QSAR,docking studies of 1,3-thiazinan-3-yl isonicotinamide derivatives for antitubercular activity

The enzyme – enoyl acyl carrier protein reductase (enoyl ACP reductase) is a validated target for antitubercular activity. Inhibition of this enzyme interferes with mycolic acid synthesis which is crucial for Mycobacterium tuberculosis cell growth. In the present work 2D and 3D quantitative structure activity relationship (QSAR) studies were carried out on a series of thiazinan–Isoniazid pharmacophore to design newer analogues. For 2D QSAR, the best statistical model was generated using SA-MLR method (r² = 0.958, q² = 0.922) while 3D QSAR model was derived using the SA KNN method (q² = 0.8498). These studies could guide the topological, electrostatic, steric, hydrophobic substitutions around the nucleus based on which the NCEs were designed. Furthermore, molecular docking was performed to gauze the binding affinity of the designed analogues for enoyl ACP reductase enzyme. Amongst all the designed analogues the binding energies of SKS 01 and SKS 05 were found to be −5.267 kcal/mol and −5.237 kcal/mol respectively which was comparable with the binding energy of the standard Isoniazid (−6.254 kcal/mol).     

Probing the binding of fluoxetine hydrochloride to human serum albumin by multispectroscopic techniques

The interaction between human serum albumin (HSA) and fluoxetine hydrochloride (FLX) have been studied by using different spectroscopic techniques viz., fluorescence, UV–vis absorption, circular dichroism and FTIR under simulated physiological conditions. Fluorescence results revealed the presence of static type of quenching mechanism in the binding of FLX to HSA. The values of binding constant, K of FLX-HSA were evaluated at 289, 300 and 310 K and were found to be 1.90 × 10³, 1.68 × 10³ and 1.45 × 10³ M^?1, respectively. The number of binding sites, n was noticed to be almost equal to unity thereby indicating the presence of a single class of binding site for FLX on HSA. Based on the thermodynamic parameters, ΔH⁰ and ΔS⁰ nature of binding forces operating between HSA and FLX were proposed. Spectral results revealed the conformational changes in protein upon interaction. Displacement studies indicated the site I as the main binding site for FLX on HSA. The effect of common ions on the binding of FLX to HSA was also investigated.     

(Vapor + liquid) equilibrium data for (carbon dioxide + 1,1-difluoroethane) system at temperatures from (258 to 343) K and pressures up to about 8 MPa

Accurate thermo-physical data are of utmost interest for the development of new efficient refrigeration systems. Carbon dioxide (R744) and 1,1-difluoroethane (R152a) are addressed here. Isothermal (vapor + liquid) equilibrium data are reported herein for (R744 + R152a) binary system in the (258–343) K temperature range and in the (0.14 to 7.65) MPa pressure range. A reliable “static-analytic” method taking advantage of two online ROLSI? micro capillary samplers is used for all thermodynamic measurements. The data are correlated using our in-house ThermoSoft thermodynamic model using the Peng–Robinson equation of state, the Mathias–Copeman alpha function, the Wong–Sandler mixing rules, and the NRTL model.     

Thermochemical data for n-alkylmonoamines functionalization into lamellar silicate Al-kanemite

Al-kanemite was synthesized by using inorganic salts as a source for silicon and aluminum in the hydrothermal synthesis of the material. The resulting solid was used as hosts for functionalization of polar n-alkylamine molecules of the general formula H₃C(CH₂)_n?NH₂ (n = 1 to 5) in aqueous solution. The compound was calorimetrically titrated with amine in 1,2-dichloroethane, requiring three independent operations: (i) titration of matrix with amine, (ii) matrix salvation, and (iii) dilution of the amine solution. From those thermal effects the variation in enthalpy was calculated as: (?6.81, ?7.76, ?8.97, ?9.94, and ?11.83) kJ · mol^?1, for n = 1 to 5, respectively. The exothermic enthalpy values reflected a favorable energetic process of amine-host functionalization in 1,2-dichloroethane. The original and modified Al-kanemite samples were characterized by elemental analysis, scanning electron microscopic (SEM), and nuclear magnetic nuclei of silicon-29 and carbon-13. The negative Gibbs free energy results supported the spontaneity of all these functionalization reactions. The positive favorable entropic values, as carbon chain size increased, are in agreement with the free solvent molecules in the solution, as the amines are progressively bonded to the crystalline inorganic matrix at the solid/liquid interface.     

Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 10⁵ · M⁻¹ at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation.     

Isothermal titration calorimetric and spectroscopic studies on (alcohol + salt) induced partially folded state of α-lactalbumin and its binding with 8-anilino-1-naphthalenesulfonic acid

Interaction of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) and isopropanol in the presence of equimolar quantities of guanidine thiocyanate (GndSCN) with bovine α-lactalbumin (α-LA) has been investigated by using a combination of isothermal titration calorimetry, circular dichroism, fluorescence, and ultra-violet spectroscopies at in 20 · 10^?3 mol · dm^?3 phosphate buffer pH 7.0. All the thermal unfolding transitions, in the presence of both the (alcohol + salt) mixtures were found to be reversible as judged by the same values of absorbance observed at different temperatures during cooling after the completion of thermal unfolding. In the presence of the 0.25 mol · dm^?3 (HFIP + GndSCN) equimolar mixture and 0.85 mol · dm^?3 (isopropanol + GndSCN) equimolar mixture, α-lactalbumin was observed to be in the partially folded state with significant loss of native tertiary structure. Intrinsic fluorescence results, acrylamide and potassium iodide quenching, 8-anilino-1-naphthalenesulfonic acid (ANS) binding, and energy transfer results also corroborate the presence of partially folded states of α-lactalbumin. Apart from the generation of the partially folded states, it was also observed that destabilizing action of GndSCN is reduced in the presence of isopropanol compared to that in HFIP. Isothermal titration calorimetry has been used to characterize the energetics of ANS binding to the partially folded states of the protein. ITC results indicate that ANS binds to these partially folded states at pH 7.0 due to the presence of two sequentially binding sites on the protein under the solvent conditions employed. For example, ANS binds to the 0.25 mol · dm^?3 (HFIP + GndSCN) induced partially folded state with affinity constants K₁ = (858 ± 220), K₂ = (1.12 ± 0.25) · 10³; enthalpies of binding ΔH₁ = (4.4 ± 1.0) kJ · mol^?1, ΔH₂ = (2.1 ± 0.2) kJ · mol^?1; and entropies of binding ΔS₁ = 70 J · K^?1 · mol^?1 and ΔS₂ = 65 J · K^?1 · mol^?1, respectively at these two sequential binding sites. In light of the fluorescence results, possible binding sites where ANS can bind to the protein have also been suggested.     

The role of water in the thermodynamics of drug binding to cyclodextrin

The thermodynamic parameters, Δ_BG^∘, Δ_BH^∘, Δ_BS^∘, and Δ_BC_p, of the drugs flurbiprofen (FLP), nabumetone (NAB), and naproxen (NPX) binding to β-cyclodextrin (βCD) and to γ-cyclodextrin (γCD) in 0.10 M sodium phosphate buffer were determined from isothermal titration calorimetry (ITC) measurements over the temperature range from 293.15 K to 313.15 K. The heat capacity changes for the binding reactions ranged from −(362 ± 48) J · mol⁻¹ · K⁻¹ for FLP and −(238 ± 90) J · mol⁻¹ · K⁻¹ for NAB binding in the βCD cavity to 0 for FLP and −(25.1 ± 9.2) J · mol⁻¹ · K⁻¹ for NPX binding in the larger γCD cavity, implying that the structure of water is reorganized in the βCD binding reactions but not reorganized in the γCD binding reactions. Comparison of the fluorescence enhancements of FLP and NAB upon transferring from the aqueous buffer to isopropanol with the maximum fluorescence enhancements observed for their βCD binding reactions indicated that some localized water was retained in the FLP–βCD complex and almost none in the NAB–βCD complex. No fluorescence change occurs with drug binding in the larger γCD cavity, indicating the retention of the bulk water environment in the drug–γCD complex. Since the specific drug binding interactions are essentially the same for βCD and γCD, these differences in the retention of bulk water may account for the enthalpically driven nature of the βCD binding reactions and the entropically driven nature of the γCD binding reactions.     

Marine derived compounds as binders of the White spot syndrome virus VP28 envelope protein: In silico insights from molecular dynamics and binding free energy calculations

White spot syndrome virus (WSSV) remains as one of the most dreadful pathogen of the shrimp aquaculture industry owing to its high virulence. The cumulative mortality reaches up to 100% within in 2–10 days in a shrimp farm. Currently, no chemotherapeutics are available to control WSSV. The viral envelope protein, VP28, located on the surface of the virus particle acts as a vital virulence factor in the initial phases of inherent WSSV infection in shrimp. Hence, inhibition of envelope protein VP28 could be a novel way to deal with infection by inhibiting its interaction in the endocytic pathway. In this direction, a timely attempt was made to recognize a potential drug candidate of marine origin against WSSV using VP28 as a target by employing in silico docking and molecular dynamic simulations. A virtual library of 388 marine bioactive compounds was extracted from reports published in Marine Drugs. The top ranking compounds from docking studies were chosen from the flexible docking based on the binding affinities (ΔGb). In addition, the MD simulation and binding free energy analysis were implemented to validate and capture intermolecular interactions. The results suggested that the two compounds obtained a negative binding free energy with −40.453 kJ/mol and −31.031 kJ/mol for compounds with IDs 30797199 and 144162 respectively. The RMSD curve indicated that 30797199 moves into the hydrophobic core, while the position of 144162 atoms changes abruptly during simulation and is mostly stabilized by water bridges. The shift in RMSD values of VP28 corresponding to ligand RMSD gives an insight into the ligand induced conformational changes in the protein. This study is first of its kind to elucidate the explicit binding of chemical inhibitor to WSSV major structural protein VP28.     

Serum albumin ligand binding volumes using high pressure denaturation

The pressure shift assay (PSA, also termed either PressureFluor or differential pressure fluorimetry) was used to study the thermodynamics of decanoate and dodecanoate lipid binding to human serum albumin (HSA) in the temperature range from 25 °C to 80 °C and the pressure range from 0.1 MPa to 400 MPa. The ligands stabilized HSA against both pressure and temperature denaturation. The P–T phase diagram for HSA bound to saturated fatty acids is shown. Pressure induced HSA denaturation reversibility is demonstrated via either intrinsic tryptophan or extrinsic probe 1,8-anilinonaphthalene sulfonate (ANS) fluorescence. The effect of guanidinium in a PSA was studied. PSA provides information on ligand binding volumes. The volume changes from protein–ligand binding are thermodynamically important and could be used in designing compounds with specific volumetric binding properties.     

Quantitative aspects of recognition of the antibiotic drug oxytetracycline by bovine serum albumin: Calorimetric and spectroscopic studies

A quantitative understanding of the mode of interaction of drugs with target proteins provides a guide for the synthesis of new drug molecules. The binding of the antibiotic drug oxytetracycline with serum albumin has been studied by a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), steady-state and time-resolved fluorescence spectroscopy, and circular dichroism spectroscopy. The values of the binding constant (K), enthalpy change (ΔH), entropy (ΔS), and stoichiometry of binding have been determined along with the associated conformational changes in the protein. Oxytetracycline binds to bovine serum albumin with a 1:1 stoichiometry and with a weakly temperature dependent association constant of 1.8 · 10⁴ at T = 298.15 K. The effect of ionic strength, tetrabutylammonium bromide, and sucrose on the thermodynamic parameters obtained from ITC and DSC measurements indicate involvement of predominantly ionic and hydrophobic interactions with a minor hydrogen bonding contribution in the drug-protein complexation. The DSC results on the binding of oxytetracycline with bovine serum albumin in the absence and presence of these additives provide quantitative information on the effect of drugs on the stability of bovine serum albumin, and suggest preferential complexation of one of the domains of the protein. The results further indicate that the drug occupies binding site II on bovine serum albumin.     

Electronic and vibrational circular dichroism spectroscopic study of non-covalent interactions of meso-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin with (dG-dC)10 and (dA-dT)10

The non-covalent interactions of (dG-dC)₁₀ and (dA-dT)₁₀ with 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP) were studied using the combination of electronic circular dichroism (ECD), vibrational circular dichroism (VCD) spectroscopy, and UV–vis and IR absorption spectroscopy at different ratios of both components r = [oligonucleotide]/[TMPyP] = 2/1–10/1 where [oligonucleotide] and [TMPyP] are the amount concentrations of oligonucleotide per base-pair and TMPyP, respectively. It was shown that TMPyP with (dG-dC)₁₀ provided hemiintercalative binding mode for r = 4/1 that is manifested in vibrational spectra: The absorption band assigned to the C6O6 stretching vibration of guanine is shifted from 1683 to 1672 cm⁻¹, the corresponding VCD couplet from 1694(−)/1674(+) to 1684(−)/1663(+) cm⁻¹ and its intensity decreases. The absorption band assigned to the C2O2 stretching vibration of cytosine is shifted from 1652 to 1644 cm⁻¹ and its intensity increases. TMPyP with (dA-dT)₁₀ provided three binding modes: (i) external binding to the phosphate backbone, (ii) external minor groove binding for the ratios >6/1 and (iii) external major groove binging associated with the partial B- to Z-transition for the ratios <4/1. The major groove binding is manifested in VCD spectra by the intensity decrease of the bands 1655 and 1638 cm⁻¹ assigned to the thymine vibrations while the bands assigned to the adenine vibrations are unchanged. In the (dA-dT)₁₀–TMPyP complexes, the external binding to the phosphate backbone accompanied by self-stacking of porphyrins along the phosphate backbone chain is preferred at temperatures higher than 40 °C.     

Identification of pyrazosulfuron-ethyl binding affinity and binding site subdomain IIA in human serum albumin by spectroscopic methods

Pyrazosulfuron-ethyl (PY) is a sulfonylurea herbicide developed by DuPont which has been widely used for weed control in cereals. The determination of PY binding affinity and binding site in human serum albumin (HSA) by spectroscopic methods is the subject of this work. From the fluorescence emission, circular dichroism and three-dimensional fluorescence results, the interaction of PY with HSA caused secondary structure changes in the protein. Fluorescence data demonstrated that the quenching of HSA fluorescence by PY was the result of the formation of HSA–PY complex at 1:1 molar ratio, a static mechanism was confirmed to lead to the fluorescence quenching. Hydrophobic probe 8-anilino-1-naphthalenesulfonic acid (ANS) displacement results show that hydrophobic patches are the major sites for PY binding on HSA. The thermodynamic parameters ΔH° and ΔS° were calculated to be ?36.32 kJ mol^?1 and ?35.91 J mol^?1 K^?1, which illustrated van der Waals forces and hydrogen bonds interactions were the dominant intermolecular force in stabilizing the complex. Also, site marker competitive experiments showed that the binding of PY to HSA took place primarily in subdomain IIA (Sudlow's site I). What presented in this paper binding research enriches our knowledge of the interaction between sulfonylurea herbicides and the physiologically important protein HSA.     

Binding of the bioflavonoid robinetin with model membranes and hemoglobin: Inhibition of lipid peroxidation and protein glycosylation

Recent years have witnessed burgeoning interest in plant flavonoids as novel therapeutic drugs targeting cellular membranes and proteins. Motivated by this scenario, we explored the binding of robinetin (3,7,3′,4′,5′-pentahydroxyflavone, a bioflavonoid with remarkable ‘two color’ intrinsic fluorescence properties), with egg yolk phosphatidylcholine (EYPC) liposomes and normal human hemoglobin (HbA), using steady state and time resolved fluorescence spectroscopy. Distinctive fluorescence signatures obtained for robinetin indicate its partitioning (K_p = 8.65 × 10⁴) into the hydrophobic core of the membrane lipid bilayer. HbA–robinetin interaction was examined using both robinetin fluorescence and flavonoid-induced quenching of the protein tryptophan fluorescence. Specific interaction with HbA was confirmed from three lines of evidence: (a) bimolecular quenching constant K_q ? diffusion controlled limit; (b) closely matched values of Stern–Volmer quenching constant and binding constant; (c) τ₀/τ = 1 (where τ₀ and τ are the unquenched and quenched tryptophan fluorescence lifetimes, respectively). Absorption spectrophotometric assays reveal that robinetin inhibits EYPC membrane lipid peroxidation and HbA glycosylation with high efficiency.     

Synthesis and properties of the compound: LiNi3/5Cu2/5VO4

The LiNi_3/5Cu_2/5VO₄ is synthesized by solution-based chemical method and its formation has been checked by X-ray diffraction (XRD) study. XRD study shows a tetragonal unit cell structure with lattice parameters of a = 11.6475 (18) Å, c = 2.4855 (18) Å and c/a = 0.2134 Å. Electrical properties are verified using complex impedance spectroscopy (CIS) technique. Complex impedance analysis reveals following points: (i) the bulk contribution to electrical properties up to 200 °C, (ii) the bulk and grain boundary contribution at T ≥ 225 °C, (iii) the presence of temperature dependent electrical relaxation phenomena in the material. D.c. conductivity study indicates that electrical conduction in the material is a thermally activated process.     

Fluorescence studies on the interaction of hydrophobic ligands with Momordica charantia (bitter gourd) seed lectin

The interaction of Momordica charantia (bitter gourd) seed lectin (MCL) with several nucleic acid bases has been investigated by monitoring changes induced in the protein fluorescence by ligand binding. Values of the binding constant, K_a were obtained as 1.1 × 10⁴, 1.56 × 10⁴ and 2.2 × 10³ M^?1 for adenine, cytosine and uracil, respectively. In addition, binding of 8-anilinonaphthalene 1-sulfonate (ANS) with MCL was investigated by fluorescence spectroscopy. Interaction with MCL at low pH results in a large enhancement of the fluorescence intensity of ANS with a concomitant blue shift in the emission λ_max, whereas at neutral and basic pH changes in both fluorescence intensity and emission maximum were very small, clearly suggesting that the MCL–ANS interaction is stronger at lower pH values. When excited at 295 nm in the presence of ANS, the protein fluorescence decreased with a concomitant increase in the emission intensity of ANS, suggesting resonance energy transfer from the tryptophan residues of MCL to ANS. Gel filtration profiles of MCL at pH values 2.0 and 7.4 are similar indicating that the tetrameric nature of MCL is retained even at low pH. Addition of lactose or adenine to MCL–ANS mixture did not alter the change in ANS fluorescence suggesting that lactose, adenine and ANS bind to MCL at independent and non-interacting sites. These results are relevant to understanding the functional role of MCL in the parent tissue.     

Thermodynamic properties of the methyl esters of p-hydroxy and p-methoxy benzoic acids

The vapor pressures of crystalline and liquid phases of methyl p-hydroxybenzoate and of methyl p-methoxybenzoate were measured over the temperature ranges (338.9 to 423.7) K and (292.0 to 355.7) K respectively, using a static method based on diaphragm capacitance gauges. The vapor pressures of the crystalline phase of the former compound were also measured in the temperature range (323.1 to 345.2) K using a Knudsen mass-loss effusion technique. The results enabled the determination of the standard molar enthalpies, entropies and Gibbs free energies of sublimation and of vaporization, at T = 298.15 K, as well as phase diagram representations of the (p, T) experimental data, including the triple point. The temperatures and molar enthalpies of fusion of both compounds were determined using differential scanning calorimetry and were compared with the results indirectly derived from the vapor pressure measurements. The standard (p° = 10⁵ Pa) molar enthalpies of formation, in the crystalline phase, at T = 298.15 K, of the compounds studied were derived from their standard massic energies of combustion measured by static-bomb combustion calorimetry. From the experimental results, the standard molar enthalpies of formation, in the gaseous phase at T = 298.15 K, were calculated and compared with the values estimated by employing quantum chemical computational calculations. A good agreement between experimental and theoretical results is observed. To analyze the thermodynamic stability of the two compounds studied, the standard Gibbs free energies of formation in crystalline and gaseous phases were undertaken. The standard molar enthalpies of formation of the title compounds were also estimated from two different computational approaches using density functional theory-based B3LYP and the multilevel G3 methodologies.     

Synthesis of 99mTc-gemifloxacin freeze dried kits and their biodistribution in Salmonella typhi,Pseudomonas aeruginosa and Klebsiella pneumoniae

Gemifloxacin, a novel, 4th generation fluoroquinolone derivative, was labeled with^99mTc; its freeze dried kits were prepared and used for infection imaging. Kits showed great stability with higher labeling efficiency. Kits were synthesized through a simple method; developed at room temperature without HCl and heating with low colloidal content. Reaction conditions were optimized in order to get maximum radiochemical purity. Highest labeling efficiency (99 ± 0.05)% was achieved when 1.0 mg gemifloxacin was labeled with 10 mCi sodium pertechnetate in the presence of 50 μg SnCl₂ and 300 μg D-penicillamine at room temperature. Radiolabeled antibiotic kits were preclinically assessed such as in-vitro stability, lipophilicity, protein binding, in-vitro binding with bacterial strains and pharmacokinetic investigations in animals. Kits were found highly stable for 6 h both at room temperature and at 37 °C in serum. Biodistribution showed excellent uptake of activity at infection site (in Pseudomonas aeruginosa, Salmonella typhi and Klebsiella pneumoniae). Biodistribution data showed that ^99mTc-gemifloxacin has the potential and may be used for infection imaging.     

Solubility of CO2 in the solvent system (water + monoethanolamine + triethanolamine)

This report presents a new set of values for the solubility of carbon dioxide in the solvent system {water (1) + monoethanolamine (2) + triethanolamine (3)} at T = (313.2, 333.2, 353.2, and 373.2) K and CO₂ partial pressures ranging (1.0 to 120) kPa. The results are specific to solvent systems with the following compositions: (i) ω₂ = 0.24, ω₃ = 0.06, (ii) ω₂ = 0.18, ω₃ = 0.12, (iii) ω₂ = 0.12, ω₃ = 0.18, (iv) ω₂ = 0.06, ω₃ = 0.24, and (v) ω₂ = 0, ω₃ = 0.30, where ω refers to the mass fraction of the component. The results fit the Deshmukh and Mather model well.     

Pharmacoinformatics study of Piperolactam A from Piper betle root as new lead for non steroidal anti fertility drug development

Fertility control is a burning problem all over the world to regulate population overflow and maintain ecological balance. This study is an in-silico approach to explore a non-steroidal lead as contraceptive agent in order to avoid several contraindications generated by steroidal analogues. Piperolactam A, an aristolactam isolated from Piper betle Linn. showed binding affinity towards estrogen and progesterone receptor as −8.9 and −9.0 Kcal/mol (inhibition constant K_i = 0.294 μM and 0.249 μM) respectively which is even larger than that of reported antagonists such as Rohitukine and OrgC (binding affinity −8.7 and −8.4 Kcal/mol; K_i 0.443 μM and 0.685 μM respectively). The binding site exploration displayed more hydrogen bonding of Piperolactam A (His 524, Leu 346, Thr 347) than Rohitukine and OrgC (Leu 718) with associated receptors which was further confirmed by molecular dynamics simulations. The drug-likeliness of the compound has been proved from its tally with Lipinsky’s Rule of Five and lowered toxicity such as cardiac toxicity, liver toxicity, mutagenicity and ecological toxicity. Endocrine disruptome and later docking guided molecular simulations revealed that Piperolactam A has weaker binding affinity and/or lower probability of binding with nuclear receptors especially hERG and cytochrome P450. The high Caco-2 permeability suggested more bioavailability hence more therapeutic efficacy of the drug.