Negative Binding Energy Values Research Articles

Designing plausible catalysts for synthesis of zingerone from vanillin and acetone via aldol condensation reaction on O-terminated M3C2-MXenes

Herein, high-performance O-terminated M3C2 MXene catalysts were screened for the synthesis of zingerone using vanillin and acetone. The electrochemical and electronic properties of O-terminated ordered MXenes in the form of M3C2O2(H) [M = Ti, V, and Cr (3d); Zr, Nb, and Mo (4d); and Hf, Ta, and W (5d)] were investigated using first principle density functional theory (DFT) calculations. These calculations revealed 37 stable candidates based on their negative binding energy values of ΔG*H and three O-terminated M3C2 MXene candidates with superior zingerone synthesis activity than pure precious metal (platinum), a UL > −0.4 V can guarantee high activity and low energy consumption during zingerone synthesis. Ti3C2O (FCC)), Hf3C2O2 (HCPFCC), and Nb3C2O2 (HCPHCP) exhibited higher catalytic activity than other candidates, and their performances were competitive for zingerone synthesis, with low limiting potentials of −0.37, −0.27, and −0.35 V, respectively. Zingerone synthesis via the protolysis reaction between vanillin and acetone includes two paths, i.e., induced protolysis and direct protolysis via the aldol condensation reaction. Multiple descriptors were used to evaluate and screen promising candidates for the synthesis of zingerone. For example, ΔG(*vanillin*acetone), and Bader charge, and d-band center analyses revealed the origin of zingerone synthesis activity based on binding energy and electronic structure. Importantly, binding energy and electronic structure have a strong intrinsic linear scaling relationship that can be used to screen for the optimal catalyst by controlling the scaling relationship between the intermediate binding energy and electronic properties. Indicating a scaling relationship and volcano plot were established based on ΔG(*vanillin+*acetone) and ΔG[*zingiberone] depending on Limiting potential (UL). Finally, we proposed a method for directly inducing protolysis during the aldol condensation reaction, which may be widely applicable to different biomass-derived carbonyl compounds, yielding chemicals and medicinal compounds through biomass valorization.

In silico analysis: Fulleropyrrolidine derivatives against HIV-PR mutants and SARS-CoV-2 Mpro

Abstract Approximately 37.9 million people living with HIV (PLWH) are at risk of severe consequences from COVID-19. Urgent development of tailored treatments for PLWH, who have historically been excluded from vaccine trials, is crucial. The present study introduces some modified fulleropyrrolidine derivatives with chalcogen atoms (O, S, or Se) and hydroxymethylcarbonyl (HMC) groups to target 11 single and double HIV-1 protease (HIV-PR) mutations and the main protease of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 Mpro). The inhibitory activities of these derivatives are computationally examined through molecular docking, molecular dynamic simulations for 200 ns, and Lipinski’s rule of five (RO5). Fourier-transform infrared spectroscopy spectra and thermodynamic properties are calculated and analyzed using Density Functional Theory B88-PW91 method. The results indicate that the suggested O-compounds obey three parameters of the RO5 and HMC forms hydrogen bonds with studied viral proteases. Compounds with O and S additives display a high binding affinity with negative binding energy values for HIV-PR mutations (A71V-I84V, V77I-I84V, and I84V-L90M) and SARS-CoV-2 Mpro. The compounds with S and Se additives shift to lower frequencies of the major vibrational bands. Specifically, compound 1, with two oxygen additives, emerges as the most effective in inhibiting both HIV-PR mutations and SARS-CoV-2 Mpro.

Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis.

This study investigated the potential of selected compounds as inhibitors of SARS-CoV-2 Mpro through pharmacokinetic and toxicological analyses, molecular docking, and molecular dynamics simulations. In silico molecular docking simulations revealed promising ligands with favorable binding affinities for Mpro, ranging from -6.2 to -9.5 kcal/mol. Moreover, molecular dynamics simulations demonstrated the stability of protein-ligand complexes over 200 ns, maintaining protein secondary structures. MM-PBSA analysis revealed favorable interactions between ligands and Mpro, with negative binding energy values. Hydrogen bond formation capacity during molecular dynamics was confirmed, indicating consistent interactions with Mpro catalytic residues. Based on these findings, selected ligands show promise for future studies in developing COVID-19 treatments.

Exploring the twin potential of nanostructured TiO2:SeO2 as a promising visible light photocatalyst and selective fluorosensing platform

The present work describes the development of TiO2/SeO2 nanostructure as a potential candidate for visible light photocatalysis as well as selective fluorophore for the sensing of picric acid. The obtained nanostructure consists of uniform globular nanoparticles having approximate size of 170 nm and possess an optical band gap of 2.33 eV with absorption maxima at 473 nm. The photocatalyst was able to achieve 90.34% degradation efficiency for 2, 4-dichlorophenol (2,4-DCP) with rate constant of 0.0046 min−1 in the visible region. Further the nanostructure was able to serve as a selective fluorophore for sensing of Picric acid portraying more than 95% of fluorescence quenching when the concentration of PA is 10–4 M. Theoretical calculations indicate the interaction of organic pollutants with the nanostructure and reveal that both picric acid (− 66.21 kcal/mol) and 2,4-DCP (− 12.31 kcal/mol) possess more negative binding energy values demonstrating a strong interaction of both with the nanostructure, making it suitable for the degradation as well as sensing of organic pollutants. Thus this study explains the potential of prepared catalyst for waste water treatment.

Cyclo[16]carbon through the lens of density functional theory: Role of impurity decoration in hydrogen evolution reaction

The increasing global demand for sustainable energy sources has intensified the search for cost-effective catalysts in the hydrogen evolution reaction (HER). Single-atom catalysts (SACs) supported on suitable substrates have emerged as promising alternatives. In this study, we investigate the utilization of cyclo[16]carbon (C16 nanocluster) as a support for second-row transition metals (TMs) based SACs. The exploration focuses on analyzing the geometry, electronic properties, stability, and catalytic performance of TM@C16 SACs in the context of HER. Notably, highly negative binding energy values, structural modifications, and altered dipole moments collectively affirm the strong binding between the TMs and the C16 nanocluster. The incorporation of TMs onto the C16 nanocluster substantially enhances the conductivity of the latter. Studied SACs primarily showed H2 evolution via Volmer-Heyrovsky mechanisms. Notably, Pd@C16 and Rh@C16 displayed superior catalytic performance, with ΔGHV values of −0.007 eV and 0.05 eV, respectively. The determination of the exchange current via a volcano plot as a function of Gibbs free energy for hydrogen evolution over these designed SACs further validates their efficacy. Our findings establish Pd@C16 and Rh@C16 as highly stable and efficient SACs for the HER, underscoring their potential in advancing sustainable energy technologies.

Spectroscopic and computational study of Favipiravir-Adenine cocrystallization biomolecular complex

The research focuses on the structural investigation of biomolecules and biomolecular complexes using the DFT method, spectroscopic techniques, and determining cocrystal formation. The significant difficulties in making new drug products are low oral bioavailability and poor aqueous solubility. However, the co-crystallization of biomolecules can enhance their solubility without changing their pharmacological properties. The optimized structure of the molecules is obtained using the B3LYP/6–311++G(d,p) basis set within the framework of Density Functional Theory (DFT). Various vibrational techniques such as Fourier Transform Infrared (FTIR), Raman, and Surface-Enhanced Raman Spectroscopy (SERS) are employed to characterize the monomers and their interacting system. Possible vibrational assignments along with Potential energy distribution (PED) analysis are carried out using Vibrational Energy Distribution Analysis (VEDA). Natural Bond Orbital (NBO), Non-Linear Optical (NLO), Non-Covalent Interaction (NCI), and Atoms in Molecule (AIM) study are carried out to understand the interacting mechanism in the Favipiravir-Adenine biomolecular complex. The study shows that there is charge transfer through inter and intramolecular interaction in the complex. The binding energy of protein and Ligand is investigated using the Autodock tool for the molecular docking method and the negative value of binding energy – 4.36 kcal/mol of Favipiravir-Adenine biomolecular complex exclaims good binding affinity with the chosen protein 6LU7. Lipinski's criteria for druglikeness also claim that monomers and synthesized biomolecular complexes have the potential to influence drugs with good oral bioavailability. Cocrystal formation is confirmed by the X-ray diffraction pattern. The Protox II software claims that the toxicity of the drug and synthesized biomolecular complex is class IV.

Quantum mechanical treatment for potential antiphlogistic effects from the leaf extract of Ocimum basilicum citriodorum using gas chromatography-mass spectrometry (GCMS)

Abstract The immune biological response systems and inflammation can be triggered by a number of things such as pathogens, damaged cells and toxic substances. In ethnomedicine, leaves of Lemon basil (Ocimum basilicum citriodorum) have been used for their health benefits. This study examines the anti-inflammatory properties of lemon basil stalks. In a GC/MS study, 24 plant-based bioactive compounds were identified. Comparing the activities in 24 compounds with the largest negative binding energy values helped us determine which compound was most active. It can be seen that only two compounds (Campstool and stigmasterol) with the highest binding energies interact with the 2QVD protein; consequently, the compound with the highest binding energy has superior anti-inflammatory activity. In quantum mechanics, electron energy difference between lowest-unoccupied molecular orbitals (LUMO) and highest-occupied molecular orbitals (HOMO) is described by the quantum-mechanical method, electronegativity (χ), electron affinity (A), global hardness (η), global softness (σ) and ionization potential (I) estimated from the optimized structure. Higher energy molecules are more reactive than other substances reported in this study.

Exploring glutathione transferase and Cathepsin L-like proteinase for designing of epitopes-based vaccine against Fasciola hepatica by immunoinformatics and biophysics studies.

Fasciolosis is a zoonotic infection and is considered a developing deserted tropical illness threatening ruminant productivity and causing financial losses. Herein, we applied immunoinformatics and biophysics studies to develop an epitopes vaccine against Fasciola hepatica using glutathione transferase and Cathepsin L-like proteinase as possible vaccine candidates. Using the selected proteins, B- and T-cell epitopes were predicted. After epitopes prediction, the epitopes were clarified over immunoinformatics screening, and only five epitopes, EFGRWQQEKCTIDLD, RRNIWEKNVKHIQEH, FKAKYLTEMSRASDI, TDMTFEEFKAKYLTE, and YTAVEGQCR were selected for vaccine construction; selected epitopes were linked with the help of a GPGPG linker and attached with an adjuvant through another linker, EAAAK linker. Cholera toxin B subunit was used as an adjuvant. The ExPASy ProtParam tool server predicted 234 amino acids, 25.86257 kDa molecular weight, 8.54 theoretical pI, 36.86 instability index, and -0.424 grand average of hydropathicity. Molecular docking analysis predicted that the vaccine could activate the immune system against F. hepatica. We calculated negative binding energy values. A biophysics study, likely molecular docking molecular dynamic simulation, further validated the docking results. In molecular dynamic simulation analysis, the top hit docked compounds with the lowest binding energy values were subjected to MD simulation; the simulation analysis showed that the vaccine and immune cell receptors are stable and can activate the immune system. MMGBSA of -146.27 net energy (kcal/mol) was calculated for the vaccine-TLR2 complex, while vaccine-TLR4 of -148.11 net energy (kcal/mol) was estimated. Furthermore, the C-ImmSim bioinformatics tool predicted that the vaccine construct can activate the immune system against F. hepatica, eradicate the infection caused by F. hepatica, and reduce financial losses that need to be spent while protecting against infections of F. hepatica. The computational immune simulation unveils that the vaccine model can activate the immune system against F. hepatica; hence, the experimental scientist can validate the finding accomplished through computational approaches.

ANTIVIRAL SCREENING OF AZADIRACHTA INDICA PHYTOCHEMICALS AS DENGUE NS5 INHIBITOR: A MOLECULAR DOCKING APPROACH

Dengue has been an alarming viral infection in tropical and subtropical regions of the world for the past few decades, resulting in millions of deaths. There is no effective drug to treat this arbovirus-based infection. Dengue virus non-structural protein NS5 contains N terminus methyl transferase domain and C terminus RNA-dependent RNA polymerase domain, which is involved in viral RNA replication and serves as a potential target. The current in-silico study aims to find new potential dengue virus NS5 protein inhibitors. The designed library containing eight compounds from Azadirachta Indica was used to perform molecular docking against active residues of dengue virus NS5 protein. Four compounds (Desacetyl Salanin, Azadirchtin-A, Castalagin, Vilasinin) with high negative binding energy values and zero RMSD values were selected, and their drug-likeness and ADMET analysis was performed. Among the best-docked compounds, Vilasinin (-11kcal/mol) exhibited drug-like properties as it has a molecular weight less than 500 D and has zero violation value. Moreover, it has 5 hydrogen bond donors and 10 hydrogen bond acceptors. It is well soluble in water so that it can be used as a potential inhibitor and drug candidate for the treatment of dengue infection.

Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases.

For the first time, sigma (σ)- and lone-pair (lp)-hole site-based interactions of SF4 and SeF4 molecules in seesaw geometry with NH3 and FH Lewis bases were herein comparatively investigated. The obtained findings from the electrostatic potential analysis outlined the emergence of sundry holes on the molecular entity of the SF4 and SeF4 molecules, dubbed the σ- and lp-holes. The energetic viewpoint announced splendid negative binding energy values for σ-hole site-based interactions succeeded by lp-hole analogues, which were found to be -9.21 and -0.50 kcal/mol, respectively, for SeF4···NH3 complex as a case study. Conspicuously, a proper concurrence between the strength of chalcogen σ-hole site-based interactions and the chalcogen's atomic size was obtained, whereas a reverse pattern was proclaimed for the lp-hole counterparts. Further, a higher preference for the YF4···NH3 complexes with elevated negative binding energy was promulgated over the YF4···FH ones, indicating the eminent role of Lewis basicity. The indications of the quantum theory of atoms in molecules generally asserted the closed-shell nature of all the considered interactions. The observation of symmetry-adapted perturbation theory revealed the substantial contributing role of the electrostatic forces beyond the occurrence of σ-hole site-based interactions. In comparison, the dispersion forces were specified to govern the lp-hole counterparts. Such emerging findings would be a gate for the fruitful forthcoming applications of chalcogen bonding interactions in crystal engineering and biological systems.

In silico Screening of the Potential Anti-SARS-CoV-2 Activities of Peptides from Vipera ammodytes ammodytes Venom by Molecular Docking

The coronavirus disease 2019 (COVID-19) is induced by the SARS-CoV-2 virus, which caused the global pandemic, infecting approximately 608.328.548 confirmed cases and bringing about 6.501.469 deaths worldwide, as WHO stated in September 2022. The disease is more deadly due to the lack of specific drug molecules or a treatment plan. Therefore, the development of potent pharmacological compounds is urgently required to combat COVID-19. Due to their biological actions, snake venoms constitute a source of potentially beneficial medicinal compounds. Vipera ammodytes ammodytes (VA) is a viper species whose venom has been shown to have anti-proliferative, antimetastatic, anti-cancer, and anti-microbial activities. This in silico study was conducted to evaluate the efficacy of selected VA venom proteins (Adamalysin II, Ammodytoxin A, Ammodytin L, L-amino acid oxidase) against molecular targets; Main protease (3CLpro) and Angiotensin-Converting Enzyme 2 (ACE2) by molecular docking study. Molecular docking investigations were performed by using AutoDock Vina software. All compounds displayed negative binding energy values to 3CLpro and ACE2, suggesting that their interactions with the active sites were favourable. L-amino acid oxidase had the highest binding affinity with both 3CLpro and ACE2. This study revealed for the first time that VA venom proteins are functional inhibitors of 3CLpro and ACE2 activities, and the components of VA venom can be considered potential SARS-CoV-2 inhibitors. However, more studies are needed to validate these compounds in vitro and in vivo.

In silico and in vitro assays suggests Congo red dye degradation by a Lentinus sp. laccase enzyme

Laccase is a superfamily of ligninolytic enzymes known to degrade a wide variety of xenobiotics, including synthetic dyes. Congo Red (CR) has a diazo dye function, carcinogenic and mutagenic potential, and is currently applied in clinical analysis. The objective of this work was to produce and characterize the crude extract of Lentinus sp. in semi-solid fermentation (FSS) and perform in vitro and in silico studies to assess the potential of the crude extract to discolor the CR dye. Laccase activity was determined using ABTS as substrate and characterized. The in vitro discoloration was carried out using experimental design 22 at room temperature and monitored at 340 nm for 24h. Molecular docking and molecular dynamics simulations were performed between laccase and CR. The maximum laccase activity production was 29.63 U L−1 with six days of FSS. The optimal temperature and pH were 50 °C and 3.0, respectively. Discoloration of the CR dye was obtained only in tests containing CuSO4. Laccase formed stable complexes with the dye, presenting negative binding energy values ranging from −70.94 to −63.16 kcal mol−1 and the occurrence of seven hydrogen bonds. Molecular dynamics results showed the stability of the system (RMSD ranging from 1.0 to 2.5 Ä) and protein-ligand interaction along simulation. RMSF values pointed residues at the end of chains A (residues 300 to 305, 480 to 500) and B (residues 650 to 655 and 950 to 1000) as the most flexible regions of the laccase. This study highlighted the enzymatic action in the bioremediation of CR in vitro in agreement with the in silico simulations that demonstrate the enzyme potential. Communicated by Ramaswamy H. Sarma

Liquid-assisted mechanochemical synthesis, crystallographic, theoretical and molecular docking study on HIV instasome of novel copper complexes: (µ-acetato)-bis(2,2'-bipyridine)-copper and bromidotetrakis(2-methyl-1H-imidazole)-copper bromide.

In the present work the two new Cu(II) complexes, (µ-acetato)-bis(2,2'-bipyridine)-copper [Cu(bpy)2(CH3CO2)] and bromidotetrakis(2-methyl-1H-imidazole)-copper bromide [Cu(2-methylimid)4Br]Br have been synthesized by liquid assisted mechanochemical method. The [Cu(bpy)2(CH3CO2)] complex (1) and [Cu(2-methylimid)4Br]Br complex (2) characterised by IR and UV-visible spectroscopy and the structure are confirmed by XRD diffraction studies. Complex (1) crystallized in the Monoclinic with the space group of C2/c where a = 24.312(5)Å, b = 8.5892(18)Å, c = 14.559(3)Å, α = 90°, β = 106.177(7)° and γ = 90° and Complex (2) crystallized in the Tetragonal with the space group of P4nc, a = 9.9259(2)Å, b = 9.9259(2)Å, c = 10.9357(2)Å, α = 90°, β = 90° and γ = 90°. The complex (1) has distorted octahedral geometry where the acetate ligand showed bidentate bridging with the central metal ion and complex (2) has slightly deformed square pyramidal geometry. The HOMO-LUMO energy gap value and the low chemical potential showed that the complex (2) is stable and difficult to polarize compare to complex (1). The molecular docking study of complexes with the HIV instasome nucleoprotein showed the binding energy values -7.1 and -5.3kcal/mol for complex (1) and complex (2) respectively. The negative binding energy values showed the complexes have affinity to bind with HIV instasome nucleoproteins. The in-silico pharmacokinetic study of the complex (1) and complex (2) showed non AMES toxicity, non-carcinogens and low honey Bee toxicity but weakly inhibit Human Ether-a-go-go-related gene.

Sensitive determination of benzo(a)pyrene in vegetable oils based on the electrochemiluminescence quenching of ruthenium (II) dipyrido[3,2-a:2′,3′-c]phenazine complex

A sensitive method for the determination of cancerogen benzo(a)pyrene (BaP) was proposed based on the electrochemiluminescence (ECL) property of a ruthenium(II) complex, [Ru(bpy)2dppz]2+ (Ru-dppz). With the π-π interaction between the ligand of dppz and BaP, the metal to ligand charge transfer of Ru-dppz might be disturbed, which inhibits the ECL behavior of Ru-dppz. The orientations of the π-π interaction between Ru-dppz and BaP were calculated via DFT theory. The negative value of binding energy confirmed both of the parallel displaced stacking and T-shape stacking could occur but the more negative binding energy value of parallel displaced stacking confirmed the preferred orientation. The ECL quenching yield was utilized to determine BaP, the linear range and the detection limit of BaP were estimated as 50 nM-15 μM and 2.45 nM, respectively. The recoveries of BaP in several kinds of vegetable oils were in the range of 97%∼108%, indicating the detection of BaP in fresh oils was reliable. However, the recovery of BaP in deep fried colza oil appears some deviation compared with which achieved by GC–MS, indicates the selectivity for the detection of PAHs depends on the ECL quenching of ruthenium complexes via π-π stacking still has the potential to be improved by optimizing the conjungation system of the ligands.

First principle study of benzoquinone based microporous conjugated polymers as cathode materials for high-performance magnesium ion batteries

Rechargeable magnesium-ion batteries (MIBs) can fulfill large-scale energy storage needs due to the abundance of Mg but technical challenges due to complexity of its chemistry results uncertainties about their commercialization. We for the first report benzoquinone-based microporous conjugated polymer (BQMCP) as cathode material for MIBs using density functional theory. It is dynamically and thermodynamically stable with a strong affinity for Mg-ions. The Mg ions strongly attaches to the CO group (redox-active sites) than π-bonds of BQMCP. The binding energy demonstrates that the interaction of the 2 Mg-ion system (BE = −47.32 kcal.mol−1) is stronger than the mono-Mg ion system (BE = −39.57 kcal.mol−1). The attachment of first Mg2+ to the BQMCP facilitate the attachment of another Mg ion. The BQMCP shows higher positive redox potential, which decreases with the increase of Mg atoms with the high storage capacity of twelve Mg ions/ BQMCP unit at redox-active sites without any structure distortion. Mg ions successfully entraps in bulk porous stacked BQMCP layers with higher negative binding energy values. The results demonstrates that the BQMCP is a promising cathode material for magnesium ion batteries in future.

Orofacial antinociceptive effects of perillyl alcohol associated with codeine and its possible modes of action.

This study evaluated the orofacial antinociceptive effect of (S)-(-)-perillyl alcohol (PA) associated with codeine (C) and investigated the possible molecular anchorage mechanisms of PA. Mice (n = 5 per group) were treated with PA alone and associated with codeine and assigned to the following groups: 75.0 mg/kg PA; 75.0 mg/kg PA + C 30 mg/kg; PA 37.5 mg/kg + C 15.0 mg/kg; C 30.0 mg/kg; and control. Nociception was induced by formalin, capsaicin, and glutamate, and was quantified based on the duration (in seconds) of face grooming. The possible mechanisms of action were evaluated by molecular docking study. In the formalin test, PA75/C30 presented an effect in the neurogenic (p < 0.0001) and inflammatory (p < 0.005) phases. Mice treated with PA75 (p < 0.0001) and PA75/C30 (p < 0.0005) showed a reduced nociceptive behavior in the capsaicin test. Glutamate-induced nociception also was blocked by PA75 (p < 0.0005) and C30 (p < 0.0005). The molecular anchorage analysis indicated high negative binding energy values for the evaluated receptors, especially glutamate receptors (AMPA -79.57 Kcal/mol, mGLUR6 -71.25, and NMDA -66.33 Kcal/mol). PA associated with codeine showed orofacial antinociceptive activity, with theoretical evidence of interaction with glutamate receptors.

Atom accurate structure determination of alprazolam/cyclodextrin inclusion complexes by ROESY and computational approaches

A lot of interest has been seen in computational methods that provide reliable atom accurate structures of different molecular systems. In this article, we describe the complexation of alprazolam (ALP) with three cyclodextrins, i.e., α-, β- and γ-CD. ROESY spectra showed that no complex was formed between ALP and α-CD however, ring A of ALP formed ICs with β- and γ-CD. Therefore, structures of ALP/β-CD and ALP/γ-CD were obtained by a combination of NMR (2D-ROESY) and computational methods by a quantitative ROESY approach. Here we determined the structures of CD ICs by a method recently used in our laboratory and then the structures were obtained independently by DFT (B3LYP functional and def2-TZVP basis set). The structures obtained by both methods were compared with each other. Results demonstrated that our method provides reasonable structures comparable to DFT, and can be used to obtain highly atom accurate structures of CD inclusion complexes. Quantitative ROESY analysis of MM and MD structures consume less time and are cheap as compared to DFT, which is highly CPU demanding and time taking. Negative values of binding energy showed that the process of inclusion was spontaneous and complexes formed were stable. The large negative value of binding energy for ALP/β-CD as compared to ALP/γ-CD showed a higher binding affinity of ALP towards β-CD. FMO studies also revealed the higher HOMO-LOUMO gap for inclusion complexes as compared to pure ALP. Intermolecular H-bonds formed in both the complexes are also one of the forces responsible for inclusion complex formation.

Effects of some phenolic compounds on the inhibition of α-glycosidase enzyme-immobilized on Pluronic®F127 micelles: An in vitro and in silico study

This study aimed to consider the activity of immobilized α-glycosidase, significant enzyme defined in serum glucose adjustment, on Pluronic®F127 micelles and to compare the results with theoretical molecular docking studies. The phenolic molecules were used for the activity studies, which play a crucial role in the inhibition of α-glycosidase by providing conservation against pathogen factors. The immobilization of α-glycosidase on Pluronic®F127 micelles showed higher kinetic activity towards p-nitrophenyl-D-glucopyranoside (pNPG) than the free one. The inhibition profiles from some phenolic molecules were observed impressively with IC50 values between 20.47 and 1118.68 nM and Ki values between 18.51 and 1087.53 nM against immobilized α-glycosidase. In addition, the inhibition effects of the studied phenolic compounds have been tested with calculated negative binding energies from theoretical molecular docking studies. Negative binding energy values were as − 6.1 and − 8.3 kcalmol−1 for p-coumaric acid and tetrakis compounds, respectively.

Computational modeling of inclusion complex between aromatic amine and calixarene analogs using Semiempiric Quantum Method (SQM)

PM3 Semiempiric Quantum calculation has been done in this research by using Gaussian 2009 Rev. D 01 software package to explore the capability of Calixarene and its analogs for aromatic amine extraction. The Calixarene analogs used in this research are Calixpyrrole, Calixpyridine, Thiacalixarene, Heterocalixaromatic, Calixcarbazole and Calixnaphtalene; and the aromatic amine used in this research are Aniline, 4-Chloroaniline, Toluene-2,4-diamine, 2-Naphty lamině, 4,4’-Mety lenbis(2-chloroaniline), 4,4’-Metylendianiline, N-Nitrosodiphenylamine, Benzidine, 2-Aminobiphenyl, 2-Amino-1-methyl-6-phenylimidazo[4,5-b] Pyridine, 3-Trifluoromethylaniline, p-Phenylendiamine, o-Toluidin, 4-Chloro-o-toluidin. The most suitable host molecule of calixarene analogs for extraction of aromatic amine compounds are Calixnaphthalene and Calixpyridine because all of aromatic amine compounds form inclusion complex with them spontaneously shown by negative value of binding energy.

Molecular docking study of inclusion complex between aromatic amine and Calixarene analogs

A molecular docking was performed in this research by using ArgusLab version 4.0.1. It was used to explore the capability of Calixarene analogs for aromatic amine extraction. There are 6 Calixarene analogs used in this research, i.e. Calixpyrrole, Calixpyridine, Thiacalixarene, Heterocalixaromatic, Calixcarbazole and Calixnaphtalene; and the aromatic amine used in this research are Aniline, 4-Chloroaniline, Toluene-2,4-diamine, 2-Naphtylamine, 4,4’-Metylenbis(2-chloroaniline), 4,4’-Metylendianiline, N-Nitrosodiphenylamine, Benzidine, 2-Aminobiphenyl, 2-Amino-1-methyl-6-phenylimidazo [4,5-b] Pyridine, 3-Trifluoromethylaniline, p-Phenylendiamine, o-Toluidin, 4-Chloro-o-toluidin. In this molecular docking simulation, the guest molecule of aromatic amine compounds were treated as ligand and host molecule of calixarene and its analogs were treated as binding site. This molecular docking simulation used AScore scoring function, binding sitebox size for host molecule with grid size of 0.4 Å, GA docking engine with flexible ligand, 50 population sizes, 1000 max generations, 5 elitisms, 0.2 mutation rate, and 0.8 crossover rate. Calixcarbazole and Calixnaphthelene is the best host molecule for aromatic amines extraction because the inclusion complexes formed between them have negative value of binding energy.