Researchers solve high-resolution structure of HIV co-receptor CCR5
By Andreas von Bubnoff
The fact that a drug is approved means—in most cases—that it works. But its mere approval doesn’t guarantee that anyone knows exactly how it works.
Take, for example, the antiretroviral (ARV) drug Maraviroc: It belongs to a class of ARVs called “entry inhibitors” because it keeps HIV from entering its target cells by binding to CCR5, one of the co-receptors HIV uses to slip into CD4+ cells.
Researchers know that Maraviroc binds to a part of CCR5 distinct from the part bound by HIV’s gp120 protein, so it isn’t merely outcompeting gp120 for access to CCR5. But exactly where Maraviroc binds to CCR5, and how Maraviroc binding renders CCR5 incapable of binding to HIV, has so far remained a mystery.
Now, a team of researchers led by Beili Wu, a professor at the Shanghai Institute of Materia Medica, has determined the structure of CCR5 bound to Maraviroc and appears to have solved this lingering mystery. To do so, Wu and colleagues made a protein crystal of the CCR5-Maraviroc complex and used X rays to determine its structure at a resolution of 2.7 Ångstroms—sufficient to pinpoint the interactions between individual atoms (Science 341, 1387, 2013).
The structure confirms that Maraviroc binds to CCR5—a cell surface protein that crosses the cell membrane several times—at a site distinct from that bound by HIV gp120. It reveals that Maraviroc’s binding site is deep inside CCR5, and binding by the drug stabilizes CCR5’s structure in a manner that makes it incapable of binding to HIV gp120. “Nobody knew where [Maraviroc] binds,” Wu says. “We found it binds very deeply into the receptor. I think that’s surprising.”
The finding, Wu says, could lead to the development of drugs that bind CCR5 more tightly and are therefore more effective than Maraviroc. Also, knowledge of the CCR5 structure might now enable researchers to develop a drug that blocks HIV entry by competing for the same site on CCR5 that’s used by HIV gp120, Wu adds.
While the main receptor HIV uses to enter cells is CD4, CCR5 is one of two co-receptors HIV variants use to enter cells. The other is CXCR4. During the early stages of HIV infection, most HIV variants use CCR5 to enter cells. But HIV variants that emerge in the later stages of infection often use CXCR4 to enter CD4+ cells. This switch is believed to expand the range of target cells HIV can infect and to contribute to the progression of HIV infection to AIDS.
Wu, who solved the structure of CXCR4 bound to an inhibitor when she was a postdoc at The Scripps Research Institute in La Jolla (Science 330, 1066, 2010), says that now that the structures of both co-receptors are available, it should be possible to develop drugs that inhibit HIV binding to both CCR5 and CXCR4. “We are working on a structure-based drug design to get an idea of how to make new drugs to inhibit both [co-]receptors,” she says.
A comparison of the new CCR5 structure to CXCR4, Wu says, shows small differences in the charge and position of atoms in the so-called “ligand binding pocket” of the two proteins. This pocket binds to a stretch of gp120 called V3 (see image, below), which determines whether HIV prefers to bind to CCR5 or CXCR4 to enter cells. Those differences may be what determines what kind of HIV variant can bind the two co-receptors, Wu says, adding that she was surprised that the differences were so small. This insight may now enable researchers to better understand just how the virus switches from preferring CCR5 early in infection to CXCR4 later in infection.
This image captures the predominant movement of an HIV-1 gp120 protein and the attached sugar chains during 30 nanoseconds. It was calculated by a computer simulation of the interactions of all of the 7,500 atoms and roughly 320,000 water molecules that surround this gp120 protein. The gold ribbon surface illustrates the range of movement for the protein with the outer extremes in red. The gold dotted surface illustrates the range of movement for the sugars (red sticks). The image was generated as part of a project aimed at understanding the effect of sugars on the dynamics of the gp120 protein and in particular the V3 loop, which can be seen extending downwards at the bottom. The focus on the V3 loop is due to its important role in determining whether a specific virus uses the CXCR4 or CCR5 chemokine receptor for cell entry. Image courtesy of Natasha Wood, South African National Bioinformatics Institute, University of the Western Cape.
Even though it’s been known since 1996 that HIV needs to also bind to CXCR4 or CCR5 to enter cells, it took until 2010 to determine the structure of CXCR4, and the structure of CCR5 has been determined only now. One reason it took so long, Wu says, is that both proteins are G-protein coupled receptors (GPCRs), a class of proteins that is notoriously unstable and therefore difficult to crystallize.
To make CCR5 more stable, Wu and colleagues replaced the most flexible part of CCR5 with a more rigid protein, a common trick in structural biology. CCR5 was especially challenging, Wu says, because the rigid replacement proteins that had previously worked for other GPCRs such as CXCR4 didn’t work for CCR5. So Wu and colleagues had to find a new one. Another challenge: getting sufficient amounts of the CCR5 protein to make crystals.
Now that they know how to produce large amounts of high quality CCR5, Wu says, they can use it as an immunogen in a vaccine to induce antibodies that might keep HIV from binding to CCR5 and invading cells.
P. J. Klasse, a virologist at Weill Cornell Medical College in New York City who was not connected to the study, says he was impressed by the quality of the study. “They managed to solve the structure to a very high resolution,” says Klasse, who wrote a commentary on the finding in the same issue of Science. He says the finding now enables researchers to design better CCR5 inhibitors that bind the protein more strongly than Maraviroc and perhaps perturb its structure in a different way, making it harder for the virus to escape.
Still, Klasse adds, to better understand just how HIV gp120 interacts with CCR5 to enter cells in the absence of Maraviroc, it would be valuable one day to know the structures of the CCR5 co-receptor both when it is free and when it is bound to CD4-bound gp120 (in the absence of Maraviroc).
That, Wu says, is one of the things she plans to do next.