Enzyme Models—From Catalysis to Prodrugs

Enzymes are highly specific biological catalysts that accelerate the rate of chemical reactions within the cell. Our knowledge of how enzymes work remains incomplete. Computational methodologies such as molecular mechanics (MM) and quantum mechanical (QM) methods play an important role in elucidating the detailed mechanisms of enzymatic reactions where experimental research measurements are not possible. Theories invoked by a variety of scientists indicate that enzymes work as structural scaffolds that serve to bring together and orient the reactants so that the reaction can proceed with minimum energy. Enzyme models can be utilized for mimicking enzyme catalysis and the development of novel prodrugs. Prodrugs are used to enhance the pharmacokinetics of drugs; classical prodrug approaches focus on alternating the physicochemical properties, while chemical modern approaches are based on the knowledge gained from the chemistry of enzyme models and correlations between experimental and calculated rate values of intramolecular processes (enzyme models). A large number of prodrugs have been designed and developed to improve the effectiveness and pharmacokinetics of commonly used drugs, such as anti-Parkinson (dopamine), antiviral (acyclovir), antimalarial (atovaquone), anticancer (azanucleosides), antifibrinolytic (tranexamic acid), antihyperlipidemia (statins), vasoconstrictors (phenylephrine), antihypertension (atenolol), antibacterial agents (amoxicillin, cephalexin, and cefuroxime axetil), paracetamol, and guaifenesin. This article describes the works done on enzyme models and the computational methods used to understand enzyme catalysis and to help in the development of efficient prodrugs.     

Green Synthesized Zinc Oxide Nanoparticles Based on Cestrum diurnum L. of Potential Antiviral Activity against Human Corona 229-E Virus

SARS-CoV-2 has caused more than 596 million infections and 6 million fatalities globally. Looking for urgent medication for prevention, treatment, and rehabilitation is obligatory. Plant extracts and green synthesized nanoparticles have numerous biological activities, including antiviral activity. HPLC analysis of C. dirnum L. leaf extract showed that catechin, ferulic acid, chlorogenic acid, and syringic acid were the most major compounds, with concentrations of 1425.16, 1004.68, 207.46, and 158.95 µg/g, respectively. Zinc nanoparticles were biosynthesized using zinc acetate and C. dirnum extract. TEM analysis revealed that the particle size of ZnO-NPs varied between 3.406 and 4.857 nm. An XRD study showed the existence of hexagonal crystals of ZnO-NPs with an average size of 12.11 nm. Both ZnO-NPs (IC₅₀ = 7.01 and CC₅₀ = 145.77) and C. dirnum L. extract (IC₅₀ = 61.15 and CC₅₀ = 145.87 µg/mL) showed antiviral activity against HCOV-229E, but their combination (IC₅₀ = 2.41 and CC₅₀ = 179.23) showed higher activity than both. Molecular docking was used to investigate the affinity of some metabolites against the HCOV-229E main protease. Chlorogenic acid, solanidine, and catchin showed high affinity (−7.13, −6.95, and −6.52), compared to the ligand MDP (−5.66 Kcal/mol). Cestrum dinurum extract and ZnO-NPs combination should be subjected to further studies to be used as an antiviral drug.     

Structural and orthoselectivity study of 2-hydroxybenzaldehyde using spectroscopic analysis

The orthoselectivity and high yield are two significant subjects which should be studied more in the process of hydroxybenzaldehydes or salicylaldehyde production. In this work, salicylaldehyde was synthesized by the reaction of formaldehyde and phenol magnesium methoxide complex, in an anhydrous medium. In order to achieve a selectively orthoformylated product, at first the hydroxyl group of phenol was rearranged by magnesium methoxide. The phenol magnesium salt was then formylated by paraformaldehyde. Impurities of the resulted salicylaldehyde were removed by several steps of liquid extracting via water and acid washing. The spectroscopic data of FT-IR, ¹H NMR (500 MHz), and GC/MS on the final product were recorded and interpreted. The results of FT-IR spectrum and integration value of ¹H NMR spectrum imply on the high conversion of reaction. The GC/MS spectrum also shows that the amounts of by products are low enough.     

Synthesis and Characterization of Zinc Oxide Nano-particles by Solid State Chemical Reaction Method

Several important synthetic parameters such as precursor concentration, reaction time are found to determine the growth of ZnO nanostructures. These reaction parameters can be tuned to produce a variety size of nanostructures. In this work we show the importance of these parameters on the size of synthesized zinc oxide nano-powders. ZnO nanoparticles are synthesized by the solid-state reaction using ZnSO₄·7H₂O and NaOH as the reagents. In this method Zn(OH)₂ is the intermediate product of the reaction, we show that by adjusting the molar ratio of the reagents and grinding time, we can be removed this unwanted component in the final product so for obtaining pure ZnO nanostructures the calcinations process is not necessary, also we can tune the size of ZnO nanoparticles. XRD spectra of the nanoparticles demonstrate typical diffraction peaks of a well-crystalline Wurtzite ZnO structure transmission electron microscopic observations show that these nanoparticles are of hexagonal phase ZnO mostly in round shapes and he composition analysis by EDX indicate that final product is pure ZnO. In the optimum conditions by XRD analysis we see that the mean grain size of synthesized zinc oxide nano-particles is about 44 nm.     

Aptamer-based sensor for diclofenac quantification using carbon nanotubes and graphene oxide decorated with magnetic nanomaterials

In this contribution, a novel label-free electrochemical biosensor for diclofenac (DCF) detection was developed using the unique properties of acid-oxidized carbon nanotubes (CNT), graphene oxide (GO), and Fe₃O₄ magnetic nanomaterials. The GO sheets and CNT were interlinked by ultrafine Fe₃O₄ nanoparticles forming three-dimensional (3D) architectures. The characterization of the nanocomposite was studied by scanning electron microscopy (SEM), energy-dispersive X-ray (EDS), and wavelength-dispersive X-ray (WDX) spectroscopy. Initially, aminated detection probe (aptamer) was surface-confined on the CNT/GO/Fe₃O₄ nanocomposite via the covalent amide bonds formed by the carboxyl groups on the CNT/GO and the amino groups on the oligonucleotides at the 5′ end. Our constructed folding-based electrochemical sensor was used for detection of target molecule utilizing structure-switching aptamers. Signaling arose from changes in electron transfer efficiency upon target-induced changes in the conformation of the aptamer probe. These changes were readily monitored using differential pulse voltammetry technique. This sensor exhibited binding affinities ranging from 100 to 1300 pM with a low detection limit of 33 pM.     

The electrospun poly(ε‐caprolactone)/fluoridated hydroxyapatite nanocomposite for bone tissue engineering

Biodegradable cell‐incorporated scaffolds can guide the regeneration process of bone defects such as physiological resorption, tooth loss, and trauma which medically, socially, and economically hurt patients. Here, 0, 5, 10, and 15 wt% fluoridated hydroxyapatite (FHA) nanoparticles containing 25 wt% F^? and 75 wt% OH^? were incorporated into poly(ε‐caprolactone) (PCL) matrix to produce PCL/FHA nanocomposite scaffolds using electrospinning method. Then, scanning electron microscopy (SEM), X‐ray diffraction (XRD) pattern, and Fourier transform infrared spectroscopy (FTIR) were used to evaluate the morphology, phase structure, and functional groups of prepared electrospun scaffolds, respectively. Furthermore, the tensile strength and elastic modulus of electrospun scaffolds were investigated using the tensile test. Moreover, the biodegradation behavior of electrospun PCL/FHA scaffolds was studied by the evaluation of weight loss of mats and the alternation of pH in phosphate buffer saline (PBS) up to 30 days of incubation. Then, the biocompatibility of prepared mats was investigated by culturing MG‐63 osteoblast cell line and performing MTT assay. In addition, the adhesion of osteoblast cells on prepared electrospun scaffolds was studied using their SEM images. Results revealed that the fiber diameter of prepared electrospun PCL/FHA scaffolds alters between 700 and 900 nm. The mechanical assay illustrated the mat with 10 wt% FHA nanoparticles revealed the highest tensile strength and elastic modulus. The weight loss alternation of mats determined around 1% to 8% after 30 days of incubation. The biocompatibility and cell adhesion of mats improved by increasing the amounts of FHA nanoparticles.     

Indeno[1,2-b]pyridin-5-one derivatives containing azo groups and their hydrazonal precursors: Synthesis,antimicrobial profile,DNA gyrase binding affinity,and molecular docking

The prevalence of germs that are resistant to many antibiotics is rising rapidly the world over. There is a large group of researchers actively looking for better medicines. Here, we designed two series of hydrazonal and indeno[1,2-b]pyridin-5-one bearing hydrazone and azo-groups to test their antimicrobial activity. Molecular structures of all derivatives were assured based on their spectral data and elemental analyses. Results of the antimicrobial activity of the tested hydrazone and azo compounds showed promising potential for several derivatives. The minimum inhibitory concentrations (MICs) of hydrazones 4a - h and 6a - g displayed good antibacterial reactivities with a range of 3.91–250 μg/mL and moderate antifungal activity with a range of 15.6–500 μg/mL. The most promising hydrazone 4f and azo- 6a compounds demonstrated MIC values against Streptococcus faecalis and Escherichia coli equal to 3.91 and 7.81 μg/mL, respectively. Moreover, azo compound 6a showed MIC value equal to 3.91 μg/mL against Enterobacter cloacae species. Additionally, derivative 4f exhibited a significant inhibitory profile against the E. coli gyrase A enzyme (IC₅₀ = 5.53 μg/mL). On the other hand, compound 6a (IC₅₀ 14.05 μg/mL) exhibited the lowest DNA gyrase inhibitory activity as compared to compounds 4f and reference standard drug novobiocin, IC₅₀ 5.53 and 1.88 μg/mL, respectively. Pharmacokinetic and pharmacodynamic profiles and molecular docking studies for the two most promising molecules 4f and 6a were computed and revealed that both compounds have good ADME profiles and high binding affinity to DNA gyrase binding site.     

Isolation and synthesis of N-acyladenine and adenosine alkaloids from a southern Australian marine sponge, Phoriospongia sp.

Chemical fractionation of the southern Australian marine sponge Phoriospongia sp. (CMB-03107) yielded phorioadenine A (1) as a nematocidal agent and the first reported example of a 6-N-acyladenine natural product. The structure of 1 was confirmed by spectroscopic analysis and the chemical synthesis of racemic (1a) and enantiomeric (1b) analogues. HPLC–ESIMS analysis of the crude sponge extract with comparisons to the synthetic 6-N-acyladenosine 2a provided evidence that the biosynthetically related adenosine, phorioadenosine A (2), was present as a trace co-metabolite. The rare starfish metabolite asterubine (3) was also isolated as a co-metabolite, and its structure confirmed by spectroscopic analysis and chemical synthesis. Biological investigations confirmed that natural products 1–3 and synthetic analogues 1a–e and 2a were not cytotoxic to multiple mammalian cancer cell lines, or Gram-positive or -negative bacteria. Nematocidal activity (inhibition of larval development of Haemonchus contortus) detected in the Phoriospongia sp. extract was attributed to 1 (LD₉₉ 31 μg/mL), with preliminary structure–activity relationship investigations confirming the importance of the N-acyl side chain.     

Green synthesis of silver nanoparticles using aqueous extract of Stachys lavandulifolia flower,and their cytotoxicity,antioxidant, antibacterial and cutaneous wound‐healing properties

In a biological process where the herbal tea (Stachys lavandulifolia) aqueous extract was applied as a capping and reducing agent, nanoparticles (NPs) of silver (Ag) were synthesized. These AgNPs were characterized using Fourier transform‐infrared spectroscopy, field emission‐scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, transmission electron microscopy and ultraviolet–visible spectroscopy. The synthesized AgNPs had great cell viability dose‐dependently [investigating the effect of the plant on human umbilical vein endothelial cell line] and indicated this method was non‐toxic. In this study, the 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) free radical scavenging test was carried out to examine antioxidant properties, which revealed similar antioxidant properties for AgNPs and butylated hydroxytoluene. Agar diffusion tests were applied to determine the antibacterial characteristics. The macro‐broth tube test was run to determine minimum inhibitory concentration. All data of antibacterial and cutaneous wound‐healing examinations were analyzed by SPSS 21 software (Duncan post hoc test). AgNPs showed higher antibacterial property than all standard antibiotics (p ≤ 0.01). Also, AgNPs prevented the growth of all bacteria at 2–8 mg/ml concentrations and destroyed them at 2–16 mg/ml concentrations (p ≤ 0.01). For the in vivo experiment, after creating the cutaneous wound, the rats were randomly divided into six groups: untreated control; treatment with Eucerin basal ointment; treatment with 3% tetracycline ointment; treatment with 0.2% AgNO₃ ointment; treatment with 0.2% S. lavandulifolia ointment; and treatment with 0.2% AgNPs ointment. These groups were treated for 10 days. For histopathological and biochemical analysis of the healing trend, a 3 × 3‐cm section was prepared from all dermal thicknesses at day 10. Use of AgNPs ointment in the treatment groups substantially reduced (p ≤ 0.01) the wound area, total cells, neutrophil, macrophage and lymphocyte, and remarkably raised (p ≤ 0.01) the wound contracture, hydroxyl proline, hexosamine, hexuronic acid, fibrocyte and fibrocytes/fibroblast rate compared with other groups. Seemingly, AgNPs can be used as a medical supplement owing to their non‐cytotoxic, antioxidant, antibacterial and cutaneous wound‐healing properties.