Use of Receptor-Based Drug Design and Applications in the Study of finding antagonists for MD-2/TLR4, GLP and CXCR4 Open Access

Liu, Jin (2012)

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Paclitaxel (PTX) mimics the action of lipopolysaccharide (LPS) in mice but not in human immune system. Recent experiments show that activation of TLR4 by PTX requires the mouse MD-2 protein, and is independent of TLR4 species, indicating that the mouse MD-2/PTX interaction is a key to TLR4 activation. To define the structural differences for MD-2/TLR4 activation, the electrostatic potential and lipophilic surfaces of human and mouse MD-2 have been assessed. The computational docking of PTX to each species supports the hypothesis that PTX, as an antagonist in human MD-2, stabilized loop 123-130, especially the Phe126, to prevent TLR4/MD-2 dimerization.

Lipopolysaccharide (LPS) signals through a membrane bound-complex of the lipid binding protein MD-2 and the receptor TLR4. When LPS binds MD-2, the complex activates the key transcriptional regulator NF-κB, resulting in the production of inflammatory cytokines. TLR4 dimerization is an essential step in signal transduction. In this study, we identified the human and mouse TLR4/MD-2 dimerization model by computation - Rosetta Protein-Protein docking. The Meningococcal LOS binding modes in human TLR4/MD-2 dimer were also predicted. KDO moiety is crucial for meningococcal LOS bioactivity. PEA group can be added at 1-PO4 or 4-PO4 site to make more tightly binding.

The Gilman reagent can be used for selective creation of carbon-carbon bonds in organic chemistry. We performed density functional calculations to propose a reasonable mechanism for the reaction between Me2CuLi·LiX (X=I, SCH3, CN) and CH3I. The tetracoordinate, square-planar intermediate proves to be an intermediate species in the calculation. Based on our calculations, the reaction goes through an asymmetric, non-planar transition state to reach the long proposed "copper (III) intermediate". Then the intermediate overcomes a fairly low barrier to create ethane. The schematic potential energy surface for this reaction illustrates the mechanism for new carbon-carbon bond formation.

Histone lysine methylation plays a key epigenetic role in the regulation of chromatin and gene expression. BIX-01294 (a diazepin-quinazolin-amine derivative) inhibits activities of G9a and G9a-like protein (GLP) lysine methyltransferase. Efforts to improve the potency of BIX-01294 employed the X-ray structure of the GLP/BIX-01294 complex as a template for structure-based design. After the molecular modeling to guide the design, synthesis, and validation of new BIX derivatives, we found that adding a lysine mimic proved to be 5-10 fold more potent than the original compound.

G-protein coupled receptor (GPCR) CXCR4 and the chemokine stromal cell-derived factor-1 (SDF-1/CXCL12) play a crucial role in physiological processes. The interaction of SDF-1 with CXCR4 has implications in cancer metastasis. Several benzenesulfonamide analogs were designed and synthesized to find anti-CXCR4 agents to disrupt of the interaction of SDF-1 with CXCR4. The docking scores of these analogs correlated with the effective concentration of these compounds blocking TN14003 binding on CXCR4.

Table of Contents

Table of Contents
List of Figures...X
List of Tables...XII
Chapter 1: Introduction...1

1.1 Introduction to drug design...1
1.2 Outline for subsequent chapters...4

Chapter 2: Paclitaxel binding to Human and Mouse MD-2...6

2.1 Introduction...6
2.2 Computational Methods...11

2.2.1 Homology Modeling...11
2.2.2 Computational Ligand-Protein Docking...11
2.2.3 Molecular Volumes...12

2.3 Results and Discussion...13

2.3.1 MD-2 models and Glide Docking...13
2.3.2 Induced Fit Docking of PTX into MD-2...19
2.3.3 Discussion...23

Chapter 3: TLR4/MD-2 dimerization Model...27

3.1 Introduction...27
3.2 Computational Methods...29

3.2.1 Homology Modeling...29
3.2.2 Protein-Protein Docking...29

3.3 Results and Discussion...30

Chapter 4: Lipopolysaccharide (LPS) binding to TLR4/MD-2 dimer...36

4.1 Introduction...36
4.2 Computational Methods...38
4.3 Results and Discussion...38

4.3.1 KDO group effect...38
4.3.2 PEA group adding to LPS...43

Chapter 5: Density Functional Calculation of Cross-Coupling Reaction between series of Gilman Cuprates and CH3I...47

5.1 Introduction...47
5.2 Results and Discussion...48

Chapter 6: Structure-based design and synthesis of inhibitors of histone lysine methyltransferase (H3K9me2)...53

6.1 Introduction...53
6.2 Structure-based Modeling of GLP Ligands...56

6.2.1 Computational Methods...56
6.2.2 Structure-based Prediction of BIX-Analog Binding Poses...57

6.3 Conclusion...66

Chapter 7: Benzenesulfonamides as a New Class of Chemokine Receptor Type 4 Inhibitors...67

7.1 Introduction...67
7.2 Results and Discussion...69

7.2.1 Structure-Activity Relationship (SAR) Study...69
7.2.2 Computational Protein-Ligand Docking...70
7.2.3 Mapping of the CXCR4 Antagonists Binding and SDF-1 N-terminus Binding...70
7.2.4 Prediction of Benzene sulfonamide derivatives Binding Poses...72


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