Subject(s)
Hydrocarbons, Chlorinated/chemical synthesis , Hydrocarbons, Halogenated/chemical synthesis , Myosins/antagonists & inhibitors , Pyrroles/chemical synthesis , Allosteric Regulation , Binding Sites , Catalysis , Computer Simulation , Crystallography, X-Ray , Cyclization , Dictyostelium/enzymology , Hydrocarbons, Chlorinated/chemistry , Hydrocarbons, Halogenated/chemistry , Molecular Conformation , Myosins/metabolism , Pargyline/analogs & derivatives , Pargyline/chemistry , Propylamines/chemistry , Pyrroles/chemistry , Silver/chemistryABSTRACT
We have identified pentabromopseudilin (PBP) as a potent inhibitor of myosin-dependent processes such as isometric tension development and unloaded shortening velocity. PBP-induced reductions in the rate constants for ATP binding, ATP hydrolysis and ADP dissociation extend the time required per myosin ATPase cycle in the absence and presence of actin. Additionally, coupling between the actin and nucleotide binding sites is reduced in the presence of the inhibitor. The selectivity of PBP differs from that observed with other myosin inhibitors. To elucidate the binding mode of PBP, we crystallized the Dictyostelium myosin-2 motor domain in the presence of Mg(2+)-ADP-meta-vanadate and PBP. The electron density for PBP is unambiguous and shows PBP to bind at a previously unknown allosteric site near the tip of the 50-kDa domain, at a distance of 16 A from the nucleotide binding site and 7.5 A away from the blebbistatin binding pocket.
Subject(s)
Myosins/metabolism , Pyrroles/pharmacology , Adenosine Triphosphate/metabolism , Animals , Chickens , Kinetics , Models, Molecular , Myosins/antagonists & inhibitors , Myosins/chemistry , Myosins/drug effects , Protein Binding , Protein Conformation , Rats , Sensitivity and SpecificityABSTRACT
The human secretory phospholipase A2 group IIA (PLA2-IIA) is a lipolytic enzyme. Its inhibition leads to a decrease in eicosanoids levels and, thereby, to reduced inflammation. Therefore, PLA2-IIA is of high pharmacological interest in treatment of chronic diseases such as asthma and rheumatoid arthritis. Quercetin and naringenin, amongst other flavonoids, are known for their anti-inflammatory activity by modulation of enzymes of the arachidonic acid cascade. However, the mechanism by which flavonoids inhibit Phospholipase A2 (PLA2) remained unclear so far. Flavonoids are widely produced in plant tissues and, thereby, suitable targets for pharmaceutical extractions and chemical syntheses. Our work focuses on understanding the binding modes of flavonoids to PLA2, their inhibition mechanism and the rationale to modify them to obtain potent and specific inhibitors. Our computational and experimental studies focused on a set of 24 compounds including natural flavonoids and naringenin-based derivatives. Experimental results on PLA2-inhibition showed good inhibitory activity for quercetin, kaempferol, and galangin, but relatively poor for naringenin. Several naringenin derivatives were synthesized and tested for affinity and inhibitory activity improvement. 6-(1,1-dimethylallyl)naringenin revealed comparable PLA2 inhibition to quercetin-like compounds. We characterized the binding mode of these compounds and the determinants for their affinity, selectivity, and inhibitory potency. Based on our results, we suggest C(6) as the most promising position of the flavonoid scaffold to introduce chemical modifications to improve affinity, selectivity, and inhibition of PLA2-IIA by flavonoids.
Subject(s)
Drug Design , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Flavonoids/chemistry , Flavonoids/pharmacology , Phospholipases A2, Secretory/antagonists & inhibitors , Catalytic Domain , Computer Simulation , Computer-Aided Design , Enzyme Inhibitors/chemical synthesis , Flavonoids/chemical synthesis , Humans , Ligands , Models, Molecular , Phospholipases A2, Secretory/chemistry , ThermodynamicsABSTRACT
Based on the identification of actin as a target protein for the flavonol quercetin, the binding affinities of quercetin and structurally related flavonoids were determined by flavonoid-dependent quenching of tryptophan fluorescence from actin. Irrespective of differences in the hydroxyl pattern, similar Kd values in the 20 microM range were observed for six flavonoids encompassing members of the flavonol, isoflavone, flavanone, and flavane group. The potential biological relevance of the flavonoid/actin interaction in the cytoplasm and the nucleus was addressed using an actin polymerization and a transcription assay, respectively. In contrast to the similar binding affinities, the flavonoids exert distinct and partially opposing biological effects: although flavonols inhibit actin functions, the structurally related flavane epigallocatechin promotes actin activity in both test systems. Infrared spectroscopic evidence reveals flavonoid-specific conformational changes in actin which may mediate the different biological effects. Docking studies provide models of flavonoid binding to the known small molecule-binding sites in actin. Among these, the mostly hydrophobic tetramethylrhodamine-binding site is a prime candidate for flavonoid binding and rationalizes the high efficiency of quenching of the two closely located fluorescent tryptophans. The experimental and theoretical data consistently indicate the importance of hydrophobic, rather than H-bond-mediated, actin-flavonoid interactions. Depending on the rigidity of the flavonoid structures, different functionally relevant conformational changes are evoked through an induced fit.
Subject(s)
Actins/chemistry , Actins/metabolism , Cell Nucleus/metabolism , Cytoplasm/metabolism , Flavonoids/chemistry , Flavonoids/pharmacology , Models, Chemical , Models, Molecular , Binding Sites , Cell Nucleus/drug effects , Computer Simulation , Cytoplasm/drug effects , HeLa Cells , Humans , Protein Binding , Protein Conformation/drug effectsABSTRACT
We compared an antisense-oligodeoxynucleotide and four DNAzymes directed to the prothrombin mRNA for their efficiency to reduce prothrombin transcript level in HepG2 cells. The DNAzymes have different binding arm symmetry and cleavage sites, but are directed to the identical target site of the antisense-oligodeoxynucleotide. The nucleic acid-based inhibitors were transfected into HepG2 cells and prothrombin transcript level was quantified and normalized to the beta-actin transcript level by multiplex PCR. All nucleic acid-based inhibitors reduced prothrombin transcript level and the effect was in almost all cases, strongest 24 h after transfection, but still remarkable up to 68 h after transfection. The antisense-oligodeoxynucleotide was more effective than the DNAzymes tested.
Subject(s)
Nucleic Acids/chemistry , Nucleic Acids/pharmacology , Polymerase Chain Reaction/methods , Prothrombin/genetics , Transcription, Genetic/drug effects , Base Sequence , Cell Line, Tumor , DNA, Catalytic/metabolism , Humans , Molecular Sequence Data , Nucleic Acid Conformation , Oligodeoxyribonucleotides, Antisense/genetics , Prothrombin/biosynthesis , RNA, Messenger/genetics , Substrate SpecificityABSTRACT
INTRODUCTION: The development of novel antithrombotic agents directly affecting gene expression requires well established, reliable and useful in vitro model systems for initial validation of drug effects. Since most proteins involved in coagulation are synthesized by the liver, the hepatoblastoma cell line Hep G2 is introduced, here, as a model system to test nucleic acid based coagulation inhibitors. METHODS: Hep G2 cells were characterized with respect to prothrombin, tissue factor and factor VIII expression in dependence of cell culture conditions. Reliable enzyme linked immuno sorbent assays as well as viability tests were introduced that allow drug screening procedures with multiple probes in microplate format. Furthermore, a multiplex PCR-procedure has been presented that offers the possibility to simultaneously detect the effects of a selected compound on two coagulation proteins in comparison to a house keeping gene. RESULTS: Hep G2 cells were not affected in viability by cell culture conditions, while proliferation and the expression patterns of some coagulation factors were affected by the adhesion factor collagen. The prothrombin expression characteristics allowed us to choose a specific time point for the transfection of Hep G2 cells with prothrombin specific antisense oligonucleotides. Antisense oligonucleotides inhibited prothrombin expression independent from culture conditions and the effects were detected on protein-and mRNA-level. DISCUSSION: Nucleic acid based agents require cellular in vitro model systems since they affect the process of gene expression and not the gene product. Hep G2 cells are a useful model to study effects of novel nucleic acid based coagulation inhibitors with an antisense mechanism of action on protein and mRNA level.
Subject(s)
Blood Coagulation Factors/biosynthesis , Cell Culture Techniques/methods , Gene Expression Regulation/physiology , Gene Expression Regulation/drug effects , Humans , Oligonucleotides, Antisense/pharmacology , Tumor Cells, CulturedABSTRACT
The development of antisense oligonucleotides (AS-ODN) always had the limitation that because of complex mRNA secondary structures, not every designed AS-ODN inhibited the expression of its target. There have been many investigations to overcome this problem in the last few years. This produced a great deal of theoretical and empirical findings about characteristics of effective AS-ODNs in respect to their target regions but no standardized selection procedure of AS-ODN target regions within a given mRNA or standardized design of AS-ODNs against a specific target region. We present here a standardized method based on secondary structure prediction for target site selection and AS-ODN design, followed by validation of the antisense effect caused by our predicted AS-ODNs in cell culture. The combination of theoretical design and experimental selection procedure led to an AS-ODN that efficiently and specifically reduces prothrombin mRNA and antigen.
