The human immunodeficiency virus, HIV, is a retrovirus. In other words, it integrates its RNA genome into the host DNA with the help of specialized proteins and enzymes. According to the CDC, approximately 1.1 million people were living with HIV in the United States by the end of 2015. HIV-1 gains entry to target cells by binding to the envelope glycoprotein gp120 and simultaneously binding to two co-receptors, CCR5 or CXCR4, which are essential co-receptors that facilitate HIV-1 entry (Brelot, and Chakrabarti 2559). Viruses that employ CCR5 are called R5-tropic viruses while viruses that employ CXCR4 are called X4-tropic viruses (Ray 151). CCR5 is one of the most commonly employed chemokine receptors that assist in the process of HIV-1 infection. It is a member of the ? -chemokines that are characterized by the two conserved cysteines that are adjacent to each other in the N terminus, hence the term CC chemokines. CCR5 aids in the search of leukocytes for the immune system (Brelot and Chakrabarti 2557).
Maraviroc is an antagonist of CCR5, meaning that it inhibits the function of the CCR5 co-receptor with the HIV-1 gp120 and it was approved in 2007 as a chemokine receptor inhibitor (Brelot and Chakrabarti 2556). The mechanism for maraviroc is still poorly understood but it is known to use allosteric modification. Due to its inhibiting function, it has been used as an HIV treatment to stop viral cells from replicating within the body. However, patients whose HIV uses the CXCR4 are not advised to take maraviroc.
The purpose of this work was to propose a ligand-binding site for chemokines and gp120. By providing a structure of the CCR5-Maraviroc complex, it was apparent that steric hindrances in the binding pockets as well as net charges aid in the process of concisely understanding the inhibiting mechanism behind maraviroc. In addition, these charge distributions and structural conformations are critical for HIV-1 co-receptor tropism.
Structure Comparison of CCR5 and CXCR4The crystal structure of CCR5-Maraviroc was determined at a resolution of 2.7 Å using X-ray crystallography and it was expressed in the organism Spodoptera frugiperda. CCR5 shares structural features with class A G protein-coupled receptor (GCPRs), which are membrane receptors that contain seven transmembrane ?-helices (I-VII), three extracellular loops (ECL1-3) as well as three intracellular loops (ICL1-3). The structure was compared to the structure of CXCR4 bound to IT1t, which is a small molecule inhibitor for CXCR4, to demonstrate what structural differences make CCR5 to be the preference for viral invasion. The structural comparison is shown in Figure 1.
Figure 1. Comparison of the CCR5-maraviroc complex with CXCR4. CCR5 is shown in blue, rubredoxin is light cyan, maraviroc as orange spheres and disulfide bonds are shown as yellow sticks. Zinc ions are shown as gray spheres. Image obtained from Science ECL2 is the largest loop in CCR5 and it forms a ?-hairpin as it is seen from the top of Figure 1A. Accounting for the stability of the extracellular loops (ECLs), there are two disulfide bonds that link Cys-101 and Cys-178 as well as Cys-20 with Cys-269, which hold the ECLs and N terminal in place and are represented as yellow sticks in Figures 1A, 1B and 1C.
However, there are differences that can be observed as well. In CCR5 there is a small ?-helix VIII whereas in CXCR4 the C terminus takes on a disordered form after helix VII and extends itself outwards (Figure D). This structural difference after helix VII is attributed to an ?-helical sequence in CCR5’s helix VIII that is modified in CXCR4. In the other hand, helix IV’s intracellular portion of CCR5 is shorter than that of CXCR4 by 1.5 turns. This portion of helix IV forms an ?-helix that exists as a ?-helix in CXCR4. In Figure 1D, ICL2 of CCR5 shows to have a two-turn ?-helix whereas in CXCR4 the ICL2 takes on an unstructured form. Phe-135 and Ala-136 in the ?-helix form hydrophobic interactions around the end of helix III with Leu-128 and Ala-129. This hydrophobic cluster allows for the stability of ICL2.
The binding pocket in CCR5 encompasses residues from helices I, II, III, V, VI and VII. The stability of the binding pocket lies on salt bridges, hydrogen bonds and hydrophobic interactions between residues, in addition to interactions with a water molecule that is located in the pocket area.
The difference in the size of the binding pocket for both co-receptors is visible in Figure 2. The CCR5 binding pocket was found to have a wider opening as well as a larger and deeper inner pocket (Figures 2A and 2B). This leads to no interactions between maraviroc and the extracellular loops (ECLs) of CCR5. In the other hand, the CXCR4 shows to have a narrower opening and tighter inner arrangement.
Figure 3. Comparison of the binding pockets of the CCR5-maraviroc complex and the CXCR4-IT1t complex. CCR5 is shown in blue, CXCR4 is shown in green. Maraviroc and IT1t are represented in stick configuration; maraviroc is shown in orange, IT1t is shown in pink. (A,D) demonstrate the width of the binding pocket opening for CCR5-maraviroc and CXCR4-IT1t complexes, respectively. (B,C) show the depth of the binding pocket for the ligand. (C,F) represent surface of CCR5 and CXCR4 through electrostatic potential; red represents the negative electrostatic potential and blue represents the positive electrostatic potential.
Another important difference is derived from the salt bridge that is formed between residues Asp-97 and Arg-183 in ECL2 which cause the ?-hairpin of ECL2 to move toward the binding pocket, accounting for a central placement and a binding pocket that is less deep compared to that of CCR5. This salt bridge among Asp-97 and Arg-183 is absent om CCR5 because of the presence of Tyr-89 and His-175. Therefore, the more covered feature of CXCR4’s binding pocket is due to the N terminus and the ECL2’s placement in the opening of the ligand binding pocket. However, it is this depth in the CCR5 structure that could facilitate proper binding when stable interactions are present during complex formation.
In the CCR5-maraviroc complex, there is a tropane group present, whose nitrogen was found to form a salt bridge with Glu-283. The nitrogen that forms the carboxamide hydrogen bonds to Tyr-251. There is a triazole group present whose amine moiety forms hydrogen bonds with Tyr-37 as well as the water molecule (Figure 3). Two fluorines are attached to the cyclohexane ring which form additional hydrogen bonds with residues Thr-195 and Thr-259. In the other hand, Maraviroc contains a phenyl group that forms a hydrophobic interaction with Tyr-108, Phe-109, Phe-112, Trp-248 and Tyr-251. This hydrophobic interaction with Trp-248 specifically is said to prevent its “activation-related motion”, which could make Trp-248 a target residue for drug development since it plays an important role in viral activation.
Besides Trp-248’s role in activation, Trp-248 and Tyr-244 are thought to play a major role in the stabilization of the CCR5-maraviroc complex. Because these two residues are conserved among class A GCPRs, their conformations in inactive states allow for a better understanding of the stabilization of CCR5-maraviroc. Both residues are in charge of taking on conformational changes in the ligand-binding pocket. It was observed that the conformations of these residues in the CCR5-maraviroc complex are very similar to those conformations taken in other inactive structures of GCPRs by the same residues. These inactive conformations are all different from the conformations during an active state.
Although maraviroc’s mechanism is not well understood, it is known to function through negative allosteric modification, meaning that its binding to CCR5 causes conformational changes which reduce the affinity of CCR5 to the glycoprotein gp120 which is essential for viral entry.
Figure 4. Key interactions in the CCR5-maraviroc complex. CCR5 residues are displayed in blue, maraviroc is displayed with orange carbons by stick representation. Oxygen is represented in red, nitrogen in dark blue, sulfur in yellow, fluorine in light cyan. Image obtained from Science.
The V3 loop is characterized by its ?-hairpin and is located in the glycoprotein gp120 which mediates viral fusion by binding to CD4 cells as well as a co-receptor. It has been recognized as a very important factor in co-receptor selectivity for the viral cell. The V3 loop has been shown to bind to the N-terminus of the co-receptor, CCR5 or CXCR4. Studies were carried out on the V3 region that shows that in X4-tropic viruses the V3 loop is more acidic than the V3 loop in R5-tropic viruses. These acidic residues in CXCR4 among which are Asp97, Asp-171, Asp-187, Asp 193 and Asp-262 are critical for ligand binding which renders them vital for HIV-1 infectivity.
However, in CCR5 these residues are replaced by uncharged residues, making it less acidic by using residues such as Tyr-89, Gly-163, Ser-179, Gln-188 and Asn-258, respectively. The N terminus of CXCR4 shows to be more acidic by having nine acidic residues while CCR5 only has three. This difference in the charges of co-receptor shows that charge distribution is of high importance to HIV-1 infectivity. This was supported by performing mutations to various uncharged residues which were Trp-86, Trp-94, Tyr-108, Trp-248 and Tyr-251 and were found to affect the binding of gp120 to CCR5 which proves that the net charge of the V3 loop plays a role in the co-receptor selectivity of the virus towards either co-receptor. These uncharged residues cluster together in the binding pocket of CCR5 (Figure 5) which could imply the binding site for gp120, demonstrating the importance of the availability of these residues for gp120 to bind to CCR5 and consequently lead to HIV entry into the target cell. Thus, this decision of HIV-1 strains to use the CCR5 receptor over the CXCR4 could be partially attributed to a preference of the virus to a more neutral or less acidic environment to bind to.
Figure 5. Mutations to uncharged residues Trp-86, Trp-94, Tyr-108, Trp-248 and Tyr-251 affected binding of gp120 to CCR5, demonstrating how the net charge is critical for co-receptor selectivity. Image generated by me using spdbv. PDB ID: 4MBS
The importance of this work could pave the way to the improvement of already existing treatment as well as innovative drug development using a structural approach that targets the key residues mentioned in this work as well as inhibiting certain CCR5 conformations to prevent HIV entry. A question that could help with life-changing drug development is the process behind selectivity of the virus to use either CCR5 or CXCR4. Given that these two receptors are structurally stable, there must be a portion of the HIV virus that varies per viral cell which allows for a preference of CCR5 over CXCR4. This proposal can be considered for future research purposes due to the high mutation rate that characterizes HIV. However, this answer remains unanswered as of today.
Nevertheless, the findings of this work increase the structural possibilities for understanding HIV tropism and by targeting said residues, entry and activation can be inhibited. The net charge of the V3 loop residues were found to be important for gp120 binding which, in turn, is critical for HIV infectivity. In addition, Trp-248 has shown to play a vital role in HIV tropism through gp120 binding, its stabilizing contribution that is shared among class A GCPRs as well as its role in activation. Trp-248 was of great importance in preventing activation when the phenyl group of maraviroc formed a hydrophobic interaction with it, demonstrating its possible activation-inhibitor properties.
The disulfide bonds hold the ECLs and the N-terminal in place by the strong covalent bonds of such. The ECLS, specifically ECL2, were also proven to be important for the binding pocket conformation that is taken upon the salt bridge formation between Asp-97 and Arg-183 mentioned earlier. As for the CCR5-maravirox complex, a variety of forces account for its stability in order to properly function as an inhibitor by implementing salt bridge formation between residues, hydrogen bonds among residues and the water molecule located between them as well as hydrophobic interactions, with the Phe-135 from maraviroc being of great importance.
The simultaneous collaboration of ECL2 and the N terminal of CCR5 were found to be critical for chemokine ligand recognition by interacting with the core of the chemokine. Lastly, the net charge distribution in the V3 loop of gp120 was found to be essential for HIV-1 tropism.
This finding raises the question of whether HIV-1 prefers less acidic environments, since it tends to use the CCR5 co-receptor whose V3 loop has been shown to be less than that of X4- tropic viruses. The answer to this question could open a new world of drug innovations by helping understand the HIV entry mechanism as well as the selectivity of this virus.
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