together with availability of these nutrients, signaling molecules that respond to environmental signals, such as mTOR, AMPK, and stress-regulated transcription factors, modulate the HBP. This review discusses the regulation of GFAT, the key enzyme of the de novo HBP, as well as other metabolic enzymes that catalyze the reactions to produce UDP-GlcNAc. We also examine the contribution of the salvage mechanisms in the HBP and how dietary supplementation of the salvage metabolites glucosamine and N-acetylglucosamine could reprogram metabolism and have therapeutic potential. We elaborate on how UDP-GlcNAc is utilized for N-glycosylation of membrane and secretory proteins and how the HBP is reprogrammed during nutrient fluctuations to maintain proteostasis. We also consider how O-GlcNAcylation is coupled to nutrient availability and how this modification modulates cell signaling. We summarize how deregulation of protein N-glycosylation and O-GlcNAcylation can lead to diseases including cancer, diabetes, immunodeficiencies, and congenital disorders of glycosylation. We review the current pharmacological strategies to inhibit GFAT and other enzymes involved in the HBP or glycosylation and how engineered prodrugs could have better therapeutic efficacy for the treatment of diseases related to HBP deregulation.

Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics?

Although the prevalence of antibiotic resistance is increasing at an alarming rate, there are a dwindling number of effective antibiotics available. Thus, the development of novel antibacterial agents should be of utmost importance. Peptidoglycan biosynthesis has been and is still an attractive source for antibiotic targets; however, there are several components that remain underexploited. In this review, we examine the enzymes involved in the biosynthesis of one such component, UDP-N-acetylglucosamine, an essential building block and precursor of bacterial peptidoglycan. Furthermore, given the presence of a similar biosynthesis pathway in eukaryotes, we discuss the current knowledge on the differences and similarities between the bacterial and eukaryotic enzymes. Finally, this review also summarises the recent advances made in the development of inhibitors targeting the bacterial enzymes.

Mechanisms of coordinating hyaluronan and glycosaminoglycan production by nucleotide sugars

Hyaluronan is a versatile macromolecule capable of an exceptional range of functions from cushioning and hydration to dynamic signaling in development and disease. Because of its critical roles, hyaluronan production is regulated at multiple levels including epigenetic, transcriptional, and post-translational control of the three hyaluronan synthase (HAS) enzymes. Precursor availability can dictate the rate and amount of hyaluronan synthesized and shed by the cells producing it. However, the nucleotide-activated sugar substrates for hyaluronan synthesis by HAS also participate in exquisitely fine tuned cross talking pathways that intersect with central carbohydrate metabolism. Multiple UDP-sugars have alternative metabolic fates and exhibit coordinated and reciprocal allosteric control of enzymes within their biosynthetic pathways to preserve appropriate precursor ratios for accurate partitioning among downstream products, while also sensing and maintaining energy homeostasis. Since the dysregulation of nucleotide sugar and hyaluronan synthesis is associated with multiple pathologies, these pathways offer opportunities for therapeutic intervention. Recent structures of several key rate-limiting enzymes in the UDP-sugar synthesis pathways have offered new insights to the overall regulation of hyaluronan production by precursor fate decisions. The details of UDP-sugar control and the structural basis for underlying mechanisms are discussed in this review.

Targeting UDP-Glycosyltransferase, Glucosamine-6-Phosphate Synthase and Chitin Synthase by Using Bioactive 1,8 Cineole for “Aspergillosis” Fungal Disease Mutilating COVID-19 Patients: Insights from Molecular Docking, Pharmacokinetics and In-vitro Studies

SARS-CoV-2 (COVID-19)-associated co-infections like “Aspergillosis”, has recently baffled the world. Due to its key role in cell wall synthesis, in the present study UDP-glycosyltransferase, glucosamine-6-phosphate synthase and chitin synthase have been chosen as appropriate targets for molecular docking. The objective of the present study was molecular docking of eucalyptus essential oil component 1,8 cineole against cell wall enzymes followed by in vitro validation. For molecular docking, patch-dock web based online tool was used. Ligand–Protein 2D and 3D Interactions were also studied. Drug likeliness, toxicity profile and cancer cell line toxicity were also studied. Molecular docking results indicated that 1,8 cineole form hydrogen bonding and hydrophobic interactions with UDP-glycosyltransferase, glucosamine-6-phosphate synthase and chitin synthase enzymes. 1,8 cineole also depicted drug likeliness by showing compliance with the LIPINSKY rule, sufficient level of bioactivity and cancer cell line toxicity thus signifying its role as a potent anti-fungal drug.

Essential oil from Cymbopogon citratus exhibits "anti-aspergillosis" potential: in-silico molecular docking and in vitro studies

BACKGROUND

Aspergillosis, has recently confounded some states of India. Due to major role in fungal cell wall synthesis, in the present study UDP-glycosyltransferase, Glucosamine-6-phosphate synthase and chitin synthase were chosen as an appropriate sites to design drug. The objective of present study was molecular docking of lemon grass essential oil component citral and in vitro validation. GC-FID analysis was used to find out aromatic profile. For docking, Patch-dock analysis was used. Ligand Protein 2D and 3D Interactions were also studied. Drug likeliness, and toxicity profile were also studied. Docking analysis indicated effective binding of citral to UDP-glycosyltransferase, Glucosamine-6-phosphate synthase and chitin synthase. In vitro validation was performed by fungal strain Aspergillus fumigatum.

RESULTS

GC-FID profiling revealed the presence of citral as major bioactive compound. Interactions results indicated that, UDP-glycosyltransferase, Glucosamine-6-phosphate synthase and chitin synthase enzymes and citral complexes forms hydrogen and hydrophobic interactions. Citral also depicted drug likeliness by LIPINSKY rule, sufficient level of bioactivity, drug likeliness and toxicity.

CONCLUSION

In vitro results revealed that lemon grass oil was able to inhibit growth of fungal strains toxicity thus signifying its role as potent anti-fungal drug.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s42269-022-00711-5.

Microwave assisted one-pot synthesis, photophysical and physicochemical studies of novel biologically active heterocyclic Donor (D)-π-Acceptor (A) chromophore

A donor-π-acceptor (D-π-A) chromophore, 2-amino-4-(9-ethyl-9H-carbazol-3-yl)-8-methoxy-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (AEDQ) was synthesized from the condensation of 6-methoxy-3,4-dihydronaphthalen-1(2H)-one, 9-ethyl-9H-carbazole-3-carbaldehyde, malononitrile and NH₄OAc in ethanol. Spectroscopic techniques and elemental analysis were employed to establish the structure of AEDQ. Photophysical parameters and fluorescence quantum yield were calculated in the different polarity solvents to evaluate the interactions of the solvent with AEDQ chromophore. Further, the interaction of the AEDQ with cationic and anionic surfactants (CTAB, SDS) were also evaluated by using fluorescence spectroscopy techniques. The intensity of the fluorescence spectrum increased as the concentration of surfactants increased, suggesting that strong interaction occurs between AEDQ with surfactants, and this interaction arises from electrostatic forces. As a result, the AEDQ chromophore could be used to determine the CMC of surfactants. The disc diffusion and minimal inhibitory concentration (MIC) technique were used to test in-vitro antibacterial activity against Gram +ve and Gram -ve bacteria, and the results are compared with the standard drug, tetracycline. AEDQ also showed good ADMET, pharmacokinetics and drug-likeness properties, which are desirable for a good drug candidate. The molecule also fits well in the DNA gyrase A active pocket site with the binding free energy of -17.92 kcal/mol, which testifies its good antibacterial activity.

Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1

The hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for glycosylation processes in mammals. It modulates the ER stress response and HP activation extends lifespan in Caenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the rate-limiting HP enzyme. GFAT-1 activity is modulated by UDP-GlcNAc feedback inhibition and via phosphorylation by protein kinase A (PKA). Molecular consequences of GFAT-1 phosphorylation, however, remain poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels in C. elegans. In human GFAT-1, the R203H substitution interferes with UDP-GlcNAc inhibition and with PKA-mediated Ser205 phosphorylation. Our data indicate that phosphorylation affects the interactions of the two GFAT-1 domains to control catalytic activity. Notably, Ser205 phosphorylation has two discernible effects: it lowers baseline GFAT-1 activity and abolishes UDP-GlcNAc feedback inhibition. PKA controls the HP by uncoupling the metabolic feedback loop of GFAT-1.

Molecular Docking Study of Active Diazenyl Scaffolds as Inhibitors of Essential Targets Towards Antimicrobial Drug Discovery

BACKGROUND

The diazenyl compounds (-N=N- linkage) have been reported to have antimicrobial activity. In modern drug discovery, the drug-receptor interactions are generally explored by the molecular docking studies.

MATERIALS AND METHODS

Three categories of diazenyl scaffolds were screened for the docking studies to explore the binding mechanism of interaction with various microbial targets. The diazenyl Schiff bases (SBN-20, SBN-21, SBN-25, SBN-33, SBN-39, SBN-40 and SBN-42), naphthol pharmacophore based diazenyl Schiff bases (NS-2, NS-8, NS-12, NS-15, NS-21, and NS-23), morpholine based diazenyl chalcones (MD-6, MD-9, MD-14, MD-16, MD-20, and MD-21) were docked against various bacterial and fungal proteins in comparison with different standard drugs. Further, the drug likeliness and ADME properties of these molecules were predicted by QikProp module of the Schrodinger software.

RESULTS

Most of the derivatives had shown less docking scores and binding energies towards bacterial proteins, such as dihydropteroate synthase (PDB:2VEG), glucosamine-6-phosphate synthase (PDB:2VF5), dihydrofolate reductase (PDB:3SRW) in comparison with the standard drugs. The naphthol based diazenyl Schiff bases NS-21 and NS-23 were predicted to act on the cytochrome P450 sterol 14-alpha-demethylase (CYP51) (PDB:5FSA) involved in sterol biosynthesis, an essential target for antifungal drugs. The derivative MD-6, NS-2, NS-21, and NS-23 had shown high docking scores against bacterial DNA topoisomerase (PDB:3TTZ) in comparison with the standard drug ciprofloxacin. Further, most of the synthesized derivatives had shown drug like characters.

CONCLUSION

Hence, these compounds can be developed as novel antibacterial agents as potent DNA topoisomerase inhibitors and antifungal agents as CYP51 inhibitors.

Potential of 2-Chloro-N-(4-fluoro-3-nitrophenyl)acetamide Against Klebsiella pneumoniae and In Vitro Toxicity Analysis

Klebsiella pneumoniae causes a wide range of community and nosocomial infections. The high capacity of this pathogen to acquire resistance drugs makes it necessary to develop therapeutic alternatives, discovering new antibacterial molecules. Acetamides are molecules that have several biological activities. However, there are no reports on the activity of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide. Based on this, this study aimed to investigate the in vitro antibacterial activity of this molecule on K. pneumoniae, evaluating whether the presence of the chloro atom improves this effect. Then, analyzing its antibacterial action more thoroughly, as well as its cytotoxic and pharmacokinetic profile, in order to contribute to future studies for the viability of a new antibacterial drug. It was shown that the substance has good potential against K. pneumoniae and the chloro atom is responsible for improving this activity, stabilizing the molecule in the target enzyme at the site. The substance possibly acts on penicillin-binding protein, promoting cell lysis. The analysis of cytotoxicity and mutagenicity shows favorable results for future in vivo toxicological tests to be carried out, with the aim of investigating the potential of this molecule. In addition, the substance showed an excellent pharmacokinetic profile, indicating good parameters for oral use.

Docking Related Survey on Heterocyclic Compounds Based on Glucosamine-6- Phosphate Synthase Inhibitors and their Antimicrobial Potential

The synthetic heterocyclic compounds have their importance due to their wide applications in various fields of science. The heterocyclic compounds have been reported for their anticancer, antitubercular, insecticides, analeptics, analgesic, anti-bacterial, anti-viral, anti-fungal, and weedicidal activity. Researchers have tried various newer targets in search of better antimicrobials acting via novel mechanisms. Glucosamine-6-Phosphate synthase is an enzyme present in microbial cells. The inactivation of G-6-P synthase may serve as a novel approach to find better antimicrobials. The increasing demands development of newer and effective antimicrobial drugs has reported in search of newer techniques for the generation of new drugs. Hence, the molecular docking technique shall be explored to find or investigate the newer target finding the novel compounds which can be an active antimicrobial compound. The present review has focused on the reported heterocyclic compounds which have been evaluated for their antimicrobial potential using G-6-P synthase as a target. The results of in silico methods and in vitro methods have been compared and critically discussed.

Loss of GFAT-1 feedback regulation activates the hexosamine pathway that modulates protein homeostasis

Glutamine fructose-6-phosphate amidotransferase (GFAT) is the key enzyme in the hexosamine pathway (HP) that produces uridine 5′-diphospho-N-acetyl-d-glucosamine (UDP-GlcNAc), linking energy metabolism with posttranslational protein glycosylation. In Caenorhabditis elegans, we previously identified gfat-1 gain-of-function mutations that elevate UDP-GlcNAc levels, improve protein homeostasis, and extend lifespan. GFAT is highly conserved, but the gain-of-function mechanism and its relevance in mammalian cells remained unclear. Here, we present the full-length crystal structure of human GFAT-1 in complex with various ligands and with important mutations. UDP-GlcNAc directly interacts with GFAT-1, inhibiting catalytic activity. The longevity-associated G451E variant shows drastically reduced sensitivity to UDP-GlcNAc inhibition in enzyme activity assays. Our structural and functional data point to a critical role of the interdomain linker in UDP-GlcNAc inhibition. In mammalian cells, the G451E variant potently activates the HP. Therefore, GFAT-1 gain-of-function through loss of feedback inhibition constitutes a potential target for the treatment of age-related proteinopathies.

Mutations in the hexosamine pathway key enzyme glutamine fructose-6-phosphate amidotransferase (GFAT-1) improve protein quality control and extend C. elegans lifespan. Here the authors present the crystal structures of full-length human GFAT-1 alone and with bound ligands and perform activity assays, which show that gain-of-function in the longevity-associated G451E variant is caused by a loss of feedback regulation.

Probing the antibacterial and anticancer potential of tryptamine based mixed ligand Schiff base Ruthenium(III) complexes

Development of new chemotherapeutic agents to treat microbial infections and recurrent cancers is of pivotal importance. Metal based drugs particularly ruthenium complexes have the uniqueness and desired properties that make them suitable candidates for the search of potential chemotherapeutic agents. In this study, two mixed ligand Ru(III) complexes [Ru(Cl)₂(SB)(Phen] (RC-1) and [Ru(Cl)₂(SB)(Bipy)] (RC-2) were synthesised and characterized by elemental analysis, IR, UV-Vis, ¹H, ¹³C NMR spectroscopic techniques and their molecular structure was confirmed by X-ray crystallography. Antibacterial activity evaluation against two Gram-positive (S. pneumonia and E. faecalis) and four Gram-negative strains (P. aurogenosa, K. pneumoniae, S. enterica, and E. coli) revealed their moderate antibacterial activity with MIC value of ≥250 μg/mL. Anticancer activity evaluation against a non-small lung cancer cell line (H1299) revealed the tremendous anticancer activity of these complexes which was further validated by DNA binding and docking results. DNA binding profile of the complexes studied by UV-Visible and fluorescence spectroscopy showed an intercalative binding mode with CT-DNA and an intrinsic binding constant in the range of 3.481-1.015× 10⁵ M^-1. Both the complexes were also found to exert weak toxicity to human erythrocytes by haemolytic assay compared to cisplatin. Potential of these complexes as anticancer agents will be further delineated by in vivo studies.

Synthesis, Molecular Docking and in Vitro Screening of Some Newly Synthesized Triazolopyridine, Pyridotriazine and Pyridine⁻Pyrazole Hybrid Derivatives

A series of novel pyridine and fused pyridine derivatives have been prepared starting from 6-(3,4-dimethylphenyl)-2-hydrazinyl-4-(thiophen-2-yl)-pyridine-3-carbonitrile 1 which on treatment with appropriate formic acid, acetic acid/acetic anhydride, benzoyl chloride and/or carbon disulfide afforded the corresponding triazolopyridine derivatives 2–5. Also, treatment of hydrazide 1 with diethyloxalate, chloroacetyl chloride, chloroacetic acid and/or 1,2-dichloroethane yielded the corresponding pyridotriazine derivatives 7–10. Further transformation of compound 1 with a different active methylene group, namely acetyl acetone, diethylmalonate, ethyl cyanoacetate, ethyl benzoylacetate and/or ethyl acetoacetate, produced the pyridine–pyrazole hybrid derivatives 11–15. These newly synthesized compounds (1–15) were subjected to in silico molecular docking screenings towards GlcN-6-P synthase as the target protein. The results revealed moderate to good binding energies of the ligands on the target protein. All the newly prepared products exhibited antimicrobial and antioxidant activity.

Facile one-pot multicomponent synthesis and molecular docking studies of steroidal oxazole/thiazole derivatives with effective antimicrobial, antibiofilm and hemolytic properties

A series of steroidal oxazole and thiazole derivatives have been synthesized employing thiosemicarbazide/semicarbazide hydrochloride and ethyl 2-chloroacetoacetate with a simple and facile one-pot multicomponent reaction pathway. The antimicrobial activity of newly synthesized compounds were evaluated against four bacterial strains namely Gram-negative (Escherichia coliand Pseudomonas aeruginosa) and Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) in addition to pathogenic fungi (Candida albicans and Cryptococcus neoformans). Bioactivity assay manifested that most of the compounds exhibited good antimicrobial activity. To provide additional insight into antimicrobial activity, the compounds were also tested for their antibiofilm activity against S. aureus biofilm. Moreover, molecular docking study shows binding of compounds with amino acid residues of DNA gyrase and glucosamine-6-phosphate synthase (promising antimicrobial target) through hydrogen bonding interactions. Hemolytic activity have been also investigated to ascertain the effect of compounds over RBC lysis and results indicate good prospects for biocompatibility. The expedient synthesis of steroidal heterocycles, effective antibacterial and antifungal behavior against various clinically relevant human pathogens, promising biocompatibility offer opportunities for further modification and potential applications as therapeutic agents.

Angular Phenozaxine Ethers as Potent Multi-microbial Targets Inhibitors: Design, Synthesis, and Molecular Docking Studies

The reaction of diaza-5H-benzo[a]phenoxazin-5-one and 5H-benzo[a]phenoxazin-5-one with various phenols catalyzed by Pd/t-BuXPhos/K3PO4 system gave previously unknown ether derivatives (7a-f and 8a-f) in good yields. UV-visible, FTIR, and 1H NMR data were used to confirm structures of the synthesized compounds. The parent compounds and the derivatives were screened in-silico for their drug-likeness and binding affinities to the microbial targets through molecular docking. Molinspiration software and AutoDock were used for the drug-likeness and docking studies, respectively. All the synthesized compounds showed strong drug-likeness. They also showed excellent binding affinities with glucosamine-6-phosphate synthase (2VF5), AmpC beta-lactamase (1KE4), and Lanosterol-14α-demethylase (3JUV), with compound 7e having the highest binding energies -9.5, -9.3, and -9.3 kcal/mol, respectively. These were found to be higher than the binding energies of the standard drugs. The binding energies of ciprofloxacin with 2VF5 and 1KE4 were -7.8 and -7.5 kcal/mol, respectively, while that of ketoconazole with 3JUV was -8.6 kcal/mol. The study showed that the synthesized compounds have multi-target inhibitory effects and can be very useful in multi-drug resistance cases. A 2D quantitative structural activity relationship (QSAR) model against target Glucosamine-6-phosphate synthase (2VF5) was developed using partial least squares regression (PLS) with good internal prediction (R2 = 0.7400) and external prediction (R2_ predicted = 0.5475) via Molecular Operating Environment (2014).

Design, synthesis, in silico and in vitro antimicrobial screenings of novel 1,2,4-triazoles carrying 1,2,3-triazole scaffold with lipophilic side chain tether

BACKGROUND

1,2,4-Triazoles and 1,2,3-triazoles have gained significant importance in medicinal chemistry.

RESULTS

This study describes a green, efficient and quick solvent free click synthesis of new 1,2,3-triazole-4,5-diesters carrying a lipophilic side chain via 1,3-dipolar cycloaddition of diethylacetylene dicarboxylate with different surfactant azides. Further structural modifications of the resulting 1,2,3-triazole diesters to their corresponding 1,2,4-triazole-3-thiones via multi-step synthesis has been also investigated. The structures of the newly designed triazoles have been elucidated based on their analytical and spectral data. These compounds were evaluated for their antimicrobial activities. Relative to the standard antimicrobial agents, derivatives of 1,2,3-triazole-bis-4-amino-1,2,4-triazole-3-thiones were the most potent antimicrobial agents with compound 7d demonstrating comparable antibacterial and antifungal activities against all tested microorganisms. Further, the selected compounds were studied for docking using the enzyme, Glucosamine-6-phosphate synthase.

CONCLUSIONS

The in silico study reveals that all the synthesized compounds had shown good binding energy toward the target protein ranging from - 10.49 to - 5.72 kJ mol-1 and have good affinity toward the active pocket, thus, they may be considered as good inhibitors of GlcN-6-P synthase.

Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc

Glucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes of it a potential target for anti-fungal, anti-bacterial and anti-diabetic therapy. The crystal structure of isomerase domain from human pathogenic fungus Candida albicans has been solved recently but it doesn't reveal the molecular mechanism details of inhibition taking place under UDP-GlcNAc influence, the unique feature of eukaryotic enzyme. The following study is a continuation of the previous research based on comparative molecular dynamics simulations of the structures with and without the enzyme's physiological inhibitor (UDP-GlcNAc) bound. The models used for this study included fructose-6-phosphate, one of the enzyme's substrates in its binding pocket. The simulation results studies demonstrated differences in mobility of the compared structures. Some amino acid residues were determined, for which flexibility is evidently different between the models. Importantly, it has been confirmed that the most fixed residues are related to the inhibitor binding process and to the catalysis reaction. The obtained results constitute an important step towards understanding of the inhibition that GlcN-6-P synthase is subjected by UDP-GlcNAc molecule.

Design, synthesis and pharmacological studies of some new quinoline Schiff bases and 2,5-(disubstituted-[1,3,4])-oxadiazoles

G6P-Ligand (4f) and (5b) interactions as visualized using Chimera (Version 1.8).

Antimicrobial activity of aroylhydrazone-based oxido vanadium(v) complexes: in vitro and in silico studies

A series of oxido vanadium(v) complexes have been synthesized and evaluated from the point of experimental and theoretical antimicrobial activity.

Synthesis, spectral characterization, structural studies, molecular docking and antimicrobial evaluation of new dioxidouranium(vi) complexes incorporating tetradentate N2O2 Schiff base ligands

Two new uranyl(vi) Schiff base complexes were synthesized and characterized by physicochemical and spectroscopic methods. The antimicrobial activities of these complexes were also investigated against microorganisms.

A molecular pathway for the egress of ammonia produced by nitrogenase

Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.

Characterization of a UDP-N-acetylglucosamine biosynthetic pathway encoded by the giant DNA virus Mimivirus

Mimivirus is a giant DNA virus belonging to the Megaviridae family and infecting unicellular Eukaryotes of the genus Acanthamoeba. The viral particles are characterized by heavily glycosylated surface fibers. Several experiments suggest that Mimivirus and other related viruses encode an autonomous glycosylation system, forming viral glycoproteins independently of their host. In this study, we have characterized three Mimivirus proteins involved in the de novo uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) production: a glutamine-fructose-6-phosphate transaminase (CDS L619), a glucosamine-6-phosphate N-acetyltransferase (CDS L316) and a UDP-GlcNAc pyrophosphorylase (CDS R689). Sequence and enzymatic analyses have revealed some unique features of the viral pathway. While it follows the eukaryotic-like strategy, it also shares some properties of the prokaryotic pathway. Phylogenetic analyses revealed that the Megaviridae enzymes cluster in monophyletic groups, indicating that they share common ancestors, but did not support the hypothesis of recent acquisitions from one of the known hosts. Rather, viral clades branched at deep nodes in phylogenetic trees, forming independent clades outside sequenced cellular organisms. The intermediate properties between the eukaryotic and prokaryotic pathways, the phylogenetic analyses and the fact that these enzymes are shared between most of the known members of the Megaviridae family altogether suggest that the viral pathway has an ancient origin, resulting from lateral transfers of cellular genes early in the Megaviridae evolution, or from vertical inheritance from a more complex cellular ancestor (reductive evolution hypothesis). The identification of a virus-encoded UDP-GlcNAc pathway reinforces the concept that GlcNAc is a ubiquitous sugar representing a universal and fundamental process in all organisms.

Utilization of protein intrinsic disorder knowledge in structural proteomics

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed.