Docking Addictions With Mcfabz Protein

TLC Analysis of Analgesic Drugs Author: Monique Amanda Mendez Lab Instructor: Wenmo Sun Organic Chemistry Lab 243A: Section 038 Date Work Performed: 02 September 2015 Discussion: Lab 1a - TLC Analysis of Analgesic Drugs Discuss the relative polarities of the components of the analgesic drugs based on their functional groups The relative polarity of the analgesic drugs depends on their functional groups. Polarity of the drugs depends on several differentiating factors which include how the compound can hydrogen bond to itself or another compound, the number of electronegative atoms that are present within the structure of the compound, the net dipole moment of the molecule and the polarizability of the bonds or atoms that are present within the compound, which can highly define how polarizable the compound is or will be. The more polar the functional group, the stronger the bond is to the stationary phase, making it slower for the molecules to move down the TLC plate, thus the stronger it will be absorbed on the surface of the solid phase.

between Lys235 and the substrate carboxyl group, the Lys235 side chain reoriented and the intramolecular H-bonds between Gln229, Asp215, Lys235 and Asn255 were established. As a consequence, the magnesium cation changed its position and anchored between the amino acid substrate carboxyl group and the a-phosphate group of ATP (Fig. 4). Such an arrangement represents an unproductive way of substrate binding. The above-mentioned amino acid triad, Gln229, Asp215, Lys235, is preserved in both Bj Gly:CP and At Ala:CP ligases. However, in methanogenic M. barkeri SerRS this triad is not present.

When studying medicine it is important to know how the pharmaceutical drug will affect the body, how quickly the drug will work, and what are the short term and long term effects of the drug on the disease. It is important to know the structure of the molecules, to see exactly where the inhibitor will bind, or if it will even bind at all. In the experiment, Structure Based Approach to the Development of Potent and Selective Inhibitors of Dihydrofolate Reductase from Cryptosporidium, they studied the crystal structures of the inhibitors and used computational analysis to determine which in inhibitor would bind the best. The overall goal is to make sure that the inhibitor binds to the correct active site, and that it is the only site.

The active site contains residues that form complementary interactions to MP-10 (Figure 3B), there are several hydrophobic interactions, from certain amino acid residues in the active site of PDE10A to the MP-10 inhibitor, in particularly the quinoline and pyridine moieties. There are also two hydrogen bonds between the active site and MP-10, which is via the phenol group (donor) on the tyrosine (Tyr683) residue to the nitrogen (acceptor) in the quinoline moiety and to the ether oxygen (acceptor) within MP-10.6

The delivery pathway and depth of insertion of inhibitors will be affected by the mechanistic property and porosity of fungal cell walls, which can be examined by measuring the mobility and hydration of biomolecules. Our preliminary 1D data have revealed a very distinct dynamical profile for cell wall molecules for A. fumigatus (Fig. 3). The 1H-13C INEPT spectrum (Fig.3, top) showed quite a few sharp resonances belonging to very mobile molecules, while the 1H-13C cross polarization spectrum (Fig 3, bottom) contained only broad peaks from the rigid molecules, including chitins. These results led us to hypothesize that chitin forms the rigid scaffold whereas glucans form a relatively mobile matrix. We will also measure transverse and longitudinal relaxation times, chemical shift anisotropy, and dipolar couplings with site-specific resolutions. The combined measurements cover a wide range of motions happening from nanoseconds to milliseconds, including both local reorientation and collective motion of multiple sugar rings. It is particularly interesting to know whether dynamical heterogeneity is present for the same molecule. For example, for β-1,3-glucan, some disordered chains could fill the interstitial space between chitin microfibrils while other partially oriented chains can hydrogen bond to the chitin surface becoming partially rigidified. If this scenario occurs, we will observe

On the basis of structural composition, the presence of numerous reactive cysteines residue on actin, it cannot be excluded that allyl compounds may induce redox modifications also at the actin level. Based on theinvolvement of cytoskeleton in NAD(P)H oxidase activation, as well as in cell adhesion and motility, it could have a critical role in the induction of cell cycle arrest and apoptosis by destabilizing the imperative cytoskeletal filaments of the

Histone deacetylases (HDACs), a family of enzymes deacetylating lysines on core histones and other cellular proteins, play an key role in epigenetic regulation of gene transcription and control other cellular functions including cell death, proliferation, and motility.

For this Learning Journal I’ve chosen to research the mechanism of action of methotrexate, an antimetabolite drug that is used mainly in the treatment of cancer and rheumatoid arthritis. This week we’ve studied how specific molecules can bind to enzymes to inhibit their activity in either a reversible or irreversible way; the main difference between these two inhibitions is that in the irreversible one the inhibitor bound tightly to the target enzyme, thus eventually dissociating very slowly, while in reversible inhibition the inhibitor quickly dissociated from the target enzyme. Moreover, reversible inhibition can be competitive, when the inhibitor resembles the substrate and binds to the active site of the target enzyme or non-competitive, where the inhibitor binds at a different binding site, thus both the inhibitor and the substrate

Such drugs are known as PKC inhibitors. This includes staurosporine, a microbial alkaloid and precursor to many novel PKC inhibitors which compete at PKC's ATP binding site. Newer drugds like N-benzoyl-staurosporin and -hydroxystauro-sporin improve selectivity and demonstrated better therapeutic effect in vivo. (21) The problem for existing PKC inhibitors is that they are relatively non-selective in their actions. In the future better drugs can be developed if they target specific isozymes in order to differentially inhibit PKC functions. (21) Some other researchers study the down stream products of PKC pathway, like vimentin, as a anti-cancer therapeutic target. For example, withaferin-A increases apoptosis and vimentin cleavage in vimentin expressing tumor cells and it has been proved that this drug has pronounced anti-antiogenic effect with little adverse effect in non-proliferating endothelial cells. (22) It also significantly blocks soft tissue sarcoma growth and

We have selected different hPodxl mutants to generate (Figure 5). 1) PodxlDTHL: Podxl mutant lacking the C-terminal PDZ docking site, the docking site for NHERF1/2. This mutant will allow us to determine whether or not the ability to bind NHERF1/2 is critical for tumor progression. 2) PodxlTail, lacking all but three aminoacids of the cytoplasmic tail and, therefore, eliminating all intracellular binding (ezrin, NHERF1/2 and other potential unknown ligands). 3) PodxlEC missing the whole extracellular domain, allowing us to account for the lack of the highly negatively charged glycosylated portion as well as the stalk domain.

Although the decreased interaction of TUs 1 and 8 with DMMP than TUs 2 and 4, respectively, can be explained by the phenyl’s adverse effect, it is still not clear why N-benzyl-substituted TU 4 is better than unsubstituted TU 2 (or TU 8 better than TU 1). Since a N-benzyl-substituted TU has a similar donor strength as that of N-alkyl-substituted TU, we suspect that a secondary interaction may exist between TU 4-DMMP in order to have a larger association constant. To gain further insight into the binding mechanism between N-benzyl-substituted TU 4 and DMMP, density functional theory (DFT) calculation was performed using B3LYP functional with empirical dispersion of Grimme (B3LYP-D3BJ) and d3 basis set employing the Gaussian0920 suite of programs. As shown in Figure 4, the DFT calculation revealed the possible existence of CH-π interactions from

Statins have extra hydrophobic regions which have an additional hydrophobic interaction with a hydrophobic binding region present in the enzyme.

The free hydroxyl group of galactose at 6th carbon is essential for galectin binding49.Another very significant structural feature of ST6Gal-I is that it contains six cysteine residues which are also involving disulfide linkages, Cys142-Cys406, Cys184-Cys335, and Cys353-Cys364. These disulfide bonds give important features such as hydrophobicity and rigidity. The other major structural feature of this enzyme is containing a large glycan (with ten monosaccharide units) covalently bonded to Asn149. This specific glycan is also the acceptor for the reaction catalyze by ST6Gal-I. Therefore, The ST6Gal-I is acting as an enzyme as well as a

Beauvericin is a cyclooligomer depsipeptide ionophore that helps in the transportation of monovalent cations across membranes as a free carrier uncoupling oxidative phosphorylation (20). Beauvericin shows an important biological activities as antifungal and antibiotic properties in vitro (21), and antifungal agents in combinatorial therapies (22). Along with above functions, In 2004 Jow et al., (23) reported beauvericin as a broad-spectrum antiproliferative agent which fight against different human cancer cell lines by activating calcium sensitive cellular apoptotic pathways. It also inhibits the directional cell motility or haptotaxis which is essential for the formation of new blood vessels in case of on tumor or cancer tissues at subcytotoxic concentrations (22), invasion of other tissues by cancer cells, and metastasis (24). Wang and Xu, (25) reported that beauvericin has antitumour activity against cancer cell lines. During the molecular docking studies of about 36 protein structures of cancer molecules retrieved from PDB are docked with the anticancer drug beauvericin and negative binding energy of the docked complex was calculated. Binding free energy reveals the drug resistance of anticancer and finds the interaction between the active site and substrate of oncogene. These findings provide useful information for understanding the

Surfactant protein-D (SP-D) is a C-type lectin which is synthesized in various parts of the body. SP-D plays a key role in the auto immune disorders, lung infections and also helpful in the postnatal pregnancy. This also plays an active role in the host-defense mechanisms. In the host defense mechanism SP-D binds with various micro-organisms and other particles that enter the human body and act against them. In our present study we targeted on the interactions of surfactant protein –D with the lipid molecules where their interaction plays an important role in the defense mechanism. In our study lipid molecules were docked against the SP-D protein and interaction studies were carried-out. Mutations were generated at sites F335G and R343V and interactions of the lipids with the mutated protein molecules were studied. Among the wild and the mutant protein molecules, mutant protein F335G showed highest interaction with the lipid molecule distearoylphosphatidylcholine with cDocker energy of 94.726. These studied showed that mutant molecules are showing highest binding with the lipid molecules when compared to the wild protein molecule. Among all ligand molecules chosen, distearoylphosphatidylcholine showed highest interaction followed by dilaurylphosphatidylcholine, dipalmitoylphosphatidylcholine with tocopherol showing the least binding affinity with both wild and the mutant protein molecules.