Cheminformatics Study on Structural and Bactericidal Activity of Latest Generation β-Lactams on Widespread Pathogens

Raman spectra of oxacillin (OXN), carbenicillin (CBC), and azlocillin (AZL) are reported for the first time together with their full assignment of the normal modes, as calculated using Density Functional Theory (DFT) methods with the B3LYP exchange-correlation functional coupled to the 6-31G(d) and 6-311+G(2d,p) basis sets. Molecular docking studies were performed on five penicillins, including OXN, CBC, and AZL. Subsequently, their chemical reactivity and correlated efficiency towards specific pathogenic strains were revealed by combining frontier molecular orbital (FMO) data with molecular electrostatic potential (MEP) surfaces. Their bactericidal activity was tested and confirmed on a couple of species, both Gram-positive and Gram-negative, by using the disk diffusion method. Additionally, a surface-enhanced Raman spectroscopy (SERS)—principal component analysis (PCA)-based resistogram of A. hydrophila is proposed as a clinically relevant insight resulting from the synergistic cheminformatics and vibrational study on CBC and AZL.     

Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)‐2‐Benzyl‐3‐dehydroquinic Acids

The binding mode of several substrate analogues, (2R)‐2‐benzyl‐3‐dehydroquinic acids 4 , which are potent reversible competitive inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by structural and computational studies. The crystal structures of Mycobacterium tuberculosis and Helicobacter pylori DHQ2 in complex with one of the most potent inhibitor, p‐methoxybenzyl derivative 4 a , have been solved at 2.40 Å and 2.75 Å, respectively. This has allowed the resolution of the M. tuberculosis DHQ2 loop containing residues 20–25 for the first time. These structures show the key interactions of the aromatic ring in the active site of both enzymes and additionally reveal an important change in the conformation and flexibility of the loop that closes over substrate binding. The loop conformation and the binding mode of compounds 4 b – d has been also studied by molecular dynamics simulations, which suggest that the benzyl group of inhibitors 4 prevent appropriate orientation of the catalytic tyrosine of the loop for proton abstraction and disrupts its basicity.     

Biological Evaluation of Potent Triclosan‐Derived Inhibitors of the Enoyl–Acyl Carrier Protein Reductase InhA in Drug‐Sensitive and Drug‐Resistant Strains of Mycobacterium tuberculosis

New triclosan (TRC) analogues were evaluated for their activity against the enoyl–acyl carrier protein reductase InhA in Mycobacterium tuberculosis (Mtb). TRC is a well‐known inhibitor of InhA, and specific modifications to its positions 5 and 4′ afforded 27 derivatives; of these compounds, seven derivatives showed improved potency over that of TRC. These analogues were active against both drug‐susceptible and drug‐resistant Mtb strains. The most active compound in this series, 4‐(n‐butyl)‐1,2,3‐triazolyl TRC derivative 3 , had an MIC value of 0.6 μg mL^?1 (1.5 μM ) against wild‐type Mtb. At a concentration equal to its MIC, this compound inhibited purified InhA by 98 %, and showed an IC₅₀ value of 90 nM . Compound 3 and the 5‐methylisoxazole‐modified TRC 14 were able to inhibit the biosynthesis of mycolic acids. Furthermore, mc²4914, an Mtb strain overexpressing inhA, was found to be less susceptible to compounds 3 and 14 , supporting the notion that InhA is the likely molecular target of the TRC derivatives presented herein.     

Discovery of an Acyclic Nucleoside Phosphonate that Inhibits Mycobacterium tuberculosis ThyX Based on the Binding Mode of a 5‐Alkynyl Substrate Analogue

The urgent need for new antibiotics poses a challenge to target un(der)exploited vital cellular processes. Thymidylate biosynthesis is one such process due to its crucial role in DNA replication and repair. Thymidylate synthases (TS) catalyze a crucial step in the biosynthesis of thymidine 5‐triphosphate (TTP), an elementary building block required for DNA synthesis and repair. To date, TS inhibitors have only been successfully applied in anticancer therapy due to their lack of specificity for antimicrobial versus human enzymes. However, the discovery of a new family of TS enzymes (ThyX) in a range of pathogenic bacteria that is structurally and biochemically different from the “classic” TS (ThyA) has opened the possibility to develop selective ThyX inhibitors as potent antimicrobial drugs. Here, the interaction of the known inhibitor 5‐(3‐octanamidoprop‐1yn‐1yl)‐2′‐deoxyuridine‐5′‐monophosphate ( 1 ) with Mycobacterium tuberculosis ThyX enzyme is explored using molecular modeling starting from published crystal structures, with further confirmation through NMR experiments. While the deoxyuridylate (dUMP) moiety of compound 1 occupies the cavity of the natural substrate in ThyX, the rest of the ligand (the “5‐alkynyl tail”) extends to the outside of the enzyme between two of its four subunits. The hydrophobic pocket that accommodates the alkyl part of the tail is formed by displacement of Tyr 44.C, Tyr 108.A and Lys 165.A. Changes to the resonance of the Lys 165 NH₃ group upon ligand binding were monitored in a titration experiment by 2D HISQC NMR. Guided by the results of the modeling and NMR studies, and inspired by the success of acyclic antiviral nucleosides, compounds where a 5‐alkynyl uracyl moiety is coupled to an acyclic nucleoside phosphonate (ANP) were synthesized and evaluated. Of the compounds evaluated, sodium (6‐(5‐(3‐octanamidoprop‐1‐yn‐1‐yl)‐2,4‐dioxo‐3,4‐dihydropyrimidin‐1(2H)‐yl)hexyl)phosphonate ( 3 e ) exhibited 43 % of inhibitory effect on ThyX at 50 μM . While only modest activity was achieved, this is the first example of an ANP inhibiting ThyX, and these results can be used to further guide structural modifications to this class to develop more potent compounds with potential application as antibacterial agents acting through a novel mechanism of action.     

Reexamination of the Ergothioneine Biosynthetic Methyltransferase EgtD from Mycobacterium tuberculosis as a Protein Kinase Substrate

Ergothioneine has emerged as a crucial cytoprotectant in the pathogenic lifestyle of Mycobacterium tuberculosis. Production of this antioxidant from primary metabolites may be regulated by phosphorylation of Thr213 in the active site of the methyltransferase EgtD. The structure of mycobacterial EgtD suggests that this post-translational modification would require a large-scale change in conformation to make the active-site residue accessible to a protein kinase. In this report, we show that, under in vitro conditions, EgtD is not a substrate of protein kinase PknD.     

生产过程检测点的故障诊断

阐述利用微机进行生产控制检测点故障诊断的简易、可行方法。     

Chemoenzymatic Synthesis and Antibody Binding of HIV-1 V1/V2 Glycopeptide-Bacteriophage Qβ Conjugates as a Vaccine Candidate

The broadly neutralizing antibody PG9 recognizes a unique glycopeptide epitope in the V1V2 domain of HIV-1 gp120 envelope glycoprotein. The present study describes the design, synthesis, and antibody-binding analysis of HIV-1 V1V2 glycopeptide-Qβ conjugates as a mimic of the proposed neutralizing epitope of PG9. The glycopeptides were synthesized using a highly efficient chemoenzymatic method. The alkyne-tagged glycopeptides were then conjugated to the recombinant bacteriophage (Qβ), a virus-like nanoparticle, through a click reaction. Antibody-binding analysis indicated that the synthetic glycoconjugates showed significantly enhanced affinity for antibody PG9 compared with the monomeric glycopeptides. It was also shown that the affinity of the Qβ-conjugates for antibody PG9 was dependent on the density of the glycopeptide antigen display. The glycopeptide-Qβ conjugates synthesized represent a promising candidate of HIV-1 vaccine.     

Recent Advances in the Research of Heterocyclic Compounds as Antitubercular Agents

Tuberculosis (TB) is a major health problem, with approximately one‐third of the world′s population infected with Mycobacterium tuberculosis, eight million people in the active disease state, and two million dying annually. Furthermore, the prevalence of TB/HIV co‐infection, and the emergence of multidrug‐resistant tuberculosis (MDR‐TB) and extensively drug‐resistant tuberculosis (XDR‐TB) have further aggravated the spread of this disease and thus mortality by it. There is an urgent need for novel antitubercular agents with improved properties, such as lower toxicity, shortened duration of therapy, rapid bactericidal action, and enhanced activity against MDR strains. Fortunately, a number of new potential antitubercular candidate drugs with heterocyclic rings, which are most likely to be effective against resistant strains, have entered clinical trials in recent years. This review highlights recent advances in the research of novel heterocyclic compounds, with particular focus on their antimycobacterial activity, mechanisms of action, toxicity, and structure–activity relationships (SARs).     

Mo–V–Nb mixed oxides as catalysts in the selective oxidation of ethane

Mo–V–Nb–O mixed metal oxides, obtained by heat-treatment in N₂ at 425 °C, have been studied as catalysts in the oxidative dehydrogenation of ethane. They present higher catalytic activity, while maintaining the same selectivity to ethylene, than the corresponding metal oxides calcined under air. Both amorphous and crystalline phases are present on active and selective catalysts. The implications of the presence of these phases as well as their physicochemical characteristics on the nature of active and selective sites are discussed.     

Determination of 3‐MCPD esters in edible oil – methods of analysis and comparability of results

The discovery of fatty acid esters of 3‐chloropropane‐1,2‐diol (3‐MCPD) in edible oil products initiated food monitoring campaigns in many EU Member States. As the determination of 3‐MCPD esters was new to most laboratories, questions on the reliability of the produced analysis data were raised. In response to this, the Institute for Reference Materials and Measurements (IRMM) of the European Commission's Joint Research Centre (JRC) organised a proficiency test on the determination of 3‐chloropropane‐1,2‐diol esters (3‐MCPD esters) in edible oils. The aim of this proficiency test was to scrutinise the capabilities of official food control laboratories, private food control laboratories as well as laboratories from food industry to determine the 3‐MCPD esters content of edible oils. The study was carried out in accordance with “The International Harmonised Protocol for the Proficiency Testing of Analytical Chemistry Laboratories” and ISO Guide 43. The test materials dispatched to the participants were: refined palm oil, extra virgin olive oil spiked with 3‐chloropropane‐1,2‐dioleate and 3‐MCPD standard solution in sodium chloride. Altogether 41 laboratories from 11 EU Member States, Switzerland and Macedonia subscribed for participation in the study. The analysis task was to determine the 3‐MCPD esters content as total 3‐MCPD content of the test samples. Participants were free to choose their analysis methods. In total, 34 laboratories reported results to the organisers of the study. The performance of laboratories in the determination of 3‐MCPD esters in edible oils was expressed by z‐scores. About 56% of the participants performed satisfactorily in the determination of 3‐MCPD esters in palm oil and 85% for the spiked extra virgin olive oil test sample. The study revealed that the direct transesterification of the sample without the prior removal of glycidol esters might lead to strong positive bias.     

Porous glasses in the 21st century––a short review

This article reviews recent studies concerning the preparation, modification, characterization, modeling and application of porous glasses on the basis of phase-separated alkali borosilicate glasses.     

Locating double bonds in lipids – New approaches to the use of ozonolysis

Since the location of double bonds within a lipid molecule is critical to its biological function, methods that reveal details of this structural arrangement are of importance. Ozone can react with double bonds resulting in ozonolysis products that have masses characteristic of the exact location of these double bonds within fatty acid residues. This paper describes the use of the ozonolysis reaction for the assignment of double bond positions, with a focus on the recent developments in coupling ozonolysis reactions in‐situ and in‐line with mass spectrometry, even for use with complex lipid samples.     

On the so-called “semi-ionic” C–F bond character in fluorine–GIC

The short-range structures of fluorine–graphite intercalation compounds with stage-1 structures, C_xF (x = 2.47, 2.84, 3.61), were analyzed by means of neutron diffraction. It has been shown that the so-called “semi-ionic” C–F bond character in C_xF is essentially covalent with the bond length of 0.140 nm, and the original planar graphene sheets are buckled at the sp³-hybridized carbon atoms bound to fluorine atoms. Conjugated C–C double bonds with the bond length of 0.142 nm are preserved between the carbon atoms unbound to fluorine atoms in C_xF, while other C–C bonds are single bonds with the bond lengths of 0.153 nm. The C–F bond order in C_xF is slightly lower than those in poly(carbon monofluoride) ((CF)_n) and poly(dicarbon monofluoride) ((C₂F)_n), which is explained by the hyperconjugation involving the C–C bonds on the carbon sheets and C–F bond.     

Preliminary Evaluation of Artemisinin–Cholesterol Conjugates as Potential Drugs for the Treatment of Intractable Forms of Malaria and Tuberculosis

To evaluate the feasibility of developing drugs that may be active against both malaria and tuberculosis (TB) by using in part putative cholesterol transporters in the causative pathogens and through enhancement of passive diffusion in granulomatous TB, artemisinin–cholesterol conjugates were synthesized by connecting the component molecules through various linkers. The compounds were screened in vitro against Plasmodium falciparum (Pf) and Mycobacterium tuberculosis (Mtb). Antimalarial activities (IC₅₀) against Pf drug‐sensitive NF54, and drug‐resistant K1 and W2 strains ranged from 0.03–2.6, 0.03–1.9, and 0.02–1.7 μm . Although the compounds are less active than the precursor artemisinin derivatives, the cholesterol moiety renders the compounds relatively insoluble in the culture medium, and variation in solubilities among the different compounds may reflect in the range of efficacies observed. Activities against Mtb H37Rv were assessed using a standardized colony‐forming unit (CFU) assay after 24 h pretreatment of cultures with each of the compounds. Percentage inhibition ranged from 3–38 % and 18–52 % at 10 and 80 μm , respectively. Thus, in contrast to the comparator drug artemether, the conjugates display enhanced activities. The immediate aims include the preparation of conjugates with enhanced aqueous solubilities, assays against malaria and TB in vivo, and for TB, assays using an infected macrophage model and assessment of granuloma influx.     

Phage Display to Identify Nedd8‐Mimicking Peptides as Inhibitors of the Nedd8 Transfer Cascade

The Nedd8 activating enzyme (NAE) launches the transfer of the ubiquitin‐like protein Nedd8 through an enzymatic cascade to covalently modify a diverse array of proteins, thus regulating their biological functions in the cell. The C‐terminal peptide of Nedd8 extends deeply into the active site of NAE and plays an important role in the specific recognition of Nedd8 by NAE. We used phage display to profile C‐terminal mutant sequences of Nedd8 that could be recognized by NAE for the activation reaction. We found that NAE can accommodate diverse changes in the Nedd8 C‐terminal sequence (⁷¹LALRGG⁷⁶), including Arg and Ile replacing Leu71, Leu, Ser, and Gln replacing Ala72, and substitutions by bulky aromatic residues at positions 73 and 74. We also observed that short peptides corresponding to the C‐terminal sequences of the Nedd8 variants can be activated by NAE to form peptide～NAE thioester conjugates. Once NAE is covalently loaded with these Nedd8‐mimicking peptides, it can no longer activate full‐length Nedd8 for transfer to the neddylation targets, such as the cullin subunits of cullin‐RING E3 ubiquitin ligases (CRLs). We have thus developed a new method to inhibit protein neddylation by Nedd8‐mimicking peptides.