Molecular Dynamics Studies On The Drug/Gene-Carriers Interactions

Molecular dynamics(MD)has been widely adopted in drug/gene delivery to provide explanations for drug/gene delivery experimental results and to optimize the design of drug/gene delivery systems.MD simulation has the potential to become an important tool that facilitates the development of nanomedicine and gene therapy.Our research group has developed many successful drug/gene delivery systems.For example,our recent work in Nature Nanotechnology reported y-glutamyl transpeptidase(GGT)-responsive polymer-drug conjugate PBEAGA18-CPT5 and proposed a new mechanism called active penetration of nanomedicine.However,due to various factors such as the lack of real-time tracking and characterizing experimental methods and/or tools,the dynamics and mechanisms are still unclear.Therefore,this thesis has carried out molecular dynamics simulation studies on several of those delivery systems,aiming at understanding the mechanisms and dynamics for further optimization and rational design of drug/gene delivery systems.The first chapter introduced the methods and algorithms of MD simulation,including the basic workflow,a brief introduction of force field used in the biological systems,etc.Molecular docking and molecular mechanics-Poisson Boltzmann surface area calculation(MM-PBSA)method of free energy calculation were also introduced.The relevant literature of MD simulation used in drug/gene delivery systems were briefly introduced.The second chapter adopted MD simulation to study the effects of the modification of the surface lysine residues of bovine serum albumin(BSA)with phenethyl isothiocyanate(PEITC).The purpose of this modification of BSA was to improve the the paclitaxel(PTX)loading and to improve the pharmacokinetic properties.The experimental results showed that BSA-PEICT35 conjugates(i.e.,on average,one BSA was chemically modified with 35 PEITC molecules)effectively loaded PTX and formed highly stable BSA-PEITC35/PTX nanoparticles.Compared with BSA/PTX nanoparticles formed by native BSA and PTX,BSA-PEITC35/PTX achieved higer drug delivery efficiency.Molecular docking between drugs and carriers were performed on BSA/PTX and BSA-PEITC35/PTX.The MM-PBSA method was used to calculate the binding free energies of BSA/PTX and BSA-PEITC35/PTX.The simulation showed that compared with the lysine residues,the modified lysine of PEITC improved the binding affinity for PTX,leading to the more stable loading of PTX.The third chapter studied our newly developed fusogenic lipidic polyplex gene delivery system,which could fusion with the cell membrane to deliver polyplex particles into the cytosol.Molecular dynamics simulation was adopted to study the mechanisms of the membrane fusion of liposomes.The lipid layer of the lipidic polyplexes was composed of distearoyl-phosphatidylethanolamine-polyethylene glycol 2000,dioleoylphosphatidylethanolamine and succinate monoester cholesterol(CHEMS).The in vitro experiments showed that the lipidic polyplexes with a high ratio of CHEMS were more difficult to fusion with the cell membrane.In this chapter,three lipidic membranes with different lipid ratios consistent with the experiments were constructed,and the binding capacity of membranes with different CHEMS contents to sodium ions in solution was calculated.The MD simulation results showed that the lipidic polyplexes with a higher proportion of CHEMS had stronger adsorption capacity for sodium ions,which bound more water and formed water-cushion;the higher CHEMS content also reduced the lipid layer fluidity.Because the fusion requires the interaction between the lipid layer and cell membrane and shape adjustment and change of the lipid layer,the above two factors may account for the reduced fusion at high ratios of CHEMS.The fourth chapter adopted MD simulation to study the effects of charge density and hydrophobicity of polycations on the complexation of polycations and nucleic acids and the stability of the formed complexes.Our group synthesized a series of cationic polymethacrylates gene carriers with different charge densities,including poly[(2-(dimethylamino)ethyl methacrylate](denoted as A100)and a copolymer of 2-(tetramethyleneimino)ethyl methacrylate and 2-(diisopropyl-amino)ethyl methacrylate at a 75:25 feed molar ratio(denoted as B75D25).The charge density of B75D25 is lower than that of A100.The previous experiment showed that compared to the A100/nucleic acid complex,the B75D25/nucleic acid complex showed higher gene transfection efficiency.In this chapter,we used MD simulation to explore the complexation processes of B75D25/DNA and A100/DNA,and described the complexation processes and the corresponding complex structures.The MD results showed that the low-charge-density B75D25s bound to DNA and formed multi-layer structure around DNA,which would effectively cover and protect DNA.In contrast,high-charge-density A100s bound to DNA and formed loose single-layer structure around DNA.The MD results showed that the stability of B75D25/DNA complex stemed mainly from the hydrophobic interactions among B75D25 polymers.The fifth chapter studied the effect of core molecule topologies on the properties of poly-L-lysine(PLL)dendrimers.Our group synthesized PLL dendrimers with planar shaped perylenediimide(PDI)and cubic shaped polyhedral oligomeric silsesquioxane(POSS)as core-forming molecules.There are differences in the topologies of POSS and PDI.This chapter used molecular dynamics simulation methods to study the structures of POSS-PLL and PDI-PLL from G1 to G7 and used different methods to analyze the differences in their properties,including the shape and size,density distribution,hydrogen bonding,interfacial water,self-diffusion coefficient,internal water,the proportion of surface atoms,proportion of buried atoms.The effects of nuclear topological differences on high-generation PLL dendrimers are generally weaker than those on low-generation PLL dendrimers.The sixth chapter studied the effects of the compositions of GGT-responsive polymer-camptothecin conjugate on its GGT sensitivity.Our group synthesized GGT-responsive polymer-drug conjugate PBEAGA18-CPT5 by the polymerization of 2-(1-?-glutamyl-l-a-aminobutyrylamino)ethyl acrylamide(BEAGA)monomer and methacrylated camptothecin(MMA-CPT)monomer.Previous experiments showed that the enzyme sensitivity of PBEAGA18-CPT5 was much higher than that of PBEAGA18-CPT2,while PBEAGA23 showed the lowest sensitivity.In this chapter,we adopted MD simulation to study the bindings of the polymers mentioned above to GGT.The MD simulation results showed that the probability of catalysis reaction for PBEAGA18-CPT5/GGT was the strongest,while the probability of catalysis reaction for PBEAGA23/GGT was the weakest.In comparison to PBEAGA18-CPT2 and PBEAGA23,PBEAGA18-CPT5 underwent a clear intramolecular collapse transition from a relatively open structure to a compact one due to the hydrophobic interactions of MMA-CPT units.The compact structure of PBEAGA18-CPT5 facilitated the close contact of y-glutamyl moity of the polymer to the active site of GGT,thereby increasing the chance of the catalysis reaction.