Serda Kecel-Gunduz

Structural and vibrational study of primidone based on monomer and dimer calculations

Primidone (Mysoline), with the chemical formula 5-ethyl-5-phenyl-hexahydropyrimidine- 4,6-dione (C12H14N2O2), has been a valuable drug in the treatment of epilepsy. In the present work, the experimental IR and Raman spectra of solid phase primidone were recorded, and the results were compared with theoretical wavenumber values of monomer and dimer forms of the title molecule. Vibrational spectral simulations in the dimer form were carried out to improve the assignment of the bands in the solid phase experimental spectra. The possible stable conformers of free molecule were searched by means of torsion potential energy surfaces scan studies through two dihedral angles. The molecular geometries of the monomer and dimer forms of title molecule were optimized using DFT method at B3LYP/6-31++G(d,p) level of theory. Using PEDs determined the contributions of internal (stretching, bending, etc.) coordinates to each normal mode of vibration. Further, HOMO–LUMO energy gap and NBO properties of the investigated molecule in monomer and dimer forms were also calculated.

Structural and vibrational spectroscopic elucidation of sulpiride in solid state

The study on the conformational and vibrational behaviors of sulpiride molecule which is known as a neuroleptic or antipsychotic drug that is widely used clinically in the treatment of schizophrenic or depressive disorders is an important scientific and practical task. In here, a careful enough study of monomer and dimeric forms of sulpiridine {5-(aminosulfonyl)-N-[(1-ethyl-2-pyrrolidinyl) ethyl]-2-methoxy-benzamide (C15H23N3O4S)} is undertaken by density functional theory (DFTB3LYP) method with the B3LYP/6-31G(d,p) basis set. The conformations of free molecule were searched by means of torsion potential energy surfaces scan studies through dihedral angles D1 (8 N, 18C, 20C, 23 N), D2 (18C, 20C, 23 N, 25C) and D3 (28C, 30C, 41S, 44 N) in electronically ground state, employing 6-31G basic set. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G(d,p) theory level. Afterwards, the possible dimer forms of the molecule were formed and their energetically preferred conformations were investigated. Moreover, the effect of basis set superposition error on the structure and energy of the three energetically favourable sulpiride dimers has been determined. The optimized structural parameters of the most stable monomer and three low energy dimer forms were used in the vibrational wavenumber calculations. Raman and IR (4000–400 cm−1) spectra of sulpiride have been recorded in the solid state. The assignment of the bands was performed based on the potential energy distribution data. The natural bond orbital analysis has been performed on both monomer and dimer geometries in order to elucidate delocalization of electron density within the molecule. The predicted frontier molecular orbital energies at DFT/B3LYP/6-31G(d,p) theory level show that charge transfer occurs within the molecule. The first-order hyperpolarizability (β0) and related properties (μ and α) of the title molecule were also calculated.

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with −.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.

Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies

Background N-acetylcarnosine (NAC), a dipeptide with powerful antioxidant properties that is extensively used as a pharmaceutical prodrug for the treatment of cataract and acute gastric disease, was investigated by molecular dynamics with the GROMACS program in order to understand the solvent effect on peptide conformation of the peptide molecule used as a component of a drug and which presents substantial information on where drug molecules bind and how they exert their effects. Besides, molecular docking simulation was performed by using the AutoDock Vina program which identify the kind of interaction between the drug and proteins. A delivery system based on poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with NAC (NAC-PLGA-NPs) for the treatment of cataract was prepared for the first time in this study in order to enhance drug bioavailability and biocompatibility. The objective of this work was to prepare and evaluate the structural formulation, characterization, and cytotoxicity studies of NAC-loaded NPs based on PLGA for cataract treatment. Methods PLGA and NAC-loaded PLGA NPs were prepared using the double emulsion (w/o/w) method, and characterizations of the NPs were carried out with UV–Vis spectrometer to determine drug concentration, the Zeta-sizer system to analyze size and zeta potential, FTIR spectrometer to determine the incorporation of drug and PLGA, and TEM analysis for morphological evaluation. Results NAC-loaded PLGA NPs were successfully obtained according to UV–Vis and FTIR spectroscopy, Zeta-sizer system. And it was clearly observed from the TEM analysis that the peptide-loaded NPs had spherical and non-aggregated morphology. Also, the NPs had low toxicity at lower concentrations, and toxicity was augmented by increasing the concentration of the drug. Discussion The NAC molecule, which has been investigated as a drug molecule due to its antioxidant and oxidative stress-reducing properties, especially in cataract treatment, was encapsulated with a PLGA polymer in order to increase drug bioavailability. This study may contribute to the design of drugs for cataract treatment with better reactivity and stability.

Structural analysis, spectroscopic characterization and molecular docking studies of the cyclic heptapeptide

The theoretically possible stable conformer of the cyclic heptapeptide, that has significant anti-metastatic activity, was examined by conformational analysis followed by DFT calculations. Experimental infrared and Raman spectroscopy, together with theoretical DFT (6-31G (d,p) basis set)-based quantum chemical calculations, have been used to understand the structural and spectral characteristics of cyclo(Gly-Arg-Gly-Asp-Ser-Pro-Ala) {cyclo(GRGDSPA)}. A complete analysis of the vibrational spectrum has been reported on the basis of potential energy distribution (PED%) data of the vibrational modes. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound. The simulated spectra satisfactorily coincide with the experimental spectra. In addition, molecular electrostatic potential and frontier molecular orbital analysis were investigated using theoretical calculations. The stability of the molecule, arising from hyperconjugative interaction and charge delocalization, has been analyzed using natural bond orbital analysis and a high E(2) value reveals the presence of strong interaction between donors and acceptors. Molecular docking studies with fibronectin were performed on cyclo(GRGDSPA) in order to understand its inhibitory nature. The results indicate that the docked ligand {cyclo(GRGDSPA)} forms a stable complex with human fibronectin and gives a binding affinity value of −7.7 kcal/mol, which points out that cyclo(GRGDSPA) might exhibit inhibitory activity against the attachment of melanoma cells to human fibronectin.

Computational design of Phe-Tyr dipeptide and preparation, characterization, cytotoxicity studies of Phe-Tyr dipeptide loaded PLGA nanoparticles for the treatment of hypertension

Phe-Tyr dipeptide which was investigated in Wakame food with greatest ACE-inhibitory activity is used as a pharmaceutical drug for the treatment of hypertension, cardiovascular diseases, and diabetic nephropathy. To improve the bioavailability of Phe-Tyr, a delivery system based on poly (lactic-co-glycolic acid) (PLGA) nanoparticles loaded with Phe-Tyr (Phe-Tyr-PLGA NPs) for treating hypertension and cardiovascular diseases was prepared in this study. In the experiments, poly(lactic-co-glycolic acid) (PLGA) and Phe-Tyr dipeptide-loaded PLGA nanoparticles were prepared using the double emulsion (w/o/w) method. The characterizations of the nanoparticles were performed with a UV–vis spectrometer, the Zeta-sizer system, and FTIR spectrometer. The optimum size of the Phe-Tyr dipeptide-loaded PLGA nanoparticle was obtained with a 213.8 nm average particle size, and a 0.061 polydispersity index, −19.5 mV zeta potential, 34% of loaded and 90.09% of encapsulation efficiency. From TEM analysis, it was clearly seen that the dipeptide loaded nanoparticles had the spherical and non-aggregated morphology and Phe-Tyr dipeptide loaded-PLGA nanoparticles were obtained successfully. Cell toxicity of nanoparticles at different concentrations was assayed with XTT methods on L929 fibroblast cells. This study determined that the nanoparticles have low toxicity at lower concentration and toxicity augmented with increasing concentration of dipeptide. To analyze the effect of solvents on structure of Phe-Tyr, Molecular dynamics simulation was performed with GROMACS program and molecular orbital calculations were carried out to obtain structural and electronic properties of dipeptide. Moreover, molecular docking calculations were also employed to model and predict protein–drug interactions.

Molecular docking of immunogenic peptide of Toxoplasma gondii and encapsulation with polymer as vaccine candidate

Abstract Toxoplasma gondii is one of the most widely spread parasitic organisms in the world. T. gondii causes primary, chronic infection and mortality. Major surface antigen 1 is the most abundant tachyzoite surface protein and highly conserved between species and causes strong humoural response. Some studies showed that the peptide sequence of surface antigen has immunity. Therefore, tachyzoite surface antigenic peptide sequence is one of the good candidates for vaccine development. However, conformational information and delivery systems are very important parameters for vaccine development. Computational chemistry which is used as an effective method to perform drug or vaccine design provides important information on structure–activity relationship, biological effects of functional groups, molecular geometry, design of enzyme inhibitors and antagonists. The interaction of immunological peptides with protein systems was carried out by means of computing the free energy of binding using the molecular docking technique. Due to the major histocompatibility complex (MHC), proteins play a substantial role for adaptive immunity, the crystal structure of a MHC class I, which plays a pivotal role in the adaptive branch of the immune system, was preferred for docking calculations. A delivery system based on poly(lactic-co-glycolic acid) (PLGA) nanoparticles and peptide loaded PLGA nanoparticles was prepared in this study to improve the bioavailability of tachyzoite surface antigenic peptide sequence. Double emulsion method (water-in-oil-in-water or w/o/w) was used for synthesis of PLGA and peptide loaded PLGA nanoparticles. The average particle size, polydispersity index and zeta potential values of PLGA and peptide loaded PLGA nanoparticles were measured with zeta-sizer by using dynamic light scattering (DLS) technique. The scanning electron microscope (SEM) (Zeiss Supra 50 V) was used for imagining the peptide loaded PLGA nanoparticles. Cell toxicity of nanoparticles was assayed on AGS (gastric adenocarcinoma) cell line. To evaluate mitochondrial activity of cells and toxicity studies, XTT methods were carried out. In this study, we aimed to obtain specific immunological peptide loaded PLGA nanoparticles and characterize the formation with FTIR, zeta sizer and SEM imaging, and evaluate cytotoxicity and carry out molecular docking calculations of peptide–MHC protein in order to enlight in vivo events as vaccine candidate against T. gondii.

15 – Practical aspects

Nanotechnology is a multidisciplinary field of applications that consists of techniques of functional design and the production of structures from atoms and molecules at nanometer scales, the examination of those structures, and their effective utilization. This chapter consists of three main sections. The first section will define the nanomaterials and their types: nanoparticles, nanospheres, nanocrystals, nanotubes, and nanoemulsions. The second section will describe the uses of the nanomaterials: cancer diagnosis and treatment, low toxicity drug carriers, eye treatments, treatment of cardiovascular diseases, treatment of neurological diseases, tissue engineering, textiles, cosmetics, electronics, computers, and food and agriculture, and the benefits of nanomaterials. Lastly, the third section will discuss the disadvantages of widely used nanomaterials on health and the environment.