[Cu(dipicolinoylamide)(NO3)(H2O)] as anti-COVID-19 and antibacterial drug candidate: Design, synthesis, crystal structure, DFT and molecular docking

Oxidation-Deformylation Cascade Catalyzed By a Mononuclear Copper Complex

In this study, two copper complexes were synthesized using N3 (arising from two pyridines and one amide group) containing ligands N-(2-picolyl)picolinamide (L1H) and bis(2-pyridylcarbonyl)amine (L2H), forming [(L1)CuII(OH2)(NO3)] (1) and [(L2)CuII(OH2)2](NO3) (2). The reaction of complex 1 with hydrogen peroxide in alcoholic solvents yielded a formate-bound complex. Studies with isotopically labeled 13C ethanol indicated that formate originates from the C1 of ethanol after C-C bond cleavage. Complex 1 was found to catalytically convert primary alcohols into formic acid probably following a two-step process: (i) alcohol oxidation to aldehyde and (ii) aldehyde deformylation. Further experiments with 2-phenylpropionaldehyde (2-PPA) confirm the ability of complex 1 to catalyze aldehyde deformylation. Both steps of the reaction are associated with significant kinetic deuterium isotope effects (KDIE), suggesting that hydrogen atom abstractions (HAA) occur during the rate-determining steps of both conversions. Overall, this system proposes a clean catalytic process for alcohol-to-formic acid conversion, operating under mild conditions, and offering potential synthetic applications.

Synthesis, Characterization, DFT Studies of Novel Cu(II), Zn(II), VO(II), Cr(III), and La(III) Chloro-Substituted Schiff Base Complexes: Aspects of Its Antimicrobial, Antioxidant, Anti-Inflammatory, and Photodegradation of Methylene Blue

A new chlorobenzylidene imine ligand, (E)-1-((5-chloro-2-hydroxybenzylidene)amino) naphthalen-2-ol (HL), and its [Zn(L)(NO₃)(H₂O)₃], [La(L)(NO₃)₂(H₂O)₂], [VO(L)(OC₂H₅)(H₂O)₂], [Cu(L)(NO₃)(H₂O)₃], and [Cr(L)(NO₃)₂(H₂O)₂], complexes were synthesized and characterized. The characterization involved elemental analysis, FT-IR, UV/Vis, NMR, mass spectra, molar conductance, and magnetic susceptibility measurements. The obtained data confirmed the octahedral geometrical structures of all metal complexes, while the [VO(L)(OC₂H₅)(H₂O)₂] complex exhibited a distorted square pyramidal structure. The complexes were found to be thermally stable based on their kinetic parameters determined using the Coats-Redfern method. The DFT/B3LYP technique was employed to calculate the optimized structures, energy gaps, and other important theoretical descriptors of the complexes. In vitro antibacterial assays were conducted to evaluate the complexes' potential against pathogenic bacteria and fungi, comparing them to the free ligand. The compounds exhibited excellent fungicidal activity against Candida albicans ATCC: 10231 (C. albicans) and Aspergillus negar ATCC: 16404 (A. negar), with inhibition zones of HL, [Zn(L)(NO₃)(H₂O)₃], and [La(L)(NO₃)₂(H₂O)₂] three times higher than that of the Nystatin antibiotic. The DNA binding affinity of the metal complexes and their ligand was investigated using UV-visible, viscosity, and gel electrophoresis methods, suggesting an intercalative binding mode. The absorption studies yielded K_b values ranging from 4.40 × 10⁵ to 7.30 × 10⁵ M^-1, indicating high binding strength to DNA comparable to ethidium bromide (value 10⁷ M^-1). Additionally, the antioxidant activity of all complexes was measured and compared to vitamin C. The anti-inflammatory efficacy of the ligand and its metal complexes was evaluated, revealing that [Cu(L)(NO₃)(H₂O)₃] exhibited the most effective activity compared to ibuprofen. Molecular docking studies were conducted to explore the binding nature and affinity of the synthesized compounds with the receptor of Candida albicans oxidoreductase/oxidoreductase INHIBITOR (PDB ID: 5V5Z). Overall, the combined findings of this work demonstrate the potential of these new compounds as efficient fungicidal and anti-inflammatory agents. Furthermore, the photocatalytic effect of the Cu(II) Schiff base complex/GO was examined.

Essential oils of Origanum compactum Benth: Chemical characterization, in vitro, in silico, antioxidant, and antibacterial activities

This study was performed to investigate the phytochemical profile, and the, in vitro, and, in silico, antioxidant and antibacterial properties of the essential oil (EO) extracted from Origanum compactum. EO phytochemical screening was examined by gas chromatography coupled to mass spectrometry. The antioxidant potential, in vitro, was assessed using reducing power(FRAP), free 2,2 diphenylpicrylhydrazyl (DPPH) radical scavenging and total antioxidant capacity tests. Antibacterial properties against two Gram (−) and two Gram (+) bacteria were assessed using the minimal inhibitory concentration (MIC) and the disc diffusion methods. By use of molecular docking, antioxidant and antibacterial activities of oregano EO were also tested. Thymol (75.53%) was the major compound among the nine compounds identified in the EO of Origanum compactum, followed by carvacrol (18.26%). Oregano EO showed an important antioxidant capacity, as tested by FRAP and DPPH assays, with EC50 and IC50 values of 13.300 ± 0.200 and 0.690 ± 0.062 mg/mL, respectively. The same EO has a total antioxidant capacity of 173.900 ± 7.231 mg AAE/g EO. The antibacterial results showed significant activity of Origanum compactum EO against all tested bacteria, especially against S. aureus (MIC = 0.25 mg/mL) and B. subtilis (MIC = 0.06 mg/mL). In silico, carvacrol was the most active molecule against nicotinamide adenine dinucleotide phosphate oxidase (2CDU) and S. aureus nucleoside diphosphate kinase (3Q8U) with a glide score of −6.082, and −6.039 kcal/mol, respectively. Regarding the inhibition of E. coli beta-ketoacyl-[acyl carrier protein] synthase (1FJ4), piperitenone was the most active molecule with a glide score of −7.112 kcal/mol. In light of the results obtained, the EO of Origanum compactum Moroccan species can be used as promising natural food conservatives and an agent to fight antibiotic-resistant nosocomial microbes.

Development of Metal Complexes for Treatment of Coronaviruses

Coronavirus disease (SARS-CoV-2) is a global epidemic. This pandemic, which has been linked to high rates of death, has forced some countries throughout the world to implement complete lockdowns in order to contain the spread of infection. Because of the advent of new coronavirus variants, it is critical to find effective treatments and vaccines to prevent the virus's rapid spread over the world. In this regard, metal complexes have attained immense interest as antibody modifiers and antiviral therapies, and they have a lot of promise towards SARS-CoV-2 and their suggested mechanisms of action are discussed, i.e., a new series of metal complexes' medicinal vital role in treatment of specific proteins or SARS-CoV-2 are described. The structures of the obtained metal complexes were fully elucidated by different analytical and spectroscopic techniques also. Molecular docking and pharmacophore studies presented that most of complexes studied influenced good binding affinity to the main protease SARS-CoV-2, which also was attained as from the RCSB pdb (Protein Data Bank) data PDB ID: 6 W41, to expect the action of metal complexes in contradiction of COVID-19. Experimental research is required to determine the pharmacokinetics of most of the complexes analyzed for the treatment of SARS-CoV-2-related disease. Finally, the toxicity of a metal-containing inorganic complex will thus be discussed by its capability to transfer metals which may bind with targeted site.

Synthesis, in silico study (DFT, ADMET) and crystal structure of novel sulfamoyloxy-oxazolidinones: Interaction with SARS-CoV-2

A new series of sulfamoyloxyoxazolidinone (SOO) derivatives have been synthesized and characterized by single-crystal X-ray diffraction, NMR, IR, MS and EA. Chemical reactivity and geometrical characteristics of the target compounds were investigated using DFT method. The possible binding mode between SOO and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that SOO crystallizes in a monoclinic system with P 2 1 space group. The binding energy of the SARS-CoV-2/Mpro-SOO complex and the calculated inhibition constant using docking simulation showed that the active SOO molecule has the ability to inhibit SARS-CoV2. We studied the prediction of absorption, distribution, properties of metabolism, excretion and toxicity (ADMET) of the synthesized molecules.

Synthesis and characterization of two new mixed-ligand Cu(II) complexes of a tridentate NN'O type Schiff base ligand and N-donor heterocyclic co-ligands: In vitro anticancer assay, DNA/human leukemia/COVID-19 molecular docking studies, and pharmacophore modeling

Two new mixed-ligand complexes with general formula [Cu(SB)(L')]ClO4 (1 and 2) were synthesized and characterized by different spectroscopic and analytical techniques including Fourier transform infrared (FT-IR) and UV-Vis spectroscopy and elemental analyses. The SB ligand is an unsymmetrical tridentate NN'O type Schiff base ligand that was derived from the condensation of 1,2-ethylenediamine and 5-bromo-2-hydroxy-3-nitrobenzaldehyde. The L' ligand is pyridine in (1) and 2,2'-dimethyl-4,4'-bithiazole (BTZ) in (2). Crystal structure of (2) was also obtained. The two complexes were used as anticancer agents against leukemia cancer cell line HL-60 and showed considerable anticancer activity. The anticancer activity of these complexes was comparable with the standard drug 5-fluorouracil (5-FU). Molecular docking and pharmacophore studies were also performed on DNA (PDB:1BNA) and leukemia inhibitor factor (LIF) (PDB:1EMR) to further investigate the anticancer and anti-COVID activity of these complexes. The molecular docking results against DNA revealed that (1) preferentially binds to the major groove of DNA receptor whereas (2) binds to the minor groove. Complex (2) performed better with 1EMR. The experimental and theoretical results showed good correlation. Molecular docking and pharmacophore studies were also applied to study the interactions between the synthesized complexes and SARS-CoV-2 virus receptor protein (PDB ID:6LU7). The results revealed that complex (2) had better interaction than (1), the free ligands (SB and BTZ), and the standard drug favipiravir.

Synthesis and crystal structures of new mixed-ligand Schiff base complexes containing N-donor heterocyclic co-ligands: molecular docking and pharmacophore modeling studies on the main proteases of SARS-CoV-2 virus (COVID-19 disease)

Three new mixed-ligand copper(II) complexes (1–3) with NN'O type unsymmetrical tridentate Schiff base ligands (SB) and N-donor heterocyclic co-ligands, with general formula [Cu(SB)(L)]ClO₄, were synthesized and characterized using single crystal x-ray diffraction (SCXRD), FT-IR and UV–Vis spectroscopy and elemental analyses. The SB ligand is the half-unit form of the condensation of 1,3-propanediamine with 5-methoxysalicylaldehyde and the co-ligands (L) are pyridine (py in (1)), 2,2′-bipyridine (bpy in (2)) and 1,10-phenanthroline (phen in (3)). Crystal structures of (2) and (3) were obtained by SCXRD. Molecular docking and pharmacophore studies were performed to study the interactions between the synthesized complexes and SARS-CoV-2 virus main proteases (PDB IDs: 6LU7, 6WQF and 6W9C). Results revealed that complex (3) with phen co-ligand showed better docking scores with the three receptors, i.e. 6LU7 (−8.05 kcal.mol⁻¹), 6W9C (−7.70 kcal.mol⁻¹) and 6WQF (−7.75 kcal.mol⁻¹). The order of the binding best energies for (3) was also as follows: 6LU7 > 6WQF > 6W9C. All of the studied complexes showed considerable performance, comparable to the standard drug, Favipiravir.

New styrylquinoxaline: synthesis, structural, biological evaluation, ADMET prediction and molecular docking investigations

The organic compound (E)-3-(4-methylstyryl)quinoxalin-2(1H)-one (SQO) with molecular formula C₁₇H₁₄N₂O was synthesized and analyzed using single crystal X-ray diffraction, ¹H, ¹³C NMR and FTIR spectroscopic techniques. The geometric parameters of the molecule was optimized by density-functional theory (DFT) choosing B3LYP with 6-31++G(d,p) basis set. For compatibility, the theoretical structure and experimental structure were overlapped with each other. Frontier molecular orbitals of the title compound were made, and energy gap between HOMO and LUMO was calculated. Molecular electrostatic potential map was generated finding electrophilic and nucleophilic attack centers using DFT method. Hirshfeld surface analysis (HSA) confirms active regions at the circumference of N1 atoms and O1 atoms that form intermolecular N1-H1···O1 hydrogen bond. The acute oral toxicity study was carried out according to OECD guideline, which approve that the compound SQO was non-toxic. In addition, this quinoxaline derivative was evaluated for its in vitro antidiabetic activity against α-glucosidase and α-amylase enzymes and for antioxidant activity by utilizing several tests as 1,1-diphenyl-2-picryl hydrazyl, (2,2'-azino-bis(3-ethyl benzthiazoline-6-sulfonicacid), reducing power test (FRAP) and hydrogen peroxide activity H₂O₂. The molecular docking studies were performed to investigate the antidiabetic activity of SQO and compared with the experimental results. SQO is a potent antidiabetic from both the experimental and molecular docking results. Finally, the physicochemical, pharmacokinetic and toxicological properties of SQO have been evaluated by using in silico absorption, distribution, metabolism, excretion and toxicity analysis prediction.

A possible potential COVID-19 drug candidate: Diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate: Docking of disordered independent molecules of a novel crystal structure, HSA/DFT/XRD and cytotoxicity

This study reports the synthesis, characterization and importance of a novel diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate (MQOAHM). Two independent molecular structures of the disordered MQOAHM have been established by XRD‑single‑crystal analysis in a ratio of 0.596(3)/0.404(3), MQOAHM (a) and MQOAHM (b), respectively. MQOAHM was characterized by means of various spectroscopic tools ESI-MS, IR, ¹H &¹³C NMR analyses. Density Functional Theory (DFT) method, B3LYP, 6-311++G(d,p) basis set was used to optimize MQOAHM molecule. The obtained theoretical structure and experimental structure were superimposed on each other, and the correlation between them was calculated. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) were created, and the energy gap between these orbitals was calculated. For analyzing intermolecular interactions, Molecular Electrostatic Potential (MEP) and Hirshfeld Surface Analysis were studied. For a fair comparative study, the two forms of the title compound were docked together with 18 approved drugs and N3 under precisely the same conditions. The disordered molecule structure's binding scores against 7BQY were -7.0 and -6.9 kcal/mol^-1 for MQOAHM (a) and MQOAHM (b), respectively. Both the forms show almost identical superimposed structures and scores indicating that the disorder of the molecule, in this study, has no obvious effect. The high binding score of the molecule was attributed to the multi-hydrogen bond and hydrophobic interactions between the ligand and the receptor's active amino acid residues. Worth pointing out here that the aim of using the free energy in Silico molecular docking approach is to rank the title molecule compared to the wide range of approved drugs and a well-established ligand N3. The binding scores of all the molecules used in this study are ranged from -9.9 to -4.5 kcal/mol^-1. These results and the supporting statistical analyses suggest that this malonate-based ligand merits further research in the context of possible therapeutic agents for COVID-19. Cheap computational techniques, PASS, Way2drug and ADMET, online software tools, were used in this study to uncover the title compound's potential biological activities and cytotoxicity.