Antiviral potential of natural compounds against influenza virus hemagglutinin

Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared. The molecular mechanics Poission-Boltzmann surface area (MM-PBSA) method is used to compare the binding free energy, its different energy components and per residue binding contribution. The H1 subtype shows higher binding preference for all the curcumin derivatives than H2 and H3. The binding capability of protein subtypes with curcumin derivatives and the binding affinity of curcumin compounds are in the order H1 > H2 > H3 and CI > CII > CIII respectively. The two -O-CH3- groups present in the CI compound help to have strong binding with HA protein than CII and CIII. The van der Waals interaction energy plays a significant role for binding in all the complexes. The hydrogen bonding interactions were monitored throughout the MD simulation. The conserved region (153–155) and the helix region (193–194) of H1, H2, H3 protein subtypes are found to possess higher binding susceptibility for binding of the curcumin derivatives.     

The synthesis of azo compounds from nitro compounds using lead and triethylammonium formate

Aromatic nitro compounds were reduced to the corresponding symmetrically substituted azo compounds using lead as catalyst and triethylammonium formate as hydrogen donor. Various azo compounds containing additional reducible substituents including halogens, nitrile, acid, phenol, ester, methoxy functions, etc, have been synthesized in a single step by the use of this reagent. The conversion is reasonably fast, clean, high yielding and occurs at room temperature in methanol.     

Effects of inorganic and organic lead compounds on chromosomal length in human lymphocytes

In vitro exposure of human lymphocyte cultures to spindle inhibitors reduce the average chromosome length^1,2. In this report chromosome length measurements were used for indirect but quantitative evaluation of the effects of inorganic and organic lead compounds on spindle function. The data indicate that organic compounds are much more powerful spindle inhibitors than inorganic lead compounds, almost as potent as colchicine. Occupational exposure to organic lead compounds may result in partial spindle inhibition, leading to a high probability of nondisjunction.     

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking,ADMET properties and molecular dynamics simulation study

Phytochemicals present in medicinal plants have a variety of biological activities that help to combat against diseases. As part of efforts to study the binding performance of different phytochemicals derived from different plants like Zingiber officinale, Citrus limon, Syzygiumaromaticum, Ocimum tenuiflorum and Curcumin. We have screened 424 molecules. The binding affinity as well as physicochemical properties of the thebaine, acacetin, indomethacin, crinamineacetate, (S)-1-Piperideine-6-carboxylate, levamisole, melatonin, nicotinicacid, curcumin, methotrimeprazine, omeprazole, and methaqualone phytocompounds were analyzed through computational study. From the molecular docking study we found that, LEU50, ASN72, PRO96, TYR154, GLY170, ALA193, ARG222, and MET274 residues of main protease play a crucial role in binding with ligands. The present study revealed a noticeable interaction of GLY446, SER477, GLY482, THR500 and LEU518 residues with mutant of spike receptor binding domain SARS-CoV-2 protein were observed. Finally, 100 ns molecular dynamics simulation were used to study their dynamic properties as well as conformational flexibility. Free energy landscape analysis was performed of the 6LU7- acacetin and 6Y2E-acacetin systems and spike RBD-acacetin system. From molecular docking study and molecular dynamics study revealed that, the compound acacetin shows promising inhibitor towards both main protease as well as mutant spike RBD of SARS-CoV-2 protein.     

Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study

Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis. The 3D structures of PPO1 and PPO2 were built through homology modeling, while the 3D crystal structures of PPO3 and PPO4 were retrieved from PDB. Pharmacophore modeling was performed using LigandScout 3.1 software and top five models were selected to screen the libraries (2601 of Aurora and 727, 842 of ZINC). Top 10 hit compounds (C1-10) were short-listed having strong binding affinities for PPO1-4. Drug and synthetic accessibility (SA) scores along with absorption, distribution, metabolism, excretion and toxicity (ADMET) assessment were employed to scrutinize the best lead hit. C4 (name) hit showed the best predicted SA score (5.75), ADMET properties and drug-likeness behavior among the short-listed compounds. Furthermore, docking simulations were performed to check the binding affinity of C1-C10 compounds against target proteins (PPOs). The binding affinity values of complex between C4 and PPOs were higher than those of other complexes (−11.70, −12.1, −9.90 and −11.20 kcal/mol with PPO1, PPO2, PPO3, or PPO4, respectively). From comparative docking energy and binding analyses, PPO2 may be considered as better target for melanogenesis than others. The potential binding modes of C4, C8 and C10 against PPO2 were explored using molecular dynamics simulations. The root mean square deviation and fluctuation (RMSD/RMSF) graphs results depict the significance of C4 over the other compounds. Overall, bioactivity and ligand efficiency profiles suggested that the proposed hit may be more effective inhibitors for melanogenesis.     

Maltase-glucoamylase inhibition potency and cytotoxicity of pyrimidine-fused compounds: An in silico and in vitro approach

The prevalence of diabetes mellitus has been incremented in the current century and the need for novel therapeutic compounds to treat this disease has been significantly increased. One of the most promising approaches is to inhibit intestinal alpha glucosidases. Based on our previous studies, four pyrimidine-fused heterocycles (PFH) were selected as they revealed satisfactory inhibitory action against mammalian α-glucosidase. The interaction of these compounds with both active domains of human maltase-glucoamylase (MGAM) and their effect on human Caco-2 cell line were investigated. The docking assessments suggested that binding properties of these ligands were almost similar to that of acarbose by establishing hydrogen bonds especially with Tyr1251 and Arg526 in both C-terminal and N-terminal MGAM, respectively. Also, these compounds indicated a stronger affinity for C-terminal of MGAM. L2 and L4 made tightly complexes with both terminals of MGAM which in turn revealed the importance of introducing pyrimidine scaffold and its hinge compartment. The results of molecular dynamics simulation analyses confirmed the docking data and showed deep penetration of L2 and L4 into the active site of MGAM. Based on cell cytotoxicity assessments, no significant cell death induction was observed. Hence, these functional MGAM inhibitors might be considered as new potential therapeutic compounds in treatment of diabetes and its complications.     

In-silico investigation of phenolic compounds from leaves of Phillyrea angustifolia L. as a potential inhibitor against the SARS-CoV-2 main protease (Mpro PDB ID:5R83) using a virtual screening method

There is currently a global COVID-19 pandemic caused by the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and its variants. This highly contagious viral disease continues to pose a major health threat global. The discovery of vaccinations is not enough to prevent their spread and dire consequences. To take advantage of the current drugs and isolated compounds, and immediately qualifying approach is required. The aim of our research is evaluation the potency for natural antiviral compounds against the SARS CoV-2 M^pro. Molecular docking of four phenolic compounds from Phillyrea angustifolia leaves with SARS-CoV-2 M^pro has been conducted. Similarly, the stability of selected ligand–protein interactions has been determined using MD simulations. Moreover, the quantitative structure–activity relationship (QSAR), MMGBSA binding energies, pharmacokinetics, and drug-likeness predictions for selected phenolic have been reported. The selected phenolic compounds (Luteolin-7-O-glucoside, Apigenin-7-O-glucoside, Demethyl-oleuropein, and Oleuropein aglycone) revealed strong binding contacts in the two active pockets of a target protein of SARS-CoV-2 M^pro with the docking scores and highest binding energies with a binding energy of ?8.2 kcal/mol; ?7.8 kcal/mol; ?7.2 kcal/mol and ?7.0 kcal/mol respectively. Both Demethyloleoeuropein and Oleuropein aglycone can interact with residues His41 and Cys145 (catalytic dyad) and other amino acids of the binding pocket of M^pro. According to QSAR, studies on pharmacokinetics and drug-like properties suggested that oleuropein aglycone could be the best inhibitor of SARS-CoV-2 for new drug design and development. Further in vivo, in vitro, and clinical studies are highly needed to examine the potential of these phenolic compounds in the fight against COVID-19.     

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future.     

Properties of molecular switch triad compounds for photoinduced intramolecular energy transfer

This paper reports the synthesis and transient absorption decay kinetics of several triad compounds, in which a sulfur aryl section is used as the spacer for intramolecular energy transfer (IET). After flash photolysis the producing sulfur radicals will provide an ‘energy trap’ to stop the IET process, after stopping flash photolysis the sulfur radicals reversibly recombine and the IET process recovers, and then a rapid photoinduced IET switchable function is realized.     

Interpolation of relative retentions as a tool for identification of perhalogenated compounds

Summary Separation of perhalogenated compounds resulting from thermolysis, photolysis or radiolysis of mixtures of halogens in carbon tetrachloride was carried out by programmed temperature gas chromatography. Plots of relative retentions (to CBr₄) vs the number of bromine atoms present for known compounds of the general formula C_xBr_yCl_z (x=1 and 2; y+z=4 or 6) gave three linear correlations (all with r>0.99). These correlations permitted projections of the identities of reaction products for which no standards were available. These projections were later confirmed by CG-MS. *** DIRECT SUPPORT *** A0732166 00010     

A green procedure for the protection of carbonyl compounds catalyzed by iodine in ionic liquid

Aldehydes and ketones are protected with ethylene glycol in the presence of a catalytic amount of iodine in PEG ionic liquid (IL 400) under mild conditions to afford the corresponding ketals in good yields. The recovery of iodine is facilitated by the ionic liquid. The recovered catalyst was reused six times with consistent activity.     

Construction of ionic liquid-Pd/C based bifunction catalysts for the synthesis of UV-P

Adding light stabilizers to polymeric materials can inhibit or delay the light aging effect and improve the light resistance of materials. 2-(2′-Hydroxy-5′-methylphenyl) benzotriazole (UV-P), as a typical benzotriazole ultraviolet absorber, is widely used in various polymer synthetic materials and products owning to its outstanding oil resistance, color change resistance and low volatility. Currently, it is of great theoretical and practical significance to develop an environmentally friendly method to produce UV-P. Here, we introduce ionic liquids, tetra-butyl ammonium hydroxide, into the palladium-based catalyst, design a “transfer hydrogenation site - alkaline site” duel active center system, and investigate the physical and chemical properties and possible mechanism of this bifunction catalyst system. Such heterogeneous catalytic transfer hydrogenation method can remain 100% conversion and 93.86% selectivity. This bifunction catalyst also shows an outstanding stability when it was used for ten times, proving a green and efficient transfer hydrogenation method for the synthesis of UV-P.     

Atomic-scale investigation of the interaction between coniferyl alcohol and laccase for lignin degradation using molecular dynamics simulations and spectroscopy

The interaction between coniferyl alcohol (CA) and laccase (LAC) was investigated using molecular dynamics (MD) simulations and spectral experiments. The mode of interaction between CA and LAC was established by MD simulations. The micro-environmental changes, stability and rigidity of the LAC-CA system were assessed by relevant parameters. These parameters include root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg). The calculated binding free energy (ΔG_binding=??19.99?kcal·mol.^?1), the van der waals (VDW) contribution (ΔG_vdw=?23.99?kcal·mol^?1) and the electrostatic energy (ΔG_ele=?23.09?kcal·mol^?1) of LAC-CA system demonstrated that the interaction of LAC-CA was a spontaneous process and the main interaction forces were van der Waal's and electrostatic forces. The values of ΔG_vdw and ΔG_ele were negative, which demonstrated that VDW interactions and electrostatic interactions were favorable for the binding of CA and LAC. The binding constants, thermodynamic parameters, molecular force types and binding distances confirmed the interaction between CA and LAC and further verified the rationality of the theoretical model by spectral experiments. The MD simulations and experimental approaches provide clues for the discovery of new mediators and useful references for the mechanism of microbial degradation of lignin and industrialization of lignocellulose.     

Structure and properties of heterocomplex compounds based on lead(II) hexafluoroacetylacetonate and copper(II) β-diketonates

Single crystal X-ray diffraction study has been performed for heterometallic complexes based on lead(II) hexafluoroacetylacetonate and copper(II) β-diketonates. Crystal data for Cu(aa)₂·Pb(hfa)₂: a = 8.741(2) Å, b = 12.124(2) Å, c = 13.741(3) Å, α = 89.70(3)°, β = 89.50(3)°, γ = 75.06(3)°, space group P-1, Z = 2, d _calc = 2.084 g/cm³; for Cu(hfa)₂ Pb(hfa)₂: a = 9.334(2) Å, b = 14.584(3) Å, c = 23.102(5) Å, β = 96.82(3)°, space group P2₁/c, Z = 4, d _calc = 2.338 g/cm³. It is demonstrated that the principal structural motif for these compounds is a chain coordination polymer, which consists of alternating molecules of the complexes. The results of a thermogravimetric study for the compounds are reported.     

In silico and in vitro identification of candidate SIRT1 activators from Indonesian medicinal plants compounds database

Sirtuin 1 (SIRT1) is a class III family of protein histone deacetylases involved in NAD⁺-dependent deacetylation reactions. It has been suggested that SIRT1 activators may have a protective role against type 2 diabetes, the aging process, and inflammation. This study aimed to explore and identify medicinal plant compounds from Indonesian Herbal Database (HerbalDB) that might potentially become a candidate for SIRT1 activators through a combination of in silico and in vitro methods. Two pharmacophore models were developed using co-crystalized ligands that allosterically bind with SIRT1 similar to the putative ligands used by SIRT1 activators. Then, these were used for the virtual screening of HerbalDB. The identified compounds were subjected to molecular docking and 50 ns molecular dynamics simulation. Molecular dynamics simulation was analyzed using MM-GB(PB)SA methods. The compounds identified by these methods were tested in an in vitro study using a SIRT-Glo™ luminescence assay. Virtual screening using structure-based pharmacophores predicted that mulberrin as the best candidate SIRT1 activator. Virtual screening using ligand-based pharmacophores predicted that gartanin, quinidine, and quinine to be the best candidates as SIRT1 activators. The molecular docking studies showed the important residues involved were Ile223 and Ile227 at the allosteric region. The MM-GB(PB)SA calculations confirmed that mulberrin, gartanin, quinidine, quinine showed activity at allosteric region and their EC₅₀ in vitro values are 2.10; 1.79; 1.71; 1.14 μM, respectively. Based on in silico and in vitro study results, mulberin, gartanin, quinidine, and quinine had good activity as SIRT1 activators.     

Correlation of thermodynamic modeling and molecular simulations for liquid-liquid equilibrium of ternary polymer mixtures based on a phenomenological scaling method

In our previous study [S.Y. Oh, Y.C. Bae, J. Phys. Chem. B 114 (2010) 8948-8953], we presented a new method to predict liquid-liquid equilibria in ternary simple liquid mixtures by using a combination of a thermodynamic model and molecular simulations. As a continuation of that effort, we extend our previously developed method to ternary polymer systems. In the simulations, we used the dummy atoms to calculate the pair interaction energy values between the polymer segments and the solvent molecules. Furthermore, a thermodynamic model scaling concept is introduced to consider the chain length dependence of the energy parameters. This method was applied to ternary mixtures incorporating low to high molecular weight polymers. The method presented here well described the experimental observations using one or no adjustable parameters.     

Live retention database for identification of compounds in capillary gas chromatographic analysis --Principle and structure

A live retention database for compound identification in isothermal and any step temperature programmed capillary gas chromatography has been developed. The database utilizes the Kovats retention indices of compounds on a given stationary phase and the retention time of n-alkanes measured at isothermal conditions on the column to be used, together with the programming parameters. Identification is performed by search operation that compares the calculated results with the retention values of unknown peaks. Cross-reference of the search results of different operating conditions is performed automatically by the database in order to increase the reliability of the identification. The error of the database conversion is ≤± 0.5 index unit, or ≤± 1% on retention time. This paper describes the principle and the structure of the database in detail. The experimental results for different calsses of compounds tested at divers operating conditions will be presented in Part Ⅱ.     

Identification of critical chemical features for Aurora kinase-B inhibitors using Hip-Hop, virtual screening and molecular docking

This study was performed to find the selective chemical features for Aurora kinase-B inhibitors using the potent methods like Hip-Hop, virtual screening, homology modeling, molecular dynamics and docking. The best hypothesis, Hypo1 was validated toward a wide range of test set containing the selective inhibitors of Aurora kinase-B. Homology modeling and molecular dynamics studies were carried out to perform the molecular docking studies. The best hypothesis Hypo1 was used as a 3D query to screen the chemical databases. The screened molecules from the databases were sorted based on ADME and drug like properties. The selective hit compounds were docked and the hydrogen bond interactions with the critical amino acids present in Aurora kinase-B were compared with the chemical features present in the Hypo1. Finally, we suggest that the chemical features present in the Hypo1 are vital for a molecule to inhibit the Aurora kinase-B activity.