Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations

Abstract

HIV-1 protease is an essential enzyme in the life cycle of the HIV-1 virus. The conformational dynamics of the flap region of the protease is critical for the ligand binding mechanism, as well as for the catalytic activity. The monoclonal antibody F11.2.32 raised against HIV-1 protease inhibits its activity on binding. We have studied the conformational dynamics of protease in its free, inhibitor ritonavir and antibody bound forms using molecular dynamics simulations. We find that upon Ab binding to the epitope region (residues 36-46) of protease, the overall flexibility of the protease is decreased including the flap region and the active site, which is similar to the decrease in flexibility observed by inhibitor binding to the protease. This suggests an allosteric mechanism to inhibit protease activity. Further, the protease mutants G40E and G40R are known to have decreased activity and were also subjected to MD simulations. We find that the loss of flexibility in the mutants is similar to that observed in the protease bound to the Ab/inhibitor. these insights highlight the role played by dynamics in the function of the protease and how control of flexibility through Ab binding and site specific mutations can inhibit protease activity.The HIV-1 protease belongs to the family of aspartyl protease. It cleaves the newly synthesized polyproteins, which is the vital step to create the mature protein components of an infectious HIV-1 virus 1 . Thus, HIV-1 protease is an essential enzyme in the life-cycle of the HIV-1 virus and a potential target for the structure-based drug design. There are several commercial drugs available in the market against the HIV-1 protease. The success rate of these drugs is low due to the occurrence of drug-resistant mutations in the HIV-1 protease 2 . For example, the thermodynamic integration (TI) and MD simulation studies by Chen and his group suggested that there is a change in the shape and conformation of the binding pocket upon certain drug-resistant mutations and this consequently reduces the binding affinity of inhibitor 3 . Also, conventional method of drug delivery targets active sites and many enzymes with related function may have very similar active sites. This may cause adverse side-effects. Therefore, there is a requirement to generate new generation drugs that can function away from active-site and these are allosteric drugs 4-7 . To identify a new target on HIV-1 protease, there is a need to understand the complete structure and dynamics of HIV-1 protease to inhibits its enzymatic activity. The HIV-1 protease is a homodimeric enzyme with each monomer comprising of 99 amino-acid residues 8 . The active site (residues Asp25, Thr26 and Gly27 from both chains A and B) of the protease is covered by two flaps (residues 43-58) from each chain 9,10 . F11.2.32 is a monoclonal antibody (mAb) raised against the HIV-1 protease. The peptide P36-46 ( 36 MNLPGRWKPKM 46 ) corresponding to the epitope/elbow region of the protease binds to the complementarity determining regions (CDRs) of ...

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“…Meanwhile, these methods can facilitate the ease of finding antiviral drugs for SARS-CoV-2[36]. In the case of HIV-1 protease, these were applied to find the loss of flexibility in the mutants which can inhibit protease activity[37].…”

Understanding The Mechanism of Mutant HIV-1 Protease Resistance Against Darunavir Using Molecular Dynamic Study

“…In contrast, the exibility of the ap-tip region in chain-B (residues Gly51-Phe53) of MUT-Pr-D was remarkably increased compared with that of WT-Pr-D. It has been shown that increasing the ap-tip exibility facilitate opening of the active-site gate, which consequently facilitate releasing the inhibitor from active-site 10,12,63 . The highly affected residues as a result of mutations in both WT-Pr and MUT-Pr complexes were illustrated by superposed 20 trajectory structures, with 10 ns intervals (Fig.…”

“…The ap-tips are glycine-rich domains with hairpin structure, which control the access of substrate/inhibitor to the activesite 7 . It has been shown both computationally and experimentally that the HIV-1 PR has three possible that are classi ed based on the distance between two ap-tips [8][9][10][11][12] . In the ligand-bound form, the aptips take a downward conformation relative to the active-site (closed state), while the free form permanently takes a semi-open conformation 13,14 .…”

“…The Asp25, Thr26 and Gly27 residues form the catalytic site in both chains 4 . HIV-1 PR has six main structural segments including fulcrum (A|B: [11][12][13][14][15][16][17][18][19][20][21][22], active-site (A|B:23-30), ap-elbow (A|B:35-42), ap-tip (A|B:43-58), cantilever (A|B:59-75) and interface (A|B:95-99) (Fig. S1) 6 .…”

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“…Lopinavir is an inhibitor of Human Immunodeficiency Virus 1 (HIV-1) protease (19). The metabolism of lopinavir can be delayed by ritonavir to enhance the anti-HIV-1 effect of lopinavir; therefore, these two drugs are often used in combination (20).…”