Antibacterial Effects of Flavonoids and Their Structure-Activity Relationship Study: A Comparative Interpretation

According to the latest report released by the World Health Organization, bacterial resistance to well-known and widely available antibacterial drugs has become a significant and severe global health concern and a grim challenge to tackle in order to cure infections associated with multidrug-resistant pathogenic microorganisms efficiently. Consequently, various strategies have been orchestrated to cure the severe complications related to multidrug-resistant bacteria effectively. Some approaches involved the retardation of biofilm formation and multidrug-resistance pumps in bacteria as well as the discovery of new antimicrobial agents demonstrating different mechanisms of action. In this regard, natural products namely alkaloids, terpenoids, steroids, anthraquinone, flavonoids, saponins, tannins, etc., have been suggested to tackle the multidrug-resistant bacterial strains owing to their versatile pharmacological effects. Amongst these, flavonoids, also known as polyphenolic compounds, have been widely evaluated for their antibacterial property due to their tendency to retard the growth of a wide range of pathogenic microorganisms, including multidrug-resistant bacteria. The hydroxylation of C5, C7, C3′, and C4′; and geranylation or prenylation at C6 have been extensively studied to increase bacterial inhibition of flavonoids. On the other hand, methoxylation at C3′ and C5 has been reported to decrease flavonoids’ antibacterial action. Hence, the latest information on the antibacterial activity of flavonoids is summarized in this review, with particular attention to the structure–activity relationship of this broad class of natural compounds to discover safe and potent antibacterial agents as natural products.     

Synthesis and Antimicrobial Activity of 2-Methyl-5-nitroaniline Derivatives:A Structure-Activity Relationship Study

A series of 2‐methyl‐5‐nitroaniline derivatives, 5a – 5k and 6a – 6f , were synthesized in order to determine their in vitro antimicrobial activity. The chemical structures of the synthesized compounds were confirmed by elemental analyses, UV‐visible, FT‐IR, ¹H NMR and ¹³C NMR spectral studies. The structure‐activity relationships of the synthesized compounds were also discussed. Among the synthesized compounds, 5f , 5d , 6b and 6e showed good antimicrobial activity compared to standard drugs.     

A Structure-Activity Relationship Study of Lapachol and Some Derivatives of 1,4-Naphthoquinones Against Carcinosarcoma Walker 256

AMI semiempirical molecular orbital calculations were carried out on lapachol and several derivatives of 1,4-naphthoquinone in order to investigate possible relationships between electronic structural parameters and activity against carcinosarcoma Walker 256 (W256). It was found that, among the calculated electronic indices, that the HOMO (highest occupied molecular orbital) coefficients for carbon atoms of the side-chain double bond have a significant influence in the activity, while the LUMO (lowest unoccupied molecular orbitals) apparently have no importance. Exploratory data analysis through hierarchical cluster (HCA) and principal component analysis (PCA) showed a clear separation of the active compounds from the inactive ones. The activity against W256 probably involves a mechanism wherein the quinone acts as a reducing agent through the participation of the -electrons of the side-chain double bond. A classification study with respect to structure-activity using KNN (K-nearest neighbors) and SIMCA (soft independent modeling of class analogy), two established chemometric methods of pattern recognition, have been used to predict activity for a series of lapachol derivatives.     

Crystal Structures of trans-Tetrahydrotetrols of Benzo[a]pyrene and Chrysene: A Possible Structure-Activity Relationship in Quasi-Planar Bay-Region Polycyclic Aromatic Hydrocarbons

The molecular structures of two racemic trans-tetrahydrotetrols formed by hydrolysis of the (±)anti-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydro derivatives of the strong carcinogen benzo[a]pyrene and the weak carcinogen chrysene have been determined by X-ray crystallographic methods.³ Focusing on the (+)isomers, the stereochemical features of the two tetrols are discussed in detail to determine structural differences, which can be related to the different biological activity of their parent hydrocarbons, since they provide a model for the hydrocarbon moiety in the major PAH-DNA adduct. As a result of this study, a tentative correlation can be stated between biological activity of quasi-planar bay-region PAHs and the presence of structural features, which can decrease the steric hindrance of the aromatic skeleton and the other hydroxy groups on the pseudo-axial O4, which mimics the position of the covalent bond to DNA. The significant structural features seem to be an out-of-plane distortion with a negative torsion angle at the bay region and a half chair conformation of the saturated ring distorted toward the envelope with C8 at the tip as in BPT, in addition to the axial and pseudo-axial conformations of the hydroxy groups at C9 and C10 due to the near bay region. They may be considered generated by trans-opening of the oxirane ring in an anti-diol epoxide biologically active because it is highly strained. The strains, derived from the activation of bay-region PAHs with a negative torsion angle, seem greater in an anti-diol epoxide relative to the syn-isomer. Thus, when the strains are released, the derived trans-tetrol occurs with structural features, which seem to better fit the target. As a consequence, the presence of a methyl group at a bay region should increase the biological activity of a PAH, imposing greater strains to the structure of the anti-diol epoxide.     

Inspection on the Mechanism of SARS-CoV-2 Inhibition by Penciclovir: A Molecular Dynamic Study

In recent years, humanity has had to face a critical pandemic due to SARS-CoV-2. In the rapid search for effective drugs against this RNA-positive virus, the repurposing of already existing nucleotide/nucleoside analogs able to stop RNA replication by inhibiting the RNA-dependent RNA polymerase enzyme has been evaluated. In this process, a valid contribution has been the use of in silico experiments, which allow for a rapid evaluation of the possible effectiveness of the proposed drugs. Here we propose a molecular dynamic study to provide insight into the inhibition mechanism of Penciclovir, a nucleotide analog on the RNA-dependent RNA polymerase enzyme. Besides the presented results, in this article, for the first time, molecular dynamic simulations have been performed considering not only the RNA-dependent RNA polymerase protein, but also its cofactors (fundamental for RNA replication) and double-strand RNA.     

In Search for Multi-Target Ligands as Potential Agents for Diabetes Mellitus and Its Complications—A Structure-Activity Relationship Study on Inhibitors of Aldose Reductase and Protein Tyrosine Phosphatase 1B

Diabetes mellitus (DM) is a complex disease which currently affects more than 460 million people and is one of the leading cause of death worldwide. Its development implies numerous metabolic dysfunctions and the onset of hyperglycaemia-induced chronic complications. Multiple ligands can be rationally designed for the treatment of multifactorial diseases, such as DM, with the precise aim of simultaneously controlling multiple pathogenic mechanisms related to the disease and providing a more effective and safer therapeutic treatment compared to combinations of selective drugs. Starting from our previous findings that highlighted the possibility to target both aldose reductase (AR) and protein tyrosine phosphatase 1B (PTP1B), two enzymes strictly implicated in the development of DM and its complications, we synthesised 3-(5-arylidene-4-oxothiazolidin-3-yl)propanoic acids and analogous 2-butenoic acid derivatives, with the aim of balancing the effectiveness of dual AR/PTP1B inhibitors which we had identified as designed multiple ligands (DMLs). Out of the tested compounds, 4f exhibited well-balanced AR/PTP1B inhibitory effects at low micromolar concentrations, along with interesting insulin-sensitizing activity in murine C2C12 cell cultures. The SARs here highlighted along with their rationalization by in silico docking experiments into both target enzymes provide further insights into this class of inhibitors for their development as potential DML antidiabetic candidates.     

Binding Models of Copper(II) Thiosemicarbazone Complexes with Human Serum Albumin: A Speciation Study

Copper(II) complexes of thiosemicarbazones (TSCs) often exhibit anticancer properties, and their pharmacokinetic behavior can be affected by their interaction with blood transport proteins. Interaction of copper(II) complexes of an {N,N,S} donor α-N-pyridyl TSC (Triapine) and an {O,N,S} donor 2-hydroxybenzaldehyde TSC (STSC) with human serum albumin (HSA) was investigated by UV–visible and electron paramagnetic resonance spectroscopy at physiological pH. Asp-Ala-His-Lys and the monodentate N-methylimidazole were also applied as binding models. Conditional formation constants were determined for the ternary copper(II)-TSC complexes formed with HSA, DAHK, and N-methylimidazole based on the spectral changes of both charge transfer and d-d bands. The neutral N-methylimidazole displays a similar binding affinity to both TSC complexes. The partially negatively charged tetrapeptide binds stronger to the positively charged Triapine complex in comparison to the neutral STSC complex, while the opposite trend was observed for HSA, which demonstrates the limitations of the use of simple ligands to model the protein binding. The studied TSC complexes are able to bind to HSA in a fast process, and the conditional constants suggest that their binding strength is only weak-to-moderate.     

A Study on the Chemistry and Biological Activity of 26-Sulfur Analogs of Diosgenin: Synthesis of 26-Thiodiosgenin S-Mono- and Dioxides,and Their Alkyl Derivatives

A chemoselective procedure for MCPBA oxidation of 26-thiodiosgenin to corresponding sulfoxides and sulfone was elaborated. An unusual equilibration of sulfoxides in solution was observed. Moreover, α-alkylation of sulfoxide and sulfone was investigated. Finally, the biological activity of obtained compounds was examined.     

Molecular Tools for the Study of ADP-Ribosylation: A Unified and Versatile Method to Synthesise Native Mono-ADP-Ribosylated Peptides

ADP-ribosylation (ADPr), as a post-translational modification, plays a crucial role in DNA-repair, immunity and many other cellular and physiological processes. Serine is the main acceptor for ADPr in DNA damage response, whereas the physiological impact of less common ADPr-modifications of cysteine and threonine side chains is less clear. Generally, gaining molecular insights into ADPr recognition and turn-over is hampered by the availability of homogeneous, ADP-ribosylated material, such as mono-ADP-ribosylated (MARylated) peptides. Here, a new and efficient solid-phase strategy for the synthesis of Ser-, Thr- and Cys-MARylated peptides is described. ADP-ribosylated cysteine, apart from being a native post-translational modification in its own right, proved to be suitable as a stabile bioisostere for ADP-ribosylated serine making it a useful tool to further biochemical research on serine ADP-ribosylation. In addition, it was discovered that the Streptococcus pyogenes encoded protein, SpyMacroD, acts as a Cys-(ADP-ribosyl) hydrolase.     

Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study

We study the influence of polymer pore interactions and focus on the role played by the concentration gradient of salt in the translocation of polyelectrolytes (PE) through nanopores explicitly using coarse-grained Langevin dynamics simulations. The mean translocation time is calculated by varying the applied voltage, the pH, and the salt concentration gradient. Changing the pH can alter the electrostatic interaction between the protein pore and the polyelectrolyte chain. The polymer pore interaction is weakened by the increase in the strength of the externally applied electric field that drives translocation. Additionally, the screening effect of the salt can reduce the strong charge-charge repulsion between the PE beads which can make translocation faster. The simulation results show there can be antagonistic or synergistic coupling between the salt concentration-induced screening effect and the drift force originating from the salt concentration gradient thereby affecting the translocation time. Our simulation results are explained qualitatively with free energy calculations.     

Dual‐Polarization Imaging of a Dual‐Fluorophore Ion Sensor: A Single‐Molecule Study

The fluorescence emission of the dual‐fluorophore Ca²⁺ ion sensor molecule, calcium‐green 2 (CG‐2), has been characterized using dual‐polarization imaging at the single‐molecule level. By comparing the fluorescence intensity of individual CG‐2 molecules in two mutually orthogonal polarization image channels, information about the relative orientation of the two constituent fluorophores in the molecule is obtained. Experimental results from polarization measurements are compared with those predicted from a geometric model based on coupled‐fluorophores that are randomly distributed in space. The results confirm previous optical spectroscopy‐based predictions of the orientation of CG‐2′s fluorophores, and the general applications of this dual‐polarization imaging approach for characterizing the optical properties of molecules containing multiple fluorophores is discussed.     

Determination of Apoptotic Mechanism of Action of Tetrabromobisphenol A and Tetrabromobisphenol S in Human Peripheral Blood Mononuclear Cells: A Comparative Study

Background: Tetrabromobisphenol A (TBBPA) is the most commonly used brominated flame retardant (BFR) in the industry. TBBPA has been determined in environmental samples, food, tap water, dust as well as outdoor and indoor air and in the human body. Studies have also shown the toxic potential of this substance. In search of a better and less toxic BFR, tetrabromobisphenol S (TBBPS) has been developed in order to replace TBBPA in the industry. There is a lack of data on the toxic effects of TBBPS, while no study has explored apoptotic mechanism of action of TBBPA and TBBPS in human leukocytes. Methods: The cells were separated from leucocyte-platelet buffy coat and were incubated with studied compounds in concentrations ranging from 0.01 to 50 µg/mL for 24 h. In order to explore the apoptotic mechanism of action of tested BFRs, phosphatidylserine externalization at cellular membrane (the number of apoptotic cells), cytosolic calcium ion and transmembrane mitochondrial potential levels, caspase-8, -9 and -3 activation, as well as PARP-1 cleavage, DNA fragmentation and chromatin condensation in PBMCs were determined. Results: TBBPA and TBBPS triggered apoptosis in human PBMCs as they changed all tested parameters in the incubated cells. It was also observed that the mitochondrial pathway was mainly involved in the apoptotic action of studied compounds. Conclusions: It was found that TBBPS, and more strongly TBBPA, triggered apoptosis in human PBMCs. Generally, the mitochondrial pathway was involved in the apoptotic action of tested compounds; nevertheless, TBBPS more strongly than TBBPA caused intrinsic pathway activation.     

Evaluation of the Structure–Activity Relationship of Rifabutin and Analogs: A Drug–Membrane Study

This work focuses on the influence of rifabutin and two novel analogs, namely, N′‐acetyl‐rifabutin and N′‐butanoyl‐rifabutin, on the biophysical properties of lipid membranes. Monolayers and multilamellar vesicles composed of egg L ‐α‐phosphatidylcholine:cholesterol in a molar ratio of 4:1 are chosen to mimic biological membranes. Several accurate biophysical techniques are used to establish a putative relationship between the chemical structure of the antimycobacterial compounds and their activity on the membranes. A combination of in situ experimental techniques, such as Langmuir isotherms, Brewster angle microscopy, polarization‐modulated infrared reflection–absorption spectroscopy, and small‐angle X‐ray scattering, is used to assess the drug–membrane interaction. A relationship between the effect of a drug on the organization of the membranes and their chemical structure is found and may be useful in the development of new drugs with higher efficacy and fewer toxic effects.     

Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO− ν(C=O) band position in this family of fragments.     

ChemInform Abstract: Novel Structures and Superconductivities of Calcium—Lithium Alloys at High Pressures: A First‐Principles Study.

The crystal structures of Ca—Li alloys are investigated in the pressure range 0—200 GPa using a structure search method based on particle‐swarm optimization algorithms in combination with DFT calculations.     

Co-Fermentation of Glucose–Xylose Mixtures from Agroindustrial Residues by Ethanologenic Escherichia coli: A Study on the Lack of Carbon Catabolite Repression in Strain MS04

The production of biofuels, such as bioethanol from lignocellulosic biomass, is an important task within the sustainable energy concept. Understanding the metabolism of ethanologenic microorganisms for the consumption of sugar mixtures contained in lignocellulosic hydrolysates could allow the improvement of the fermentation process. In this study, the ethanologenic strain Escherichia coli MS04 was used to ferment hydrolysates from five different lignocellulosic agroindustrial wastes, which contained different glucose and xylose concentrations. The volumetric rates of glucose and xylose consumption and ethanol production depend on the initial concentration of glucose and xylose, concentrations of inhibitors, and the positive effect of acetate in the fermentation to ethanol. Ethanol yields above 80% and productivities up to 1.85 g_EtOH/Lh were obtained. Furthermore, in all evaluations, a simultaneous co-consumption of glucose and xylose was observed. The effect of deleting the xyIR regulator was studied, concluding that it plays an important role in the metabolism of monosaccharides and in xylose consumption. Moreover, the importance of acetate was confirmed for the ethanologenic strain, showing the positive effect of acetate on the co-consumption rates of glucose and xylose in cultivation media and hydrolysates containing sugar mixtures.     

Pitanga (Eugenia uniflora L.) as a source of bioactive compounds for health benefits: A review

The pitangueira (Eugenia uniflora) is a tree native to Brazil but is cultivated in several subtropical countries. A great diversity of nutrients and bioactive compounds have been found in the leaves and fruits of E. uniflora, which supports its use in folk medicine to treat diseases such as stomach and intestinal disorders, fever and general inflammation. Antimicrobial, antiviral, antifungal and antioxidant effects on metabolism have been reported for this plant. This review discusses the phytochemical profile, toxicity and pharmacological action of E. uniflora leaves and fruits and points out that gaps in the literature that need to be investigated further. This review also discusses studies developed with E. uniflora demonstrating its promising therapeutic potential for several diseases with an apparent low toxicity in mammals. The compilation of the main pharmacological and toxicological results, as well as the phytochemical characterization of the varieties and constituents of E. uniflora are general aspects that this review attempts to demonstrate in order to contribute to the new approaches and developments to plant-derived natural product drug discovery. However, further studies are required to establish the nutraceutical effects and uses of E. uniflora as an important and safe supplement for human health.