Structural Studies on Proteincarbohydrate Interactions and Inhibitor Design Using Molecular Modeling Techniques

Carbohydrates are the most abundant of the four major classes of biomolecules, which also include proteins, lipids and nucleic acids. They have numerous roles in living things, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). Additionally, carbohydrates and their derivatives play major roles in the working process of the immune system, fertilization, pathogenesis, blood clotting, and development. The protein-carbohydrate interactions have been investigated in recent years through the analysis of the 3-D structures of a number of proteins and their complexes with carbohydrates, by X-ray crystallographic and NMR spectroscopic methods as well as by molecular modeling studies. In the present work the nature of interactions between proteins and carbohydrates has been explored at the molecular level using advanced molecular modeling techniques. The first chapter provides a general introduction to the field of study highlighting the lectins from different sources, drug design and molecular modeling approaches for 3-D structure prediction. The second chapter presents the general description of methods used in the present study. The third chapter presents the results and discussions on the prediction of 3-D structures of mannose-binding and glucose/galactose-binding lectins from different source, namely, animal, bacteria and fungi using homology modeling techniques based on the crystal structures of mannose-binding and glucose/galactosebinding lectins available in the database. A few newly published protein sequences have been selected for structure prediction and analysis in order to understand their functional roles. Influence of calcium ions on carbohydrate binding has also been explored wherever relevant. The fourth chapter presents the results and discussions on the prediction of 3-D structures of all known human Siglecs based on the crystal structure of human Siglec-7. Related specific sugars have been docked on to the carbohydratebinding sites to get the structures of the complexes. The natures of chemical forces involved in sugar-protein interactions were analyzed to examine the strength of such binding. The knowledge of these modeled structures and particularly of their carbohydrate recognition domains may provide valuable information in developing potent therapeutics. The fifth chapter is focused on inhibitor design of a modeled cysteine protease of Leishmania donovani using target based drug design method

Search for Glucose/galactose-binding Proteins in Newly Discovered Protein Sequences Using Molecular Modeling Techniques and Structural Analysis

Sugar moieties serve as specificity markers in a wide variety of biochemical functions, and periplasmic glucose/galactosebinding proteins (GGBPs) serve as the primary receptors for transport and chemotaxis. Recently, complete genome sequencing projects have revealed many open reading frames for such receptors. On the basis of the homology search with the known x-ray structures (PDB ID: 3GBP/1GCA) of a periplasmic receptor protein from Salmonella typhimurium, we selected four putative proteins with amino acid identities between 30 and 48% for the prediction of three-dimensional (3D) structures of the proteins as well as their complexes with glucose and galactose. We could successfully identify the key residues involved in coordination with calcium ion spanning over two loop structures. We calculated the ligand-binding affinities and hydrogen bonding patterns of the modeled structures and compared with those of the x-ray structures. The calculation of free energies of binding of the modeled structures to glucose and galactose in the presence of water suggested that two of four putative proteins can form complexes with dissociation constants in the micromolar range (1–10 mM). Electrostatic potentials on the surfaces near the sugar and calcium-binding sites of the modeled structures were predominately negative as found in case of the x-ray structure. Taken together, our results suggest that the products of two newly discovered genes would serve as receptors for the transport of glucose and galactose

Ecthyma gangrenosum in the periorbital region in a previously healthy immunocompetent woman without bacteremia

Ecthyma gangrenosum (EG) is a cutaneous lesion classically associated with potentially fatal Pseudomonas septicemia in immunocompromised patients. Other bacterial and fungal pathogens have also been implicated. Although EG typically occurs in immunocompromised or neutropenic patients, it may occasionally affect a previously healthy person. The cutaneous findings are characteristic with small indurated papulovesicles progressing rapidly to necrotic ulcers with surrounding erythema and a central black Eschar. While lesions can occur at any site, most are commonly found over the buttocks, perineum, limbs, and axillae. We describe a case of EG in periorbital region in a previously healthy woman who responded to appropriate antibiotic treatment for Pseudomonas. It is very important to establish the diagnosis early so that appropriate systemic antibiotic therapy can be initiated to reduce morbidity and potential mortality

Bilateral giant juvenile fibroadenoma of breasts

An 11-year-old girl with rapidly enlarging bilateral breast lumps is reported. It was diagnosed as a case of juvenile fibroadenoma following fine needle aspiration cytology and confirmed on histopathological examination of the excised specimens

Fluorescent copper(II) complexes: The electron transfer mechanism, interaction with bovine serum albumin (BSA) and antibacterial activity

Dinuclear copper(II) complexes with formula [Cu2(L)2(N3)2] (1) and [Cu2(L)2(NCS)2] (2) HL = (1-[(3-methyl-pyridine-2-ylimino)-methyl]-naphthalen-2-ol) were synthesized by controlling the molar ratio of Cu(OAC)2·6H2O, HL, sodium azide (1) and ammonium thiocyanate (2). The end on bridges appear exclusively in azide and thiocyanate to copper complexes. The electron transfer mechanism of copper(II) complexes is examined by cyclic voltammetry indicating copper(II) complexes are Cu(II)/Cu(I) couple. The interactions of copper(II) complexes towards bovine serum albumin (BSA) were examined with the help of absorption and fluorescence spectroscopic tools. We report a superficial solution-based route for the synthesis of micro crystals of copper complexes with BSA. The antibacterial activity of the Schiff base and its copper complexes were investigated by the agar disc diffusion method against some species of pathogenic bacteria (Escherichia coli, Vibrio cholerae, Streptococcus pneumonia and Bacillus cereus). It has been observed that the antibacterial activity of all complexes is higher than the ligand

Bilateral giant juvenile fibroadenoma of breasts

An 11-year-old girl with rapidly enlarging bilateral breast lumps is reported. It was diagnosed as a case of juvenile fibroadenoma following fine needle aspiration cytology and confirmed on histopathological examination of the excised specimens

Synthesis of biologically active cadmium (II) complex with tridentate N2O donor Schiff base: DFT study, binding mechanism of serum albumins (bovine, human) and fluorescent nanowires

The photophysical properties of luminescent tetra-coordinated cadmium (II) complex formulated as [Cd(L)Cl],HL = (1-[(3-methyl-pyridine-2-ylimino)-methyl]-naphthalen-2-ol) were synthesized and characterized by analytical and spectroscopic methods. The density function theory calculations are used to investigate the electronic structures of the ligand and its complex. The interactions of cadmium (II) complex towards bovine serum albumin (BSA) and human serum albumin (HSA) were investigated using absorption and fluorescence spectroscopic techniques at pH 7.4. The quenching constants, binding constants and number of binding sites were determined by fluorescence quenching method. The calculated thermodynamic parameters (ΔG, ΔH, and ΔS) confirmed that the binding reaction is mainly entropy-driven and hydrophobic forces played an important role in the reaction. Here, we proposed a new synthetic procedure for the preparation of BSA and HSA with cadmium complex nanowires. The scanning electron microscopy images show that BSA and HSA with cadmium complex product are wire-like in structure. The complex shows enhanced antibacterial activity compared with the free ligand and standard antibiotic chloramphenicol. Antioxidant studies showed that the complex has significant antioxidant activity against DPPH. The obtained IC50 value of the DPPH activity for complex (IC50 = 138 μg/ml) showed excellent scavenging property compared to standard ascorbic acid

Synthesis and Characterisation of Copper(II) Complexes with Tridentate NNO Functionalized Ligand: Density Function Theory Study, DNA Binding Mechanism, Optical Properties, and Biological Application

The photo physical properties of two mononuclear pentacoordinated copper(II) complexes formulated as [Cu(L)(Cl)(H2O)] (1) and [Cu(L)(Br)(H2O)] (2) HL = (1-[(3-methyl-pyridine-2-ylimino)-methyl]-naphthalen-2-ol) were synthesized and characterized by elemental, physicochemical, and spectroscopic methods. The density function theory calculations are used to investigate the electronic structures and the electronic properties of ligand and complex. The interactions of copper(II) complexes towards calf thymus DNA were examined with the help of absorption, viscosity, and fluorescence spectroscopic techniques at pH 7.40. All spectroscopy's result indicates that complexes show good binding activity to calf thymus DNA through groove binding. The optical absorption and fluorescence emission properties of microwires were characterized by fluorescence microscope. From a spectroscopic viewpoint, all compounds strongly emit green light in the solid state. The microscopy investigation suggested that microwires exhibited optical waveguide behaviour which are applicable as fluorescent nanomaterials and can be used as building blocks for miniaturized photonic devices. Antibacterial study reveals that complexes are better antimicrobial agents than free Schiff base due to bacterial cell penetration by chelation. Moreover, the antioxidant study of the ligand and complexes is evaluated by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) free-radical assays, which demonstrate that the complexes are of higher antioxidant activity than free ligand

Leydig cell tumor of testis in a child: An uncommon presentation

Leydig cell tumors (LCTs) are rare testicular tumors. Incidence is 1%–3% of all testicular neoplasms, bilateral in 10%. They are frequently hormonally active, leading to feminizing or virilizing syndromes. LCTs can be either pure or mixed with germ cell tumors or other sex cord-stromal tumors. Here, we are reporting a benign pure LCT in a 6-year-old boy presented with pseudopuberty