Molecular Dynamics Simulation Studies On The Mechanism Of Neutralizing HIV-1 Virus By A Series Of Antibodies Targeting Gp120

It is well known that HIV virus leads to AIDS,which seriously threatens public health.Although ART(antiretroviral therapy,ART)has reduced the death toll of AIDS patients and improved their quality of life for more than 30 years,there have been no available drugs preventing and eliminating AIDS.To design and produce a safe and effective HIV vaccine becomes the necessary demand of the modern society.To design and elicit broadly and potently neutralizing antibodies is a key pathway of developing vaccines.At the present,many b NAbs have been isolated and identified.Among these b NAbs,lots of antibodies target HIV-1 gp120.Although crystal structures of these b NAbs in complexion with gp120 have been reported,it is far from enough to understand the mechanism of the structural rearrangements in gp120 and inhibiting HI V infection,affected by these b NAbs,only based on the static structural information.In view of the special advantage of molecular dynamics simulation(MD)to sample conformational ensemble of the macromolecule,applying MD simulations combined with various analytical methods studies the interactions between gp120 and these b NAbs,which can reveal the molecular mechanism of neutralizing HIV virus and inhibiting the entry of the virus into host cells by antibodies.The detailed research primarily includes the following four aspects:1.The study of the molecular mechanism of the broad and potent neutralization of HIV-1 by VRC01.The first step of HIV-1 infecting host cell is the binding of gp120 and CD4.Thus,CD4 bs of gp120 is an important target for antibody design.Moreover,CD4 bs antibodies are also an important class of anti-HIV antibodies.VRC01 is a CD4 bs antibody and has about 90% neutralization breadth.Additionally,VRC01 has been on clinical trial.Based on its importance,we performed molecular dynamics simulations for apo-VRC01,apo gp120,and the gp120-VRC01 complex to study the molecular mechanism of neutralizing HI V virus by the antibody.For gp120,residue energy decomposition analysis showed that the hotspot residues Asn280,Lys282,Asp368,Ile371,and Asp457 are located in three primary loops,including the CD4-binding loop,loop D,and loop V5.For VRC01,the hotspot residues Trp47,Trp50,Asn58,Arg61,Gln64,Trp100,and Tyr91 are located at the heavy chain and light chain of the antibody,respectively.By decomposing the binding free energy into different components,intermolecular van der Waals interactions and nonpolar solvation were found to dominate the binding process.Principal component analysis of loops D and V5,which are related to neutralization resistance,indicated that the binding of VRC01 makes loops D and V5 stable.Furthermore,the conformational changes of N-terminus Glu1 of VRC01 altered the orientations of Asn461 and Asn462.This information can provide the valuable references for the design of anti-HIV-1 antibodies.2.VRC01-class antibodies are the largest class among identif ied bn Abs and include VRCPG-04 and VRC23 besides VRC01.Except for this class of antibodies,CH235 is also an important CD4 bs antibody and it has more than 90% neutralization breadth.Thus,do the two classes of antibodies have similar neutralization mechanism? Why are their neutralization abilities different? To compare the molecular mechanisms of neutralizing HI V-1 virus by the two classes of antibodies,the second part of this thesis explained the molecular mechanisms of broadly neutralizing HI V-1 by the two classes of antibodies including CH235 and VRC01-class antibodies such as VRC01,VRCPG-04,and VRC23 by molecular dynamics simulations.The calculation of binding free energy shows gp120 and CH235 have the most favorable association.The binding affinity of gp120 and VRC01 is slightly weaker than that of gp120 and CH235.The complex of gp120 and VRC23 is the most instable.The analysis of residue energy decomposition shows that loops D and V5,CD4 binding loop,and bridging sheet favorably contribute to the binding of gp120 and these b NAbs.Moreover,loops D and V5 are the most important regions.Val96-Leu100 C region of heavy chain of CH235,Asn97-Trp100 B region of heavy chain of VRC01,Tyr98-Trp100 D region of heavy chain of VRC-PG04 and Arg97-Trp100 C region of heavy chain of VRC23 are involved in favorable hydrogen bonds with loop D.These hydrogen bonds play determinative roles in the interactions of loops D and V5 of gp120 with these b NAbs,resulting in the broad neutralization ability of these b NAbs.However,different strengths of these hydrogen bonds cause discriminating neutralization ability of these b NAbs.This study identifies the origin of broad and discriminated neutralization ability of b NAbs such as CH235,VRC01,VRC-PG04,and VRC23.3.The study of the molecular mechanism of broadly neutralizing HIV-1 virus by coreceptor binding site X5 and 17 b.The coreceptor binding site plays an important role in HIV entry into host cell,moreover,it primarily consists of bridging sheet and loop V3 and its sequence is highly conserved.Thus,the coreceptor binding site is a promising and especially attractive target for the design of antibody and small molecular inhibitor.X5 and 17 b are representative of coreceptor binding site antibodies.The study of the interactions of X5 and 17 b with gp120 will be helpful for understanding in depth the mechanism of inhibiting HIV-1 entry into host cell by coreceptor binding site antibodies.Here,we performed molecular dynamics simulations for the complexes of X5 and 17 b with gp120 and CD4 to study the mechanisms of broadly neutralizing HIV-1 by X5 and 17 b.The simulated results indicate that X5 and 17 b have effects on CD4 and coreceptor binding sites.When the simulated systems are with or without CD4,X5 and 17 b have different effects on CD4 binding site.Specifically,when only the antibodies bind gp120,the binding of the antibodies increases the flexibilities of CD4 binding loop,reduces the contents of ?-sheet of loop V1/V2 and increases the distances between ?20/?21 and CD4 binding loop.These changes of CD4 bs are unfavorable for gp120-CD4 binding.When gp120 binds CD4,the binding of CD4 dominates the conformational changes of CD4 bs and the binding of the antibodies is slightly favorable for gp120-CD4 binding.The binding of the antibodies has consistent influence on the region adjacent to loop V3 despite the simulated systems with or without CD4.The binding of the antibodies enhances the interactions of the region adjacent to loop V3 with other region of gp120 and with the antibodies,which are unfavorable for the conformational rearrangements of the region adjacent to loop V3 and further binding the coreceptor.Thus,X5 and 17 b broadly neutralize HIV-1.Additionally,we also find that the interactions of loop V3 and bridging sheet with X5 lead to the close motion of loop V3 in CD4 and X5 bound form,which further block the information communications of loop V3 and other regions of gp120 and influence the rearrangements in gp120.These results obtained from this study provide the guidance in the design of the vaccines targeting the coreceptor binding site.4.The mediated mechanism of the glycans on the interactions of gp120 with CD4 and with antibody.The glycans are not only important components of gp120,but also mediate neutralization ability of many CD4 bs antibodies.Thus,the glycans are important targets of neutralizing antibodies and have been recognized as indispensable components of present and further immunogen design.234 and 276 gp120 glycans can regulate neutralization ability of many antibodies,which suggest that 234 and 276 gp120 glycans play very key roles in neutralizing the virus by the antibodies.Thus,we studied how 234 and 276 gp120 glycans mediate gp120-antibodies and gp120-CD4 interactions by molecular dynamics simulations.Our analysis results reveal that 276 gp120 glycan can enhance gp120-CD4 and gp120-antibody interactions through hydrogen-bonds links of the glycan with CD4 and antibody.234 gp120 glycan primarily reinforces gp120-antibody interactions and weakly affects gp120-CD4 interactions by its link with Phe93-Trp96,Lys227-Gly235,Glu268-Ser274 and Arg480-Leu483 regions of gp120 and Val27-Asn28 and Asp73-Ser77 regions of heavy chain of the antibody.The cooperation of two glycans signif icantly enhances gp120-CD4 and gp120-antibody associations.Enhanced associations between gp120 and antibody are attr ibuted to the fact that 234 gp120 glycan leads to move upward of two glycans and the variable region of heavy chain.This results in the hydrogen-bonds interactions of 276 gp120 glycan and CD4 are signif icantly weakened,which are favorable for the interactions of CD4 and loop V5.Thus,gp120-CD4 interactions are enhanced and the conformations of loop V5 open.The information obtained in this study can provide the guidance for the design of the vaccines targeting the glycans.Overall,in this thesis we investigated the mechanism of broadly neutralizing HIV-1 by the antibodies targeting CD4 and coreceptor binding sites of gp120 from the molecular level,and identified key structural features of these antibodies with broadly neutralizing function.Then,this thesis also indicated the glycans play key roles in gp120-CD4 and gp120-antibodies interactions.This information provides importantly theoretical and practical values.