Theoretical Studies On The Interactional Mechanism Of The Purine Riboswitch And Inhibitor Of Apoptosis Proteins With Drugs

Biomacromolecules (including polypeptides, proteins, antibody, glycan and nucleic acid), especially proteins and nucleic acid, are served as the targets for drugs design and synthesis, which are mainly used to treat human major diseases, such as tumor, AIDS, diabetes, cardio-cerebrovascular disease and so on. Research of drugs targeting biomacromolecules is thought to be one of the most promising fields and makes great progress in treatment of major diseases. The investigations on the interactions of biomacromolecules and drugs are the foundation of designing and synthesizing novel drugs, however, the interactional mechanism and structure-activity relationship are totally resolved only by virtue of experimental conditions. The theoretical chemistry and molecular simulations methods are used to study the interactions between biomacromolecules and drugs, which not only plays an important role in development and applications of computational chemistry, but also provides valuable theoretical guidance in understanding the mechanism and designing novel drugs.In recent years, riboswitch and inhibitors of apoptosis proteins are found to be important targets for drugs. Many groups have solved the crystal structures of various riboswitch with metabolites, as well as XIAP-BIR3 with Smac mimetics. They have designed and synthesized metabolites analogs according to the crystal structures. However, the structure and activity relationships of drugs with biomacromolecules are unclear, in this paper, the molecular docking and dynamics simulations methods are used to investigate systematically the interactions of the guanine rioboswitch and inhibitor of apoptosis protein with various metabolites in theory. We carried out a series of significance work on these issues and obtained valuable results, which are described as follows:(1) Interactions of modified purines and pyrimidines with mutant guanine riboswitch:Gilbert et al. demonstrated experimentally that riboswitch GR(C74U) is able to bind amino-pyrimidines other than purines, however, how the structural changes of ligands affected the binding affinity and binding modes is not explained in detail. The interactions of a mutant form of guanine riboswitch GR(C74U) with series of amino modified purines, pyrimidines and imidazole derivatives are investigated. How the number and positions of amino groups affect the binding modes and binding affinity is included. The calculating results reveal that:(1) all the amino-purines and amino-pyrimidines bind in a same cavity composed of four nucleotides including U22, U47, U51 and U74, which agrees well with the experimental results. While two imidazole derivatives, histamine and L-histidinol, adopt other binding modes and bind to another binding sites; (2) the purines are engulfed within three-way junction motifs, but most pyrimidines only form two-way junctions with the riboswitch; (3) the results further show that the number of amino groups has no significant influence on the position and orientation of six-membered ring in the binding pocket, and the decrease of number only weakens the binding affinity slightly, however, the change of position could cause a substantial loss of binding affinity; (4) five-membered ring of purine is not required for recognition, and ligands form stable complexes with riboswitch through Watson-Crick base pair interaction between six-membered ring and U51 as well as U74. These results interpret in theory that six-membered ring is the primary determinant for riboswitch recognition.(2) Studies on the guanine riboswitch interacting with guanine and its closest analogs:The guanine riboswitch could specifically bind guanine analogs, but the analogs with different structures bind to riboswitch with distinct binding affinity. To study the nature of guanine riboswitch recognizing metabolites and evaluate the binding affinities, we systematically investigate the interactions of riboswitch with twenty guanine analogs. The findings display that:(1) most guanine analogs could bind to the same binding pocket with the identical orientations, and the position of functional group hardly affects the orientation of ligand, but the subtle change of structure could cause the significant change of binding affinity, which is resulted from the hydrogen bonds between ligand and surrounding bases. (2) the two tautomers of xanthine adopt different binding modes, and the enol-tautomer shows similar binding mode and affinity of hypoxanthine, which agrees well with the experimental results.(3) the guanine analogs form the complexes with riboswitch mainly through hydrogen bonds interactions of ligands with bases U51 and U74. Although U74 is responsible for the specificity of riboswitch recognition, U51 plays an important role in stabilizing the complexes. These findings not only are helpful to understand that how the change of functional group on ligand affects the binding mode and binding affinity, but also provide the theoretical foundation for riboswitch recognizing the guanine analogs.(3) Interactional mechanism of Smac mimetics bearing seven-membered ring with XIAP-BIR3:As we know, apoptosis is an essential role in maintaining normal cell proliferation and death homeostasis of multicellular organisms. According to the crystal structures of XIAP-BIR3 with Smac/DIABLO, a series of artificial peptidic and nonpeptidic compounds (called Smac mimetics) have been designed and synthesized, which can mimic Smac N-terminal four residues Alal-Val2-Pro3-Ile4 (AVPI), compete for binding to XIAP-BIR3 with caspase-9, remove the inhibition of XIAP on caspase-9 and induce cell death. To investigate the interaction nature of XIAP-BIR3 binding the Smac mimetics, the interactions of four representative mimetics bearing seven-membered ring with XIAP-BIR3 are investigated. From docking results we can see that the orientations of these backbones of mimetics are identical with that of AVPI in the binding pocket, each ligand corresponds two competitive conformations, namely the extended and bended conformations which are determined by the orientations of terminal diphenylmethyl. When the amino-terminus of mimetics is secondary amino group, the binding affinity is the strongest. Molecular dynamics simulations reveal that XIAP-BIR3 interacting with the extended conformation is more stable in MD simulations, and the mimetics would convert its conformation from the bended to the extended form gradually. Energy decomposition displays that Thr308 is the biggest contributor to the binding, and Asp309, Glu314 and Trp323 are indispensable residues for XIAP-BIR3 binding Smac miemtics.(4) Investigations of bicyclic and tricyclic core monovalent Smac mimetics interacting with XIAP-BIR3:A series of artificial Smac mimetics could mimic the N-terminal tetrapeptide AVPI of Smac to bind to XIAP-BIR3, but these structural diverse mimetics exhibited distinct binding affinities and binding modes. We studied the structural change influencing on the binding affinity and binding modes for three kinds of mimetics interacting with XIAP-BIR3. The results reveal that these Smac mimetics are docked to the surface groove of XIAP-BIR3, and these backbones are superimposed well with that of AVPI. The phenyl ring fused to seven-membered ring has a little contribution to the binding affinity because of steric effect, but five-membered ring is very important for the binding, especially the substituent introduced to it is more beneficial to form the stable complex than to eight-membered ring. The R-tetrahydronaphtyl group is more close to the hydrophobic residue Leu292, therefore, it facilitates Smac mimetics binding. Molecular dynamics simulations also show that the complexes of XIAP-BIR3 with Smac mimetics are very stable, both the backbones of XIAP-BIR3 and ligands keep stable, but only the orientations of substituents from SMb6 and SMc3 altered gradually. The hydrogen bonds between bicyclic core segment and Thr308 play an important role in maintaining the stabilities of the complexes. The binding free energies calculated by MM_PBSA method are in good agreement with the experimental results. The Smac mimetics binding to XIAP-BIR3 is mainly derived by non-polar interactions. Our results provide evaluable information for further designing and synthesizing the Smac mimetics.The primary innovations are as follows:1. We systematically investigated the nature of the purine riboswitch recognizing diverse metabolites specifically. We studied the interacations between riboswitch and a series of ligands to drive conlusions that:the specificity of riboswitch was determined by the position and category of bases in the binding pocket, and the surrounding bases had serious influence on the recognition. Only when the ligand forms strong Watson-Crick base pair interactions with the key bases, such as C74 (or U74) and U51, the purine riboswitch can recognize the pyrimidine and purine derivatives with specificity.2. We systematically studied the rules of the structures of diverse ligands influencing on the recognizing specificity. For the pyrimidine derivatives bearing the amino groups, the number of amino groups had no significant influence on the orientations in the binding pocket, while the position changes affected the binding affinity seriously. For the purine derivatives with small functional group, when the small functional group was introduced to the 1-,2-,6- or 8-postion respectively, the orientations of ligands could not change, but the binding affinity changed with the categories and positions of substitutents.3. We investigated the mechanism of inhibitor of apoptosis protein interacting with bicyclic and tricyclic core monovalent Smac mimetics. These mimetics adopted the more stable "extended conformation" to bind to XIAP-BIR3, and their bicyclic core segments played essential roles in the binding, but the modifications on the seven-membered ring had little contributions to the binding affinity, while the hydropbohic substituent introduced to five-membered ring could enhance the binding affinity significantly. The residues Thr308, Asp309, Gli314 and Trp323 were responsible for recognizing and binding the mimetics, especially Thr308 played an important role in contributing to the binding.