Interaction of a series of nitriles with the alcohol-inducible isoform of P450: computer analysis of structure-activity relationships

Theoretical Design of New Grafted Molecules d-Glucosamine-Oxyresveratrol-Essential Amino Acids: DFT Evaluation of the Structure-Antioxidant Activity

In the pursuit of innovative high-performance materials suitable for antioxidant applications, the density functional theory was employed to design a series of compounds derived from small biodegradable organic molecules. This study involved grafting the negatively charged unit d-glucosamine (GleN) and essential amino acids onto the 3 and 4' carbons of the backbone of trans-2,4,3',5'-tetrahydroxystilbene (trans-OXY), respectively. The aim was to prevent trans-OXY degradation into the cis region and enhance its electronic and antioxidant properties. Theoretical calculations using DFT/PW91/TZP in water revealed that the designed biomolecules (GleN-OXY-AA) outperformed both free OXY units and essential amino acids in terms of antioxidant efficacy, as indicated by the bond dissociation energy (BDE) findings. Notably, GleN-OXY-Ile and GleN-OXY-Trp compounds exhibited an average BDE of 66.355 kcal/mol, translating to 1.82 times the activity of t-OXY and 1.55 times the action of ascorbic acid (Vit C). AIM analysis demonstrated that the proposed biomaterials favored the formation of quasi-rings through intramolecular H···O hydrogen bonds, promoting π-electron delocalization and stabilization of radical, cationic, and anionic forms. Quantum calculations revealed the release of hydrogen atoms or electrons from sites of reduced electronegativity, visually identified by MEP maps and estimated by Hirshfeld atomic charges.

Computational discovery of dual potential inhibitors of SARS-CoV-2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics

To find drugs against COVID-19, caused by the SARS-CoV-2, promising targets include the fusion of the viral spike with the human angiotensin-converting enzyme 2 (ACE2) as well as the main protease (Mpro). These proteins are responsible for viral entry and replication, respectively. We combined several state-of-the-art computational methods, including, protein-ligand interaction fingerprint, 3D-pharmacophores, molecular-docking, MM-GBSA, DFT, and MD simulations to explore two databases: ChEMBL and NANPDB to identify molecules that could both block spike/ACE2 fusion and inhibit Mpro. A total of 1,690,649 compounds from the two databases were screened using the pharmacophore model obtained from PLIF analysis. Five recent complexes of Mpro co-crystallized with different ligands were used to generate the pharmacophore model, allowing 4,829 compounds that passed this prefilter. These were then submitted to molecular docking against Mpro. The 5% top-ranked docking hits from docking result having scores < -8.32 kcal mol-1 were selected and then docked against spike/ACE2. Only four compounds: ChEMBL244958, ChEMBL266531, ChEMBL3680003, and 1-methoxy-3-indolymethyl glucosinolate (4) displayed binding energies < - 8.21 kcal mol-1 (for the native ligand) were considered as putative dual-target inhibitors. Furthermore, predictive ADMET, MM-GBSA and DFT/6-311G(d,p) were performed on these compounds and compared with those of well-known antivirals. DFT calculations showed that ChEMBL244958 and compound 4 had significant predicted reactivity values. Molecular dynamics simulations of the docked complexes were run for 100 ns and used to validate the stability docked poses and to confirm that these hits are putative dual binders of the spike/ACE2 and the Mpro.

Exploring the effects of mono-bromination on hole-electron transport and distribution in dibenzofuran and dibenzothiophene isomers: a first-principles study

CONTEXT

This study delves into hole-electron transport and distribution properties inherent in mono-brominated dibenzofuran (DBF) and dibenzothiophene (DBT) isomers. As determined by frontier molecular orbitals, all brominated structures have narrower bandgaps than their primary structures. The TD-DFT calculation showed that 2BDBT had the highest absorption wavelength of all molecules at 315.35 nm. Notably, the study unveils remarkably low electron and hole reorganization energies due to bromine substitution in DBF and DBT molecules. Specifically, the 4BDBF has the lowest hole reorganization energy of all DBF configurations, 0.229 eV. In addition, 3BDBF has 0.226 eV less electron reorganization energy than all other molecules. Compared to DBT, 3BDBT has the lowest electron reorganization energy of 0.254 eV. Overall, this research sheds significant light on the fundamental electronic and hole transport characteristics of bromine-substituted DBF and DBT isomers, highlighting their promising role in polymer design as donors/acceptors for advanced organic electronic applications.

METHODS

Molecular structures were optimized using Density Functional Theory (DFT) B3LYP/6-311 +  + G (d, p) level of theory, and the study further elucidates these molecules' energy levels and absorption spectra through Time-Dependent Density Functional Theory TD-DFT; these calculations were performed using Gaussian 09W software package. The key parameters such as reorganization energies, Electron Localization Function map, Laplacian Bond Order, and NCI-RDG were meticulously examined for the molecules with the results of DFT calculations were analyzed and displayed by utilizing the software packages VMD 1.9.4 and Multiwfn 3.8, aiming to comprehend their charge transport and distribution properties.

Antiplatelet activity and toxicity profile of novel phosphonium salts derived from Michael reaction

In this work, five novel phosphonium salts derived from the Michael reaction were screened for their antiplatelet activity. Our findings revealed that compounds 2a, 2b, 2c, and 2d significantly inhibit platelet aggregation triggered by ADP or collagen (P < 0.001). Notably, compound 2c inhibited the arachidonic acid pathway (P < 0.001). Moreover, the selected compounds reduce CD62-P expression and inhibit GPIIb/IIIa activation. The interactions of the active compounds with their targets, ADP and collagen receptors, P2Y12 and GPVI respectively were investigated in silico using molecular docking studies. The results revealed a strong affinity of the active compounds for P2Y12 and GPVI. Additionally, cytotoxicity assays on platelets, erythrocytes, and human embryonic kidney HEK293 cells showed that compounds 2a, 2c and 2d were non-toxic even at high concentrations. In summary, our study shows that phosphonium salts can have strong antiplatelet power and suggests that compounds 2a, 2c and 2d could be promising antiplatelet agents for the management of cardiovascular diseases.

Comparative investigation of derivatives of (E)-N-((E)-3-phenylallylidene)aniline: Synthesis, structural characterization, biological evaluation, density functional theory analysis, and in silico molecular docking

Bacterial resistance to antibiotics poses a significant global challenge for the public sector. Globally, researchers are actively investigating solutions to tackle the issue of bacterial resistance to antibiotics, with Schiff bases standing out as promising contenders in the fight against antimicrobial resistance. This study focused on synthesizing a series of Schiff bases (CA1-CA10) by reacting cinnamaldehyde with various aniline derivatives. Various analytical techniques, such as NMR, FTIR, UV-Vis, elemental analysis, and mass spectrometry, were employed to elucidate the structures of the synthesized compounds. Furthermore, crystal structure of CA8 was obtained using single crystal X-ray spectroscopy. The compounds were subjected to in vitro testing to assess their antibacterial and antifungal properties against eleven bacterial strains and four fungal strains. The results revealed diverse activity levels against the pathogens at varying concentrations, with notable potency observed in compounds CA3, CA4, CA9, and CA10, as indicated by their minimum inhibitory concentrations (MIC) values. The observed activity of the compounds seemed to be influenced by the specific substituents attached to their molecular structure. By conducting computational and molecular docking studies, the electronic properties of the compounds were investigated, further substantiating their potential as effective antimicrobial agents.

Synthesis, characterization, in vitro antimycobacterial and cytotoxicity evaluation, DFT calculations, molecular docking and ADME studies of new isomeric benzimidazole-1,2,3-triazole-quinoline hybrid mixtures

New benzimidazole-1,2,3-triazole-quinoline hybrids and their intermediates, differing in substitutions at the C-2 and/or C6 positions of the benzimidazole ring, were successfully synthesized in 55---80 % yields, with the C6-substituted ones forming as inseparable tautomeric mixtures. The synthesized compounds were fully characterised by FT-IR, 1D- and 2D-NMR, and HRMS. In-depth NMR analysis and DFT molecular calculations showed that the tautomeric mixtures formed in a ratio of almost 1:1 ratio (cis and trans), except for 5 g, where the ratio is 1:2. In vitro antimycobacterial activity evaluation against the H37Rv strain of Mycobacterial tuberculosis was undertaken on all synthesized compounds, and a selected number were further screened for their cytotoxicity on TZM-bl cell lines. Hybrid compounds showed excellent MIC90 activities ranging from 1.07 to 8.66 μM and were all more efficacious than the first-line reference drug, ethambutol (MIC90 = 9.54 μM). In particular, hybrid compounds 5b (MIC90 = 1.54 μM, CC50 = 58.89 μM and % cell viability = 14.07), 5d (MIC90 = 2.08 μM, CC50 = 0.27 μM, and % cell viability = 149.50 %) and 5 g (MIC90 = 1.49 μM, CC50 = 4.62 μM and % cell viability = 44.03) were the most promising. Significantly, 5b and 5 g were over six times more efficacious than ethambutol but exhibited cytotoxicity towards TZM-bl cell-lines compared to 5d, which was over four times more active than ethambutol. The physical combination (mimicking combination therapy) of individual pharmacophoric components making up 5 g were less active, indicating the synergistic effect of hybridization. In addition, more than 60 % of all the synthesized hybrids showed better activity than their respective pharmacophoric components. In silico ADME studies of the hybrids revealed favourable physico-chemical properties, while molecular modeling studies suggested binding interactions with Val 61, Gly 62, Glu 65, Ala 66, and Phe 69 amino acid in a reported similar manner to bedaquiline, an approved quinoline-based anti-TB drug.

Topological analysis and reactivity study of monomeric and dimeric forms of 2-methyl-4(1H)-quinolone: a computational study

CONTEXT

Quinolone derivatives have gathered major attention largely due to their wonderful biological activities. Quinolones are a class of molecules that are derived from quinolines and also extracted from natural sources. Most of these quinolones have significant medicinal properties ranging from antiallergenic and anticancer to antimicrobial activities. Some bacteria produce several 2-alkyl-4(1H)-quinolones. In past years, a variety of methods have been reported for the synthesis of quinolone derivatives. In this present work, structural, wave functional, and electronic properties of monomeric and dimeric forms of 2-methyl-4(1H)-quinolone are investigated. From the calculated binding energies, it was found that the formation of dimers is thermodynamically favorable. The analysis of reactivity parameters confirms that the keto form is more reactive than the enol form and keto-keto dimer is more reactive than compared to all monomeric and dimeric forms of our studied compound.

METHODS

Geometry optimizations of monomers and dimers of studied molecules were carried out using the B3LYP-D3(BJ)/ma-def2-TZVPP level of theory. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were calculated using the B3LYP/def2-TZVP level of theory. All DFT calculations were done with the ORCA 5.0.3 program. The reactivity parameters such as ionization potential, electron affinity, global hardness, global softness, electronegativity, chemical potential, and electrophilicity index were calculated. The nature of intermolecular interactions within the dimers was studied using topological analysis such as atoms in molecule (AIM) and reduced density gradient (RDG) surface analyses. To visualize the electron delocalization in the dimer electron localization function (ELF) and localized orbital locator (LOL) studies were also performed. The analyses such as AIM, RDG, ELF, and LOL were carried out by the multifunctional wavefunction analysis program Multiwfn 3.8.

Ternary Mixture of Pentanamide in Solvent Analogy with Halogenated Phenol: Experimental, Theoretical, and In Silico Biological Studies

This research describes the preparation of mixtures of new halogen-substituted phenol derivatives and their effects due to linkages with a fatty amide (pentanamide). The molecules were optimized using DFT, and the vibrational and electronic analysis was done subsequently. The energies of frontier molecular orbitals (FMOs) were used to estimate the global chemical reactivity parameters as we suggest that hydrogen-bonded networks may have contributed to the stability and reactivity of the compound. In addition to the experimental investigation, dielectric parameters were calculated. Fukui functions were analyzed to study the chemical reactivity. To get insight into interactions of σ → π* orbitals, natural bond orbital calculations were done. Additionally, surface analysis of the MEP and Hirshfeld charges were performed at the equivalent DFT levels. The research also indicated that both (interaction region indicator) IRI and (electron delocalize range) EDR would proficiently identify chemical-bonding and weak interaction regions, providing a significant advantage in exploring diverse chemical systems and reactions. This indicated that compounds could diffuse through noncovalent interactions, including intramolecular hydrogen bonding. Dielectric relaxation studies taken at five distinct molar ratios identified significant dielectric properties such as ε', ε″, ε0, and ε∞. The PA with FP, CP, BP, and IP molecules has potential antiviral and antioxidant benefits for carbonic anhydrase, with favorable drug-like features and diverse biological benefits. Pharmacological effects were forecasted using the PASS server, and these molecules exhibited favorable pharmacokinetic properties.

In silico drug repurposing for coronavirus (COVID-19): screening known HCV drugs against the SARS-CoV-2 spike protein bound to angiotensin-converting enzyme 2 (ACE2) (6M0J)

In this study, FDA-approved HCV antiviral drugs and their structural analogues-several of them in clinical trials-were tested for their inhibitory properties toward the SARS-CoV-2 spike protein bound to angiotensin-converting enzyme 2 (6M0J) using a virtual screening approach and computational chemistry methods. The most stable structures and the corresponding binding affinities of thirteen such antiviral compounds were obtained. Frontier molecular orbital theory, global reactivity descriptors, molecular docking calculations and electrostatic potential analysis were used to hypothesize the bioactivity of these drugs against 6M0J. It is found that an increased affinity for the protein is shown by inhibitors with large compound volume, relatively higher electrophilicity index, aromatic rings and heteroatoms that participate in hydrogen bonding. Among the tested drugs, four compounds 10-13 showed excellent results-binding affinities - 11.2 to - 11.5 kcal mol-1. These four top scoring compounds may act as lead compounds for further experimental validation, clinical trials and even for the development of more potent antiviral agents against the SARS-CoV-2. Approved HCV drugs and analogues were tested for their bioactivity towards the SARS-CoV-2 (6M0J) using virtual screening, ESP and MD analysis.

Molecular Structure, Spectral Analysis, Molecular Docking and Physicochemical Studies of 3-Bromo-2-hydroxypyridine Monomer and Dimer as Bromodomain Inhibitors

In this paper, both methods (DFT and HF) were used in a theoretical investigation of 3-bromo-2-Hydroxypyridine (3-Br-2HyP) molecules where the molecular structures of the title compound have been optimized. Molecular electrostatic potential (MEP) was computed using the B3LYP/6-311++G(d,p) level of theory. The time-dependent density functional theory (TD-DFT) approach was used to simulate the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) on the one hand to achieve the frontier orbital gap and on the other hand to calculate the UV–visible spectrum of the compound in gas phase and for different solvents. In addition, electronic localization function and Fukui functions were carried out. Intermolecular interactions were discussed by the topological AIM (atoms in molecules) approach. The thermodynamic functions have been reported with the help of spectroscopic data using statistical methods revealing the correlations between these functions and temperature. To describe the non-covalent interactions, the reduced density gradient (RDG) analysis is performed. To study the biological activity of the compound of the molecule, molecular docking studies were executed on the active sites of BRD2 inhibitors and to explore the hydrogen bond interaction, minimum binding energies with targeted receptors such as PDB ID: 5IBN, 3U5K, 6CD5 were calculated.

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsonate Salt of 4-Aminopyridine

In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C₅H₇N₂)(C₅H₈N₂)[AsO₄]·H₂O ((4-APH)(4-APH₂)[AsO₄]·H₂O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values.

Development of New Azomethine Metal Chelates Derived from Isatin: DFT and Pharmaceutical Studies

Through the condensation of isatin (indoline-2, 3-dione) and aniline in a 1:1 ratio, a Schiff base ligand was synthesized and characterized via (¹H-NMR, mass, IR, UV-Vis) spectra. Elemental analyses, spectroscopy (¹H-NMR, mass, UV-Vis), magnetic susceptibility, molar conductivity, mass spectra, scanning electron microscope (SEM), and thermal analysis have all been used to characterize a series of Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), and Cd(II) metal complexes derived from the titled ligand. The metal-to-ligand ratio is 1:1, according to the analytical data. The Schiff base ligand displayed bidentate behavior with NO coordination sites when it bonded to metal ions, as seen by the IR spectra. The magnetic moment measurement and UV-Vis spectral investigation showed the octahedral geometry of the Cr(III), Fe(III), Co(II), Ni(II), and Zn(II) complexes, whereas they suggested the tetrahedral geometry of the Mn(II), Cu(II), and Cd(II) complexes. The thermal analysis study confirmed the presence of both hydrated and coordinated water molecules in all the compounds, except for the Mn(II) complex, and showed that the complexes decomposed in three or five decomposition steps leaving the corresponding metal oxide as a residue. The ligand and its metal complexes' antibacterial efficacy were evaluated. The findings showed that the metal complexes had stronger antibacterial properties than the ligand alone. The ligand and its metal complexes' anticancer properties were also investigated. A DFT investigation is also reported to gather information regarding the electronic features of the ligand and its metal complexes. Finally, drug-likeness and ADME characteristics were also calculated as parameters.

Quantum chemical hydrogenolysis strategy for elimination of heteroatoms in biomass homologous organic compounds based on oxolane and thiolane

Bio-oils obtained from biomass contain heteroatoms compounds, like oxolane and thiolane. It is quite difficult for industrialist to purify such refractory bio-oils. One of the efficient strategies for the elimination of heteroatoms is hydrogenolysis process, which results in the formation of H₂O and H₂S residues as by-products. In this work, quantum chemical studies have been used to analyse the reaction mechanism for the removal of hetero atoms (S and O) as H₂O and H₂S. We selected B3LYP functional of DFT with Pople's basis set 6-311G(d,p) for computing the hydrogenolysis steps without catalyst. LANL2DZ basis set, is used for studying hydrogenolysis steps involving AlCl₃ and WS₃H₃⁺ as catalysts. All the reactions are analysed at the temperature of 600 K and pressure of 40 bars. Structural, thermodynamic, kinetic properties have been employed to study this process. The analysis of variations parameters during the hydrogenolysis process reveals that these two organic biomass compounds undergo sequential ring opening at C-X (X = O, S) bonds. Butanol and Butanethiol are obtained as a result of first hydrogenolysis process, and these compounds are converted to butane during second catalytic process while eliminating heteroatoms.

Theoretical investigation of some 1,2,4-triazole-based molecules synthetized

In this study, theoretical calculations were made and interpreted to obtain chemical, nonlinear optical properties and antibacterial activity parameters of 14 registered heterocyclic 4, 5-dihydro-1H-1, 2, 4-triazole-5-one derivatives in the literature. For this purpose, first of all, 14 compounds registered in the literature and two main structures were optimized to find the minimum energy and the most stable structure by using the “B3LYP/6-311++G (d, p)” methods. HOMO–LUMO energies calculated from these optimized structures, energy differences and chemical parameters derived from HOMO–LUMO energies (I; Ionization potential, A; electron affinity, ΔE; Energy Gap, χ; electronegative σ; molecular softness, ω; Electrophilic Index, ε; Nucleophilic Index, μ; Chemical Potential) values were determined. In addition to chemical parameters, polar calculations were made for nonlinear optical properties, and it was evaluated whether the compounds could be optical materials. Finally, the antimicrobial properties of the molecules were calculated theoretically and compared with the experimental results by calculating the volume.

Experimental and Computational Investigation on the Interaction of Anticancer Drug Gemcitabine with Human Plasma Protein: Effect of Copresence of Ibuprofen on the Binding

The interaction of common anticancer drug gemcitabine with human serum albumin (HSA) has been studied in detail. The effect of an omnipresent nonsteroidal anti-inflammatory drug ibuprofen was also seen on the binding of HSA and gemcitabine. A slight hyperchromic shift in the difference UV-visible absorption spectra of HSA on the addition of gemcitabine gave a primary idea of the possible complex formation between them. The inner filter effect, which happens due to the significant absorbance of the ligand at the excitation and/or emission wavelengths, played an important role in the observed fluorescence quenching of HSA by gemcitabine that can be understood by comparing the observed and corrected fluorescence intensities obtained at λex = 280 nm and 295 nm. Gemcitabine showed weak interaction with HSA, which took place via a dynamic quenching mechanism with 1:1 cooperative binding between them. Secondary structural analysis, based on circular dichroism (CD) spectroscopy, showed that low concentrations of gemcitabine did not affect the native structure of protein; however, higher concentrations affected it slightly with partial unfolding. For understanding the binding site of gemcitabine within HSA, both experimental (using site markers, warfarin and ibuprofen) as well as computational methods were employed, which revealed that the gemcitabine binding site is located between the interface of subdomain IIA and IIB within the close proximity of the warfarin site (drug site 1). The effect of ibuprofen on the binding was further elaborated because of the possibility of its coexistence with gemcitabine in the prescription given to the cancer patients, and it was noticed that, ibuprofen, even present in high amounts, did not affect the binding efficacy of gemcitabine with HSA. DFT analyses of various conformers of gemcitabine obtained from its docking with various structures of HSA (free and bounded with site markers), show that the stability of the gemcitabine molecule increased slightly after binding with ibuprofen-complexed HSA. Both experimental as well as computational results were in good agreement with each other.

Ozone oxidation of 2,4,6-TCP in the presence of halide ions: Kinetics, degradation pathways and toxicity evaluation

2,4,6-Trichlorophenol (2,4,6-TCP) is extensively consumed in industrial production and may cause environmental damages. The effect of halide ions on the decomposition of 2,4,6-TCP has often been overlooked. In this study, the bromide ion was found to have a stronger negative impact on 2,4,6-TCP degradation than chloride ion in the O₃ system, and led to the formation of adsorbable organic halogens (AOX). Kinetic modeling demonstrated that the concentration of various radicals was largely depended on the solution pH, and stronger basicity not only contributed to the mineralization of 2,4,6-TCP, but also inhibited the formation of halogenated by-products. Combining the intermediate identification and quantum chemical calculation, the degradation pathways of 2,4,6-TCP during ozone oxidation process were proposed. The toxicity test and ECOSAR simulation demonstrated that the acute toxicity of some 2,4,6-TCP degradation intermediates was relatively higher than their parent compound. With high concentrations of halide ions, the ozone-treated solution showed greater toxicity than the originator 2,4,6-TCP solution. These results illustrate that the ozone treatment of the halide-containing wastewater may cause potential ecological hazards and its application needs to be more cautious.

Evaluating anti-coronavirus activity of some phosphoramides and their influencing inhibitory factors using molecular docking, DFT, QSAR, and NCI-RDG studies

The recent prevalence of coronavirus disease in 2019 (COVID-19) has triggered widespread global health concerns.Antiviral drugs based on phosphoramides have significant inhibitory activity against the main protease (M^pro) of the virus and prevent transcription and viral replication. Hence, in order to design and introduce a group of inhibitors affecting the coronavirus, 35 phosphoramide compounds based on phospho-guanine and phospho-pyrazine derivatives were selected for molecular docking study. The results showed that most phosphoguanides containing the amino benzimidazole have a high interaction tendency with COVID-19. Among them, compound 19 was identified as the strongest inhibitor with the -9.570 kcal/mol binding energy whereas, the binding energy of Remdesivir is -6.75 kcal/mol. The quantitative structure-activity relationship (QSAR) results demonstrated that the number of aromatic rings, amide's nitrogens and their ability in π-staking, and hydrogen interactions with M^pro active sites are major factors contributing to the inhibitory activity of these compounds.Also, the NCI-RDG and DFT results were in good accordance with those of QSAR and molecular docking. The findings of this investigation can be underlying the synthesis of effective and efficient drugs against COVID-19.

Corrosion mitigation in desalination plants by ammonium-based ionic liquid

CuNi (90:10) alloy is widely used in desalination plants. CuNi alloy corrosion in sulfide-containing seawater is the fundamental problem in the desalination industry. Here we have confronted this difficulty by using ammonium-based ionic liquid (Diethyl (2-methoxyethyl)-methyl ammonium Bis(fluorosulfonyl)imide) [DEMEMA][FSI]. The results revealed that the [DEMEMA][FSI] can suppress Cu–Ni alloy corrosion in a solution of (3.5% NaCl + 10 ppm sulphide) with an efficiency of 98.4% at 120 ppm. This has been estimated by electrochemistry and gravimetry. Furthermore, [DEMEMA][FSI] inhibits the growth of sulfate-reducing bacteria SRB in saline water. Surface morphology testing confirmed [DEMEMA][FSI] adsorption on Cu–Ni surface alloys. In addition, quantum calculations have been used to theoretically predict inhibition efficiency [DEMEMA][FSI].

Experimental and computational investigation on the binding of anticancer drug gemcitabine with bovine serum albumin

This study reports the experimental and computational investigation on the binding of a common anticancer drug, gemcitabine, with the model plasma protein, bovine serum albumin (BSA). Several experimental and computational methods, such as intrinsic and synchronous fluorescence, UV-visible, and circular dichroism spectroscopies, consensus molecular docking and molecular dynamics simulation have been employed to elucidate the binding mechanism. Gemcitabine altered the UV-visible spectrum of BSA, which is a clear indication of the complex formation between them. The visual inspection of observed fluorescence quenching results at λ_ex = 280 nm and 295 nm has shown the substantial involvement of tyrosine residue, even larger than tryptophan. However, after the correction of inner filter effect of the observed data, it became clear that tyrosine has a negligible role in quenching. A 20-fold decrease in quenching constant was found in the corrected data, as compared to the observed data at λ_ex = 280 nm. There was a 1:1 weak binding between BSA and gemcitabine accompanied by dynamic quenching. The secondary structure of BSA remained almost intact in the presence of gemcitabine. The primary binding site of gemcitabine inside BSA was the drug binding site 2 or DS II, which is located in the subdomain 3 A. MD Simulation results suggested that gemcitabine doesn't affect or deviate the structure of BSA upon interaction throughout 100 ns time period. The dominating intermolecular forces were hydrophobic forces and hydrogen bonding. A small change in the frontier molecular orbitals of gemcitabine was also observed after its binding with BSA.Communicated by Ramaswamy H. Sarma.

Anti-obesity, antioxidant and in silico evaluation of Justicia carnea bioactive compounds as potential inhibitors of an enzyme linked with obesity: Insights from kinetics, semi-empirical quantum mechanics and molecular docking analysis

Obesity is a global health problem characterized by excessive fat deposition in adipose tissues and can be managed by targeting pancreatic lipase (PL) activity. In the present study, we investigated the in vitro antioxidant and anti-obesity potentials of methanolic leaf extract of Justicia carnea(MEJC) using lipase inhibition kinetics model. In silico evaluations of MEJC bioactive compounds as potential drug-like agents and inhibitors of PL were also investigated using SwissADME prediction tool, semi-empirical quantum mechanics(SQM), molecular electrostatic potential(MEP) and molecular docking analysis. Gas chromatography-mass spectrometry(GC-MS) revealed presence of campesterol, stigmasterol, beta-amyrin etc. MEJC scavenged reactive species and inhibited PL activity via a mixed inhibition pattern (K_i = 107.69 μg/mL; K_ii = 398.00 μg/mL) with IC₅₀ > orlistat's IC₅₀. Molecular docking of GC-MS identified compounds with porcine PL showed compounds 8,10,12 and 14 having high PL-binding affinity and similar binding pose with orlistat. Hydrophobic interactions and van der Waals forces were predominantly involved in the ligands' interactions with some key catalytic site amino acid residues (Ser-153,His-264). Compounds 10,12,13 and 14 indicated high drug-likeness, bioavailability, electronegativity, E_LUMO-E_HOMO energy gaps and MEP. Our findings show that MEJC is a rich natural source of antioxidant and anti-obesity agents which could be optimized for development of new anti-obesity drugs.

Exploring the molecular structure, vibrational spectroscopic, quantum chemical calculation and molecular docking studies of curcumin: A potential PI3K/AKT uptake inhibitor

The IUPAC name of curcumin is (1E, 6E)-1,7-Bis(4-hydroxy-3methoxyphenyl) hepta-1,6-e-3,5-dione (7B3M5D) and is characterized by spectroscopic profiling with FT-IR and FT-Raman spectra obtained both experimentally and theoretically. PED analysis was done for the confirmation of minimum energy obtained in the title compound. Optimized geometrical parameters are compared with experimental values obtained for 7B3M5D by utilizing B3LYP functional employing 6–311++G (d,p) level of theory. The HOMO-LUMO, MEP, and Fukui function analysis has been used to elucidate the information regarding charge transfer within the molecule. The stabilization energy and charge delocalization of the 7B3M5D were performed by NBO analysis. This article assesses that the title compound act as a potential inhibitor of the PI3K/AKT inhibitor through in silico studies, like molecular docking, molecular dynamics (MD), ADMET prediction and also this molecule obeys Lipinski's rule of five. 7B3M5D was docked effectively in the active site of PI3K/AKT inhibitor.

Crystallographic investigation, Hirshfeld surface analysis, NLO characterization and experimental spectral (UV and NMR) studies with DFT probe on(R)-9-(2-hydroxy propyl)adenine

In this study, (R)-9-(2-hydroxy propyl)adenine (HPA) is the molecule of interest for investigation. The XRD from single crystal of HPA has been used to extract its structural features. Since HPA crystallised in a non-centro symmetric space group P212121, its NLO property was studied and it was found to exhibit very good SHG activity. To explore the intermolecular interactions the generated Hirshfeld surface has been investigated along with 2D-fingerprint plots. The experimental electronic and NMR spectra taken in the UV-visible and radio frequency regions respectively for HPA have been corroborated in correlation with theoretical predictions at Density Function Theory using 6-311++g (d, p) basis set. The experimental XRD geometrical parameters, chemical shifts of 13C and 1H and λmax values of HPA fit satisfactorily with the corresponding theoretically obtained numerical values as well as the stimulated spectrograms with the experimental ones. Further to explore the electronic structure, the MESP surface has been generated and investigated. The thermodynamic, kinetic and chemical reactivity features have been explored by means of frontier molecular orbitals of HPA.