Synergizing structure and function: Cinnamoyl hydroxamic acids as potent urease inhibitors

The current investigation encompasses the structural planning, synthesis, and evaluation of the urease inhibitory activity of a series of molecular hybrids of hydroxamic acids and Michael acceptors, delineated from the structure of cinnamic acids. The synthesized compounds exhibited potent urease inhibitory effects, with IC50 values ranging from 3.8 to 12.8 µM. Kinetic experiments unveiled that the majority of the synthesized hybrids display characteristics of mixed inhibitors. Generally, derivatives containing electron-withdrawing groups on the aromatic ring demonstrate heightened activity, indicating that the increased electrophilicity of the beta carbon in the Michael Acceptor moiety positively influences the antiureolytic properties of this compounds class. Biophysical and theoretical investigations further corroborated the findings obtained from kinetic assays. These studies suggest that the hydroxamic acid core interacts with the urease active site, while the Michael acceptor moiety binds to one or more allosteric sites adjacent to the active site.

Unveiling Novel Urease Inhibitors for Helicobacter pylori: A Multi-Methodological Approach from Virtual Screening and ADME to Molecular Dynamics Simulations

Helicobacter pylori (Hp) infections pose a global health challenge demanding innovative therapeutic strategies by which to eradicate them. Urease, a key Hp virulence factor hydrolyzes urea, facilitating bacterial survival in the acidic gastric environment. In this study, a multi-methodological approach combining pharmacophore- and structure-based virtual screening, molecular dynamics simulations, and MM-GBSA calculations was employed to identify novel inhibitors for Hp urease (HpU). A refined dataset of 8,271,505 small molecules from the ZINC15 database underwent pharmacokinetic and physicochemical filtering, resulting in 16% of compounds for pharmacophore-based virtual screening. Molecular docking simulations were performed in successive stages, utilizing HTVS, SP, and XP algorithms. Subsequent energetic re-scoring with MM-GBSA identified promising candidates interacting with distinct urease variants. Lys219, a residue critical for urea catalysis at the urease binding site, can manifest in two forms, neutral (LYN) or carbamylated (KCX). Notably, the evaluated molecules demonstrated different interaction and energetic patterns in both protein variants. Further evaluation through ADMET predictions highlighted compounds with favorable pharmacological profiles, leading to the identification of 15 candidates. Molecular dynamics simulations revealed comparable structural stability to the control DJM, with candidates 5, 8 and 12 (CA5, CA8, and CA12, respectively) exhibiting the lowest binding free energies. These inhibitors suggest a chelating capacity that is crucial for urease inhibition. The analysis underscores the potential of CA5, CA8, and CA12 as novel HpU inhibitors. Finally, we compare our candidates with the chemical space of urease inhibitors finding physicochemical similarities with potent agents such as thiourea.

The influence of N-alkyl chains in benzoyl-thiourea derivatives on urease inhibition: Soil studies and biophysical and theoretical investigations on the mechanism of interaction

Ureases are enzymes produced by fungi, plants, and bacteria associated with agricultural and clinical problems. The urea hydrolysis in NH₃ and CO₂ leads to the loss of N-urea fertilizers in soils and changes the human stomach microenvironment, favoring the colonization of H. pylori. In this sense, it is necessary to evaluate potential enzyme inhibitors to mitigate the effects of their activities and respond to scientific and market demands to produce fertilizers with enhanced efficiency. Thus, biophysical and theoretical studies were carried out to evaluate the influence of the N-alkyl chain in benzoyl-thiourea derivatives on urease enzyme inhibition. A screening based on IC₅₀, binding constants, and theoretical studies demonstrated that BTU1 without the N-alkyl chain (R = H) was more active than other compounds, so the magnitude of the interaction was determined as BTU1 > BTU2 > BTU3 > BTU4 > BTU5, corresponding to progressively increased chain length. Thus, BTU1 was selected for interaction and soil application essays. The binding constants (K_b) for the supramolecular urease-BTU1 complex ranged from 7.95 to 5.71 × 10³ M^-1 at different temperatures (22, 30, and 38 °C), indicating that the preferential forces responsible for the stabilization of the complex are hydrogen bonds and van der Waals forces (ΔH = -15.84 kJ mol^-1 and ΔS = -36.61 J mol^-1 K^-1). Theoretical and experimental results (thermodynamics, synchronous fluorescence, and competition assay) agree and indicate that BTU1 is a mixed inhibitor. Finally, urease inhibition was evaluated in the four soil samples, where BTU1 was as efficient as NBPT (based on ANOVA two-way and Tukey test with 95% confidence), with an average inhibition of 20% of urease activity. Thus, the biophysics and theoretical studies are strategies for evaluating potential inhibitors and showed that increasing the N-alkyl chain in benzoyl-thiourea derivatives did not favor urease inhibition.

Recent advances on natural depsidones: sources, biosynthesis, structure-activity relationship, and bioactivities

Depsidones are a class of polyphenolic polyketides that have been proposed to be biosynthesized from oxidative coupling of esters of two polyketidic benzoic acid derivatives. They are principally encountered in fungi and lichens. In addition to their diversified structural features, they revealed varied bioactivities such as antimicrobial, antimalarial, cytotoxic, anti-inflammatory, anti-Helicobacter pylori, antimycobacterial, antihypertensive, anti-diarrheal, antidiabetic, phytotoxic, anti-HIV, anti-osteoclastogenic, and butyrylcholinesterase, tyrosinase, hyaluronidase, and acetylcholinesterase inhibition. The current work was targeted to provide an overview on the naturally reported depsidones from various sources in the period from 2018 to the end of 2022 including their structures, biosynthesis, sources, and bioactivities, as well as the reported structure-activity relationship and semisynthetic derivatives. A total of 172 metabolites with 87 references were reviewed. The reported findings unambiguously demonstrated that these derivatives could be promising leads for therapeutic agents. However, further in-vivo evaluation of their potential biological properties and mechanistic investigations are needed.

In Vitro Activity of the Arylaminoartemisinin GC012 against Helicobacter pylori and Its Effects on Biofilm

This study evaluated the in vitro activity of the arylaminoartemisinin GC012, readily obtained from dihydroartemisinin (DHA), against clinical strains of Helicobacter pylori (H. pylori) with different antibiotic susceptibilities in the planktonic and sessile state. The activity was assessed in terms of bacteriostatic and bactericidal potential. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined by the broth microdilution method. After treatment with GC012, all bacterial strains showed significantly lower MIC and MBC values compared to those of DHA. The effect of combination of GC012 with antibiotics was examined using the checkerboard method. GC012 displayed synergistic interactions with metronidazole, clarithromycin, and amoxicillin in all the strains. The antibiofilm activity was evaluated via crystal violet staining, AlamarBlue^® assay, colony-forming unit count, and fluorescence microscopy. At ½ MIC and ¼ MIC concentration, both GC012 and DHA inhibited biofilm formation, but only GC012 showed a minimal biofilm eradication concentration (MBEC) on mature biofilm. Furthermore, both compounds induced structural changes in the bacterial membrane, as observed by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). It is thereby demonstrated that GC012 has the potential to be efficacious against H. pylori infection.

'Urease immobilized single-kit' for sensing of thiourea-glucose pair employing fluorescence 'Turn off - Turn on' and as an efficient sorbent for selective sample cleanup of thiourea

The tenfold lowering in binding energy for TU-Tyrosine in immobilized urease (K_b: 4.7 × 10³) with respect to the native enzyme (K_b: 6.5 × 10⁴) begets easy desorption of thiourea (TU) by glucose (GL) with an eventual formation of a more strong TU- GL adduct; that rejuvenates the kit-material ready for the subsequent cycle(s). The sorption-desorption heeds fluorescence turn-off and turn-on in DCM for selective sensing of TU- GL pair at their respective linear range of concentration 2.5-26.1 ppm and 2.36-11.57 ppm. The process was found to be static (K_SV ≥ 2.25 × 10³ L mol^-1), exothermic (ΔH: -0.08 kJ mol^-1), spontaneous (ΔG: -21.1 kJ mol^-1) and marginally entropy gaining (ΔS: 0.07 kJ mol^-1 K^-1). The 'bulk material' (200 ± 20 μm) brilliantly preconcentrates TU with an enrichment factor of 106.2 after its selective extraction at near-neutral pH from a large volume sample (800 mL) of low concentration (30 ppm). A very dilute solution (0.05 mmol L^-1) of GL at minimum volume (6 mL) acts as a stripping agent and provides a longer life (200 cycles with good extraction efficiency) to the material. The method was found to be efficient in the analysis of fruit juice as a real sample.

Usnic acid enantiomers restore cognitive deficits and neurochemical alterations induced by Aβ1-42 in mice

Alzheimer's disease (AD) is the most prevalent form of dementia with a complex pathophysiology not fully elucidated but with limited pharmacological treatment. The Usnic acid (UA) is a lichen secondary metabolite found in two enantiomeric forms: (R)-(+)-UA or (S)-(-)-UA, with antioxidant and anti-inflammatory potential. Thus, given the role of neuroinflammation and oxidative injury in the AD, this study aimed to investigate experimentally the cognitive enhancing and anti-neuroinflammatory effects of UA enantiomers. First, the interactions of UA on acetylcholinesterase (AChE) was assessed by molecular docking and its inhibitory capability on AChE was assessed in vitro. In vivo trials investigated the effects of UA enantiomers in mice exposed to Aβ_1-42 peptide (400 pmol/mice) intracerebroventricularly (i.c.v.). For this, mice were treated orally during 24 days with (R)-(+)-UA or (S)-(-)-UA at 25, 50, or 100 mg/kg, vehicle, or donepezil (2 mg/kg). Animals were submitted to the novel object recognized, Morris water maze, and inhibitory-avoidance task to assess the cognitive deficits. Additionally, UA antioxidant capacity and neuroinflammatory biomarkers were measured at the cortex and hippocampus from mice. Our results indicated that UA enantiomers evoked complex-receptor interaction with AChE like galantamine in silico. Also, UA enantiomers improved the learning and memory of the animals and in parallel decreased the myeloperoxidase activity and the lipid hydroperoxides (LOOH) on the cortex and hippocampus and reduced the IL-1β levels on the hippocampus. In summary, UA restored the cognitive deficits, as well as the signs of LOOH and neuroinflammation induced by Aβ1-42 administration in mice.

Insights into the Design of Inhibitors of the Urease Enzyme - A Major Target for the Treatment of Helicobacter pylori Infections

Expressed by a variety of plants, fungi and bacteria, the urease enzyme is directly associated with the virulence factor of many bacteria, including Helicobacter pylori, a gram-negative bacterium related to several gastrointestinal diseases and responsible for one of the most frequent bacterial infections throughout the world. The Helicobacter pylori Urease (HPU) is a nickel-dependent metalloenzyme expressed in response to the environmental stress caused by the acidic pH of the stomach. The enzyme promotes the increase of gastric pH through acid neutralization by the products of urea hydrolysis, then critically contributing to the colonization and pathogenesis of the microorganism. At the same time, standard treatments for Helicobacter pylori infections have limitations such as the increasing bacterial resistance to the antibiotics used in the clinical practice. As a strategy for the development of novel treatments, urease inhibitors have proved to be promising, with a wide range of chemical compounds, including natural, synthetic and semisynthetic products to be researched and potentially developed as new drugs. In this context, this review highlights the advances in the field of HPU inhibition, presenting and discussing the basis for the research of new molecules aiming at the identification of more efficient therapeutic entities.

Toxicity of thimerosal in biological systems: Conformational changes in human hemoglobin, decrease of oxygen binding capacity, increase of protein glycation and amyloid's formation

Thimerosal (TH), an organomercurial compound, is used as a preservative in vaccines and cosmetics. Its interaction with human hemoglobin (Hb) was investigated under physiological conditions using biophysical and biological assays, aiming to evaluate hazardous effects. TH interacts spontaneously with Hb (stoichiometry 2:1, ligand-protein), preferably by electrostatic forces, with a binding constant of 1.41 × 10⁶ M^-1. Spectroscopic data allows to proposing that TH induces structural changes in Hg, through ethylmercury transfer to human Hb-Cys93 residues, forming thiosalicylic acid, which, in turn, interacts with the positive side of the amino acid in the Hb-HgEt adduct chain. As a consequence, inhibition of Hb-O₂ binding capacity up to 72% (human Hb), and 50% (human erythrocytes), was verified. Dose-dependent induction of TH forming advanced glycation end products (AGE) and protein aggregates (amyloids) was additionally observed. Finally, these results highlight the toxic potential of the use of TH in biological systems, with a consequent risk to human health.

Molecular interaction of sulfonamides and ovalbumin, an allergenic egg protein, exploring biophysical, theoretical and biological studies

Biophysical, theoretical and biological in vitro studies were carried out to evaluate the interaction of the main allergen protein of egg white (ovalbumin, OVA) with sulphonamides (SA): sulphathiazole (S1), sulfaquinoxaline (S2), sulfadimethoxine (S3) and sulfamethazine (S4). The binding constants for the OVA-SA supramolecular complexes ranged from 1.20 to 30.66 × 10⁵ M^-1, observing the following order of affinity: S1 > S2 > S4 > S3. The preferential forces in the stabilization of the OVA complexes with S2 and S3 were hydrogen bonds and Van der Waals forces, whereas for OVA-S1 and OVAS4, were electrostatic interactions. Interaction process led to a change in the native structure of the protein, which may potentiate its natural allergenicity. Cations Ca(II), Mg(II) and Fe(III) favor the interaction of OVA with S1 and S2. The theoretical studies performed were consistent with the spectroscopic data. Finally, it was found that the interaction process for sulfonamides evaluated with OVA change the inhibition activity profile these antibiotics against strains of Escherichia coli ATCC 25922 and Bacillus megaterium APFSG3isox, but not the minimal inhibitory concentration values.

Interactions of tetracyclines with milk allergenic protein (casein): a molecular and biological approach

Tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC) interactions with the allergenic milk protein casein (CAS) were here evaluated simulating food conditions. The antibiotics assessed interact with CAS through static quenching and form non-fluorescent complexes. At 30 °C, the binding constant (K_b) varied from 0.05 to 1.23 × 10⁶ M^-1. Tetracycline interacts with CAS preferably through electrostatic forces, while oxytetracycline and chlortetracycline interactions occur by hydrogen bonds and van der Waals forces. The interaction process is spontaneous, and the magnitude of interaction based on K_b values, followed the order: TC < CTC < OTC. The distances between the donor (protein) and the receptors (TC, OTC, and CTC) were determined by Förster resonance energy transfer (FRET) and varied from 3.67 to 4.08 nm. Under natural feeding conditions, the citrate decreased the affinity between TC and CAS; a similar effect was observed for OTC in the presence of Ca(II), Fe(III) and lactose. Synchronized and three-dimensional (3D) fluorescence studies indicated alterations in the original protein conformation due to the interaction process, which may influence allergenic processes. In addition, complexation with CAS modulated the antimicrobial activity of CTC against S. aureus, demonstrated that the interaction process possibly alters the biological properties of antibiotics and the own protein, in the food conditions.Communicated by Ramaswamy H. Sarma.

Ionic liquid-assisted synthesis of dihydropyrimidin(thi)one Biginelli adducts and investigation of their mechanism of urease inhibition

Three out of twenty-six synthesized Biginelli adducts were identified as potent competitive urease inhibitors.