Crystal structure, DFT, molecular docking and dynamics simulation studies of 4,4-dimethoxychalcone

In the current study, the compound 4,4-dimethoxychalcone (DMC) was structurally studied and analyzed by in silico approach against Mpro to investigate its inhibitory potential. The molecular structure of the compound was confirmed by the single crystal X-ray diffraction studies. The crystal structure packing is characterized by various hydrogen bonds, C-H…π and π…π stacking. Intermolecular interactions are quantified by Hirshfeld surface analysis and the electronic structure was optimized by DFT calculations;results are in agreement with the experimental studies. Further, DMC was virtually screened against SARS-CoV-2 main protease (PDB-ID: 6LU7) using molecular docking, and molecular dynamics (MD) simulations to identify its inhibitory potential. A significant binding affinity exists between DMC and Mpro with a-6.00 kcal/mol binding energy. A MD simulation of 30ns was carried out;the results predict DMC possessing strong binding affinity and hydrogen-bonding interactions within the active site during the simulation period. Therefore, based on the results of the current investigation, it can be inferred that a DMC molecule may be able to inhibit Mpro of COVID-19. © 2023 by the authors;licensee Growing Science, Canada.

Rigidity and Flexibility of Pyrazole, s-Triazole, and v-Triazole Derivative of Chloroquine as Potential Therapeutic against COVID-19

Based on the core unit of chloroquine, new types of N-heterocyclic compounds that are fused together have been made. The compounds were put into two groups. In series A, the five-member hetero-rings were directly connected to the core unit, while in series B, the CH2 group was used to make the five-member ring more flexible (series B). Using the Gaussian 09 programme, the DFT method with hybrid correlation functional (B3LYP) and 6-311 (d, p) basis sets were used to figure out how to optimize and measure the quantum chemical properties of molecules. The molecular overeating environment (MOE) programme is used to study molecular docking. The binding of flexible compounds shows that AC8, AC10, AC3, and AC5 have the strongest binding affinities compared to the other candidates, while the rigid molecules ARC10 and ARC6 have the lowest binding affinities. In general, the results of the binding affinity showed that the drugs and receptors being studied might have anti-Covid-19 properties. Likewise, the flexible compounds AC8, AC10, AC3, and AC5 had the lowest Ki values of those made and could be used as a treatment. Our virtual physicochemical evaluation of all compounds in series A and B showed that all of them met the limits for molecular weight, lipophilicity (MLogP 4.15, the octanol-water partition coefficient), and water solubility. In addition to MR, the number of H-bond acceptors and the PSA were both within the acceptable range. It seems that the number of rotatable bonds is the only physicochemical property that separates the compounds in series B. The scores of compounds AC3, AC4, AC7, AC8, AC11, and AC12 are outside the acceptable range when compared to the results of chloroquine as the parent compound. © 2023 by SPC (Sami Publishing Company).

Synthesis of Biologically Active α-Tetralone Condensate: Growth of Single Crystal, Characterization by Experimental and Simulation Methods

The exocyclic double bonded α-tetralone condensate viz. (2E)-2-(4-propoxybenzylidene)-3,4-dihydro-1(2H)-naphthalene-1-one was synthesized by the Claisen–Schmidt reaction between α-Tetralone and 4-propoxybenzaldehyde in an alkaline medium. A slow evaporation technique was used to collect the single crystals. Researchers examined the detailed information provided by spectral studies. The inter- and intra-molecular interactions of the compound were identified using the single-crystal XRD investigation. Charge transfer inside organic molecules was used to calculate HOMO and LUMO energy values. In addition, MEP, NBO, NLO, topological charge distribution, and Mulliken population studies were performed for this compound. The Hirschfeld surface study showed that nonpolar or weakly polar interactions significantly contributed to the packing forces for molecules. Then, it was tested for its antioxidant, antidiabetic, and anti-inflammatory properties. The 6yb7 protein and the (2E)-2-(4-propoxybenzylidene)-3,4-dihydro-2H-naphthalen-1-one (PBDN) ligand were docked in molecular docking research.Crystal growth and spectral studies have been performed on (2E)-2-(4-propoxybenzylidene)-3,4-dihydro-2H-naphthalen-1-one (PBDN).Simulation studies were discussed.The compound PBDN has potential anti-inflammatory and anti-diabetic properties. In-silico method reveals that the PBDN is a moderate ligand for an unliganded active site on COVID-19's main protease (PDB code: 6yb7). [ FROM AUTHOR] Copyright of Polycyclic Aromatic Compounds is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

QSAR and DFT Studies of Some Tacrine-Hydroxamate Derivatives as Inhibitors of Cholinesterase (AChEs) in the Treatment of Alzheimer's Disease

Introduction: This work was devoted to an in silico investigation conducted on twenty-eight Tacrine-hydroxamate derivatives as a potential treatment for Alzheimer's disease using DFT and QSAR modeling techniques. Method(s): The data set was randomly partitioned into a training set (22 compounds) and a test set (6 compounds). Then, fourteen models were built and were used to compute the predicted pIC50 of compounds belonging to the test set. Result(s): Al built models were individualy validated using both internal and external validation methods, including the Y-Randomization test and Golbraikh and Tropsha's model acceptance criteria. Then, one model was selected for its higher R2, R2test, and Q2cv values (R2 = 0.768, R2adj = 0.713, MSE = 0.304, R2test=0.973, Q2cv = 0.615). From these outcomes, the activity of the studied compounds toward the main protease of Cholinesterase (AChEs) seems to be influenced by 4 descriptors, i.e., the total dipole moment of the molecule (mu), number of rotatable bonds (RB), molecular topology radius (MTR) and molecular topology polar surface area (MTPSA). The effect of these descriptors on the activity was studied, in particular, the increase in the total dipole moment and the topological radius of the molecule and the reduction of the rotatable bond and topology polar surface area increase the activity. Conclusion(s): Some newly designed compounds with higher AChEs inhibitory activity have been designed based on the best-proposed QSAR model. In addition, ADMET pharmacokinetic properties were carried out for the proposed compounds, the toxicity results indicate that 7 molecules are nontoxic.Copyright © 2023 Bentham Science Publishers.

Synthesis, characterization and identification of inhibitory activity on the main protease of COVID-19 by molecular docking strategy of (4-oxo-piperidinium ethylene acetal) trioxonitrate.

In this investigation a single crystal of (4-oxo-piperidinium ethylene acetal) trioxonitrate (4-OPEAN) was synthesized by modifying the mechanism of gradual evaporation at ambient temperature. The operational groupings are found in the complex material in the elaborate substance, according to the infrared spectrum. Single crystal X-ray diffraction suggests, (4-OPEAN) with the chemical formula (C7H12NO2)NO3 belongs to the orthorhombic space group Pnma and is centrosymmetric in three dimensions with the aforementioned network configurations, a = 11.7185(8) Å, b = 7.2729(6) Å, c = 11.0163(8) Å, Z = 4, V = 938.89(12) Å3, R = 0.0725 and wR = 0.1762. Many N-H…O and C-H…O hydrogen bridges, both bifurcated and non-bifurcated, link the 4-oxo-piperidinium ethylene acetal cations to the trigonal (NO3-) anions. Molecular geometry and optimal parameters of (4-OPEAN) have been determined via DFT computations at the theory-level B3LYP/6-311 ++ G(d, p), these have been contrasted with the X-ray data already available. Hirshfeld surface analysis has made it possible for the visualization and quantification of relationships between molecules in the crystal composition. Quantum theory atoms in molecules, electron location function, decreased density gradient, and localized orbital locator research have all been used to explore non-covalent interactions in crystal structure. In order to pinpoint both the nucleophilic and electrophilic locations that support hydrogen bond formation, the molecule electrostatic potential was determined. The greatest and lowest energies of occupied and unfilled molecular orbitals, together with additional derived atomic characteristics, show the material to be extremely stable and hard. According to a molecular docking study, 4-OPEAN may exhibit inhibiting effects on the 6Y84 and 7EJY virus proteins from corona (COVID-19).

DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2.

Theoretical analyses of two phenothiazine derivatives, 10-[3-(dimethylamino)-2-methylpropyl]phenothiazine-2-carbonitrile (CYM) and 2-[4-[3-(2-chlorophenothiazin-10-yl)propyl]piperazin-1-yl]ethanol (PAZ) are reported using density functional theory (DFT) and molecular dynamics (MD) simulations. Spectroscopic studies, different electronic and chemical parameters are predicted. Red and yellow in electrostatic potential plot is in rings and oxygen atom in PAZ and C≡N and rings in CYM are sensitive to nucleophilic attacks. The blue in hydrogen atoms refer to electrophilic attack in both PAZ and CYM. Stability of the protein-ligand complex formed with these derivatives and angiotensin-converting enzyme 2 (ACE2) was investigated using MD simulation. Radius of gyration of C-alpha atom of 6VW1 displayed the conformational convergence toward a compact structure leading to stable 6VW1-ligand complex which are also in agreement with root mean square fluctuation (RMSF) values. Localized area predicts reactive sites for Au and H2O molecules interaction with these compounds for further practical applications. Charge density is localized on both molecules and also tries to move toward Au-Au dimer and water molecule and such they are expected to contribute to the sensing performance. Communicated by Ramaswamy H. Sarma.

N'-(3,4-dimethoxybenzylidene)-4-methylbenzenesulfonohydrazide derivatives: Synthesis, Quantum Chemical Method, in silico ADMET, Molecular docking and Molecular dynamic simulations

A new N'-(3,4-dimethoxybenzylidene)-4-methylbenzenesulfonohydrazide derivatives were prepared from a condensation reaction between 4-methylbenzenesulfonohydrazide and 3,4-dimethoxybenzaldehyde. The structure of DMSH was elucidated using various spectral techniques including FT-IR, 1H-NMR and 13C-NMR. The structure of DMSH bond parameters also confirmed by single crystal XRD analysis of related derivatives and optimized bond parameters are calculated by density functional theory (DFT) method at B3LYP/6-311G (d, p) level of theory. The optimized geometrical parameters obtained by DFT calculation are in good agreement with single crystal XRD data. The experimentally observed FT-IR bands were assigned to different normal modes of the molecule. The results show a good agreement with each other when these computed bond parameters are compared to XRD values of related compounds. The stability, chemical reactivity and charge transfer within the molecule was explained by frontier molecular orbital calculations. Atomic charges on the various atoms of DMSH obtained by Mulliken population analysis. Potential reactive sites of the DMSH compound have been identified by MEP which is mapped to the electron density surfaces. The reported molecule is used as a potential NLO material since it has a high μβ0 value. The theoretical UV-vis spectrum of the compound is used to study the visible absorption maxima (λ max). The molecular docking mechanism between DMSH ligand and COVID-19/6WCF and COVID-19/6Y84 receptors were studied to investigate the binding modes of this compound at the active sites. Molecular docking outcomes have shown that the DMSH molecule can be considered as a potential agent against COVID-19/6WCF-6Y84 receptors. In addition, the theoretical parameters of the bioactive molecules were calculated to establish their drug-likeness qualities and ADME/T analysis was carried out to examine the drug properties of the synthesized compound. Molecular dynamics simulation was performed for COVID-19 main protease (Mpro: 6WCF/6Y84) to understand the elements governing the inhibitory effect and the stability of interaction under dynamic conditions. The resultant complex structures were subjected to 100 ns simulation run to estimate their binding stabilities using GROMACS. The molecular dynamics simulation studies provided essential evidence that the systems were stable during the progression of 100 ns simulation run.

Antiviral Docking Analysis, Semisynthesis and Mechanistic Studies on the Origin of Stereo- and Chemoselectivity in Epoxidation Reaction of α'-trans-Himachalene

Epoxides are of great commercial relevance in several businesses due to their unique attributes. The epoxide C15H22O was synthesized via epoxidizing the α'-trans-himachalene 4 deploying meta-chloroperbenzoic acid (m-CPBA) in dichloromethane. The chemoselectivity of the reaction was investigated both experimentally and theoretically in the framework of the molecular electron density theory (MEDT). An experimental chemoselectivity with the best C3=C4 interaction was appropriately determined as predicted by the Parr functions, ELF analysis of the reactants and energetic study. In addition, the epoxidation reaction of α'-trans-himachalene 4 by m-CPBA possessed a lower activation energy in water and ethanol, which shows that this reaction can be performed in environmentally friendly solvents. The investigation of the mechanism indicates that this epoxidation reaction follows a one-step mechanism. Furthermore, a docking study has been carried out for α'-trans-himachalene 4, epoxide 5 and epoxide 6 docked in SARS-CoV2 main protease (6LU7) as compared to the Ribavirin, thus indicating that epoxide 6 could be the antiviral drug.

In situ synthesis of multivariant zeolitic tetrazolate imidazole frameworks (ZTIFs) with uncoordinated N-heteroatom sites for efficient adsorption of antiviral drugs.

The current outbreak of the coronavirus (COVID-19) pandemic has significantly increased the global usage of antiviral drugs (AVDs), leading to higher concentrations of antibiotics in water pollution. To address this current issue, a new kind of adsorbent named isostructural zeolitic tetrazolate imidazolate frameworks (ZTIFs) were synthesized by combining imidazole and tetrazolates into one self-assembly approach by adjusting pores and stability of frameworks. The incorporation of imidazole ligand progressively increased the stability of frameworks. Furthermore, increasing the content of tetrazolate ligand greatly improved the adsorption performance due to N-rich sites by increasing the pore size. The obtained adsorbent composite exhibits macroporous structure up to 53.05 nm with excellent structural stability. Owing to their macropores and highly exposed active sites, the synthesized ZTIFs exhibit the maximum adsorption capacity for oseltamivir (OT) and ritonavir (RT) of 585.2 mg/g and 435.8 mg/g, respectively. Moreover, the adsorption uptake and saturation process were rapid compared to simple MOF. Within 20 min, both pollutants achieved equilibrium. The adsorption isotherms were best interpreted by Pseudo second order kinetics. The adsorption of AVDs on ZTIFs was spontaneous, exothermic, and thermodynamically feasible. The DFT calculations and characterization results after adsorption demonstrate that π-π interaction, pore filling, surface complexation, and electrostatic interaction were the primary features of the adsorption mechanism. The prepared ZTIFs composite exhibits high chemical, mechanical and thermal stability and can be recycled multiple times without destroying its morphology and structure. The adsorbent regeneration for several cycles impacted the operational cost and the eco-friendly characteristic of the process.

Novel oxazolidinone zinc(II) complexes as antibacterial and anti-SARS-CoV-2 agents: synthesis, characterization, DFT calculations, ADMET, in silico molecular docking and biological activities

A series of Zn(II) complexes with oxazolidinone derivatives has been synthesized and characterized using spectroscopic techniques: IR, H-1 NMR, UV-Vis spectroscopy, and TGA/DTG thermal investigation. Theoretical computations were carried out using B3LYP/6-31G(d) and B3LYP/LanL2DZ to analyze the vibrational properties, NBO charges, global chemical reactivity indices and to illustrate the FOMs. TD-DFT calculations using WB97XD functional were realized with 6-31 G(d) and LAN2DZ basis set on oxazolidinone ligands and their zinc complexes. The pharmacokinetic properties and toxicity of the investigated compounds were predicted using in silico ADMET studies. Moreover, the S. aureus, E. coli, S. pneumoniae, ribosome 50S subunit, SARS-Cov-2 spike protein and ACE2 human receptor were selected for molecular docking study. The docking study shows that HL4 and ZnL4 bind better to the spike protein and hACE2 receptor. The redox properties were also studied for ligands and their corresponding complexes using cyclic voltammetry. Finally, antioxidant activity studies using DPPH radical scavenging showed efficiency for HL2 and [Zn(L-2)(2)] with low values of IC50 compared to ascorbic acid. The antimicrobial activity against B. subtilis (ATCC 9372), E. faecalis (ATCC 29212), S. aureus (ATCC 6538), E. coli (ATCC 4157), bacteria strains, C. albicans (ATCC 24433) and A. niger fungi strains were evaluated.

Insights Into the Selective Imprinted Polymer of Voriconazole from Host-Guest Interaction Perspective

The incidence of fungal coinfections, such as Aspergillus spp., in patients with COVID-19 has been widely reported. Voriconazole is the first-line treatment for aspergillosis. A challenging sample preparation process is required to perform therapeutic drug monitoring of voriconazole. Recently, Molecularly Imprinted Polymers (MIP) have been shown to improve the separation selectivity for biological samples. Monomer selection in MIP is often performed by trial and error, without a design strategy. Therefore, this study aimed to construct a high-affinity MIP for voriconazole based on its interaction with functional monomers. All structures were optimized with B3LYP/6-311G++(d,p) and DFT-D3 dispersion correction method. Calculations of vacuum and solvated frequencies were carried out using a structure with maximum binding energy from molecular docking. The results showed that complex five was the most stable, exothermic, spontaneous, and enthalpy-driven among the complexes. In addition, there are nine intermolecular interactions and one moderate hydrogen bond in the QTAIM and NBO analysis, whereas hydrogen bonds, van der Waals interactions, and hydrophobic interactions were observed in the NCI-RDG analysis. The findings of this preliminary investigation showed that voriconazole possesses high stability when combined with functional monomers. It also provides information and assistance for further laboratory MIP synthesis.

Antibacterial Activity and in Silico Investigation of 2-[(3-Substitutedphenyl) Azomethine] Phenol as anti-SARS-CoV-2 Mpro and anti-Plasmodium falciparum Agents

Imine derivatives are widely used in medicine for the treatment of several diseases causing human infections;we examined Schiff's bases derivatives: 2-[(3-methylphenyl) azomethine] phenol (L1), 2-[(3-chlorophenyl) azomethine] phenol (L2) and 2-[(3-nitrophenyl) azomethine] phenol (L3) against three human pathogenic bacterial strains according to the disk diffusion test. In addition, to revealing the importances of the in silico study of these derivatives, in particular the molecular docking which is based on the protein structures: the main protease 3CL of SARS-CoV-2 and the aminopeptidase of the M1 family. Also, a molecular dynamics simulation was performed to examine the structural stability of the best docked conformation. The evaluation of the global reactivity parameters of the molecular system of Schiff base derivatives was applied by the DFT method with the hybrid functional (B3LYP)/6-31G (d) basis set. The results of the antibacterial activity showed a strong activity in the presence of the L3 ligand against Escherichia coli (ATCC 25922) with a diameter inhibition zone equal to 11 ± 0.61 mm. Molecular docking shows that the L3 ligand formed with protein targets more stable complexes by predicting interesting interactions: hydrogen, hydrophobic and electrostatic bonds with the residues of these targets 3CLpro and PfA-M1. Further, molecular dynamics simulations confirm a strong energy contribution with these interactions. Therefore, suggesting that our ligands could contribute to the development of anti-coronavirus-2 and anti-malarial drug properties. [ FROM AUTHOR] Copyright of Polycyclic Aromatic Compounds is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

DFT, molecular docking and ADME prediction of tenofovir drug as a promising therapeutic inhibitor of SARS-CoV-2 M-pro

In the present work, at first, DFT calculations were carried out to study the molecular structure of the tenofovir at B3LYP/MidiX level of theory and in the water as solvent. The HOMO/LUMO molecular orbitals, excitation energies and oscillator strengths of investigated drug were also calculated and presented. NBO analysis was performed to illustrate the intramolecular rehybridization and electron density delocalization. In the following, a molecular docking study was performed for screening of effective available tenofovir drug which may act as an efficient inhibitor for the SARS-CoV-2 M-pro. The binding energy value showed a good binding affinity between the tenofovir and SARS-CoV-2 Mpro with binding energy of-47.206 kcal/mol. Therefore, tenofovir can be used for possible application against the SARS-CoV-2 M-pro.

Exploration of DFT and TD-DFT computation to investigate the interaction between paracetamol and lithium or its compounds.

Paracetamol is a commonly used antipyretic drug and its consumption drastically was increased during the COVID-19 times as fever was one of the symptoms. The excessive usage of paracetamol could harm humans, as the unused accumulated paracetamol can involve in the reaction with many small molecules as well as can interact with several biomolecules. Lithium chloride in its hydrated form is used as an antimanic drug and a geroprotector. It is needed in very small quantities by humans. Tetrahydrated form of lithium ion is the most stable hydrated form. Herein, the authors have investigated the interaction of paracetamol with tetrahydrated lithium chloride (1:1 and 1:2) using the DFT and TD-DFT calculations at 298 K and 310 K. The interaction of paracetamol with lithium chloride P1 (1:1), P2 (2:1), P3 (3:1) and P4 (4:1) are also studied by DFT calculations in default and CPCM model. The authors have calculated the free energy, optimization energy, dipole moment and other thermodynamic parameters of all the systems. Based on enthalpy and change in Gibbs free energy, the interaction was maximum between the paracetamol and tetrahydrated lithium chloride at 298 K as well as 310 K which indicates that the hydrated lithium chloride is being consumed by unused paracetamol. In P1 and P3, lithium showed interaction with oxygen of phenolic group and other atoms of all the paracetamol molecules present, while in P2 and P4, lithium showed these interactions with only one paracetamol molecule.

Synthesis, structural analysis, DFT and molecular docking studies of N-(6-(((E)-4-methoxybenzylidene)amino)hexyl)-1-(4-methoxyphenyl) methanimine and its hydrate as a possible 2019-nCoV protease inhibitor

N-(6-(((E)-4-methoxybenzylidene) amino) hexyl)-1-(4-methoxyphenyl) methanimine (1) and its hydrate (2) were synthesized by refluxing hexamethylene diamine and anisaldehyde in presence of catalytic amount of H-Beta zeolite in solvent methanol. Resulting imines were characterized by spectroscopic analysis augmented by Single crystal X-ray diffraction. Both compounds crystalize in monoclinic crystal systems with different point groups P 21 and C 2/c. Pair wise aromatic π-CH and CH- π interactions with distance 2.887 and 2.786 Ao and iminic CH- π interactions with the distance of 2.73 Ao are mainly responsible for extending the structure along 3 dimensions. However, hydrated structure exhibited an addition hydrogen bonding with H of water molecules with the distance of 2.030 Ao , also methoxy O is involved in hydrogen bonding interaction with CH with the distance of 2.641 Ao. Probable contact points and most important crystal packing contributions were determined by employing Hirshfeld surface analysis. H…H and C…H contacts are the most important contributors in the Hirshfeld Surface. Electronic and structural characteristics of both compounds has been calculated using B3LYP/6-311G (d,p) theory. In addition, FMO and MEPS analyses were also accomplished for optimized structures. Molecular Docking studies of compound 1 and 2 were carried out with protease enzyme of 2019-nCoV (PDB-ID 7BRO), monohydrate(2) was involved in more favourable interactions hence accounting for greater binding energy (-7.98 kcal/mol) and inhibition constant (12.96 mM) than compound 1 exhibiting inhibition constant of 39.25 mM and binding energy of -6.23 kcal/mol.

Naphtho[2,1-b]furan derived triazole-pyrimidines as highly potential InhA and Cytochrome c peroxidase inhibitors: Synthesis, DFT calculations, drug-likeness profile, molecular docking and dynamic studies

Napthofuran and its fused heterocyclic derivatives evaluated with varied biological activity functional groups comprise an important class of compounds for new chemical entities. We here in reporting synthesis of new 3-(4-substituted phenyl)naphtho[1′,2′:4,5]furo[2,3-e][1,2,4]triazolo[4,3-c]pyrimidines 6(a-f). Structures of the newly synthesized compounds were confirmed by making use of spectroscopic techniques like IR, NMR and Mass. The DFT calculations were taken for the selected molecules using B3LYP hybrid functional with a 6–31+G (d, p) all-electron basis set using the Gaussian 09 package. The bioactivity predictions were evaluated for the synthesized compounds. The In vitro biological activities were reported for the all compounds 6(a-f). The compound 6a showed high activity of anti-TB and antioxidant activity with at MIC 1.6 μg/ml and at percentage of inhibition (72.54±0.21) at 10μg/ml respectively. The compound 6f (73.21±0.11) showed antioxidant activity better than standard drug BHA (71.32±0.13) at 10 μg/ml. Furthermore, the docking studies for the newly synthesized molecules were carried out by Auto dock software with proteins InhA (4TZK),Cytochrome c peroxidase (2 × 08) and protease (Mpro) of SARS-CoV-2 Omicron (PDB ID: 7TOB). All the compounds showed a strong binding affinity for the docked proteins. The outcome of docking results showed that compound 6ahad excellent binding energies -10.8, -9.4, and -9.0 kcal/mol with 4TZK, 2 × 08, and 7TOB respectively. Lastly, the protein stability, fluctuations of APO-Protein, protein-ligand complexes were investigated through Molecular Dynamics (MD) simulations studies using Desmond Maestro 11.3 and potential lead molecules were identified. © 2023

Fast-responsive and multi-applicable fluorescent turn-off chemodosimeter for monitoring hypochlorite: application to test strips, water samples, disinfectants and bioimaging

Due to the twin-demic of COVID-19 and flu virus, disinfectants containing ClO- have been widely used nowadays. Therefore, it is urgent to develop a sensor capable of efficiently detecting toxic hypochlorite. We present the invention and assessment of a fast-responsive and multi-applicable chemodosimeter sensor ETA (2-(2-((1E,2E)-3-(4-(dimethylamino)phenyl)allylidene)hydrazineyl)-N,N,N-trimethyl-2-oxoethan-1-aminium chloride) for monitoring ClO‑. In pure water, adding ClO- to ETA caused a turn-off fluorescence within 2 sec. These changes made it possible to quickly detect ClO- with a high level of selectivity. ETA displayed a low detection limit (0.68 μM) to ClO-. Using UV-vis titrations, ESI-MS and DFT calculations, we were able to demonstrate the detection mechanism, in which ETA was cleaved by ClO-. In particular, we established the possibility for reliable ClO- detection in environmental systems such as actual water samples, disinfectants, living cells, zebrafish and celery, in addition to confirming the practicality of ETA utilizing test strips.

Structural and Computational Studies of Cobalt(II) and Copper(II) Complexes with Aromatic Heterocyclic Ligand

Two coordination complexes, a cobalt(II) complex tris(1,10-phenanthroline)-cobalt perchlorate hydrate, [Co(phen)3]·(ClO4)2·H2O(1), and a copper(II) complex tris(1,10-phenanthroline)-copper perchlorate 4-bromo-2-{[(naphthalene-1-yl)imino]methyl}phenol hydrate, [Cu(phen)3]·(ClO4)2·HL·[O] (2), [where, phen = 1,10-phenathroline as aromatic heterocyclic ligand, HL = 4-bromo-2-((Z)-(naphthalene-4-ylimino) methyl) phenol] have been synthesized and structurally characterized. Single crystal X-ray analysis of both complexes has revealed the presence of a distorted octahedral geometry around cobalt(II) and copper(II) ions. density functional theory (DFT)-based quantum chemical calculations were performed on the cationic complex [Co(phen)3]2+ and copper(II) complex [Cu(phen)3]2+ to get the structure property relationship. Hirshfeld surface and 2-D fingerprint plots have been explored in the crystal structure of both the metal complexes. To find potential SARS-CoV-2 drug candidates, both the complexes were subjected to molecular docking calculations with SARS-CoV-2 virus (PDB ID: 7BQY and 7C2Q). We have found stable docked structures where docked metal chelates could readily bound to the SARS-CoV-2 Mpro. The molecular docking calculations of the complex (1) into the 7C2Q-main protease of SARS-CoV-2 virus revealed the binding energy of −9.4 kcal/mol with a good inhibition constant of 1.834 µM, while complex (2) exhibited the binding energy of −9.0 kcal/mol, and the inhibition constant of 1.365 µM at the inhibition binding site of receptor protein. Overall, our in silico studies explored the potential role of cobalt(II) complex (1), and copper(II) complex (2) complex as the viable and alternative therapeutic solution for SARS-CoV-2.

A dispersion-corrected DFT calculation on encapsulation of favipiravir drug used as antiviral against COVID-19 into carbon-, boron-, and aluminum-nitride nanotubes for optimal drug delivery systems combined with molecular docking simulations.

Favipiravir (FAV) (6-fluoro-3-oxo-3,4-dihydropyrazine-2-carboxamide) is one of the most effective antiviral drugs which is cited for action against RNA-viral infections of COVID-19. In this study, density functional theory (DFT) calculations were used to investigate three nanotubes (NTs) with FAV drug as delivery systems. The encapsulated systems (ESs) consist of FAV drug inside carbon-carbon, aluminum nitride, and boron nitride. At B3LYP-D/6-31G(d,p) and CPCM/B3LYP-D/6-31G(d,p), the optimization of NTs, FAV, and its tautomeric forms and six ESs was investigated in gas and water environments. Five tautomeric forms of FAV were investigated, two keto forms (K1 and K2) and three enol forms (E1, E2, and E3). The results revealed that E3 and K2 isomeric forms represented the most stable structures in both media; thus, these two forms were encapsulated into the NTs. The stability and the synthesis feasibility of NTs have been proven by calculating their interaction energies. Non-covalent interactions (NCIs) were investigated in the ESs to show the type of NCI with the molecular voids. The binding energies, thermochemical parameters, and recovery times were investigated to understand the mechanism of FAV encapsulation and release. The encapsulated AlNNT systems are more favorable than those of BNNTs and CNTs in gas and aqueous environments with much higher binding energies. The quantum theory of atoms in molecules (QTAIM) and recovery time analysis revealed the easier releasing of E3 from AlNNT over K2 form. Based on molecular docking simulations, we found that E3 and K2 FAV forms showed a high level of resistance to SARS-CoV-6M3M/6LU7/6W9C proteases. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-023-02182-4.

Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach.

During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.