Molecule of the Month: Lenacapavir

A potent and long-acting drug that targets the HIV capsid

Lenacapavir (cyan) binds in a pocket between individual CA monomers in a HIV capsid hexamer (yellow), from pdb_00006v2f.
Lenacapavir (cyan) binds in a pocket between individual CA monomers in a HIV capsid hexamer (yellow), from pdb_00006v2f.
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The AIDS epidemic, which started in the early 1980s, is caused by human immunodeficiency virus (HIV), a retrovirus that attacks the immune system. Although there is currently no cure for HIV, antiretroviral therapy can suppress viral replication when taken consistently, preventing disease progression and transmission and allowing HIV-positive individuals to live long and healthy lives. Maintaining a strict and life-long daily medication regimen, however, can pose a challenge for many people living with HIV, and lapses in adherence can lead to viral proliferation and allow the virus to be transmitted. While the number of new HIV infections has dropped significantly since its peak in the 1990s, the AIDS epidemic persists globally, with an estimated 1.3 million people newly infected with HIV in 2024.

Discovering a drug that targets the capsid

For decades, HIV drug development focused on targeting viral enzymes such as reverse transcriptase, protease, and integrase, or on structural proteins on the viral surface, such as envelope protein. CA protein, which self-assembles to form a conical capsid protein shell around the viral genome, was not widely considered a "druggable" target. Starting in the late 1990s, however, a growing body of scientific studies from HIV researchers described the structure of CA and the capsid shell and showed that viral replication was dependent on the integrity of the capsid. These findings convinced a team at Gilead Sciences to initiate a program to discover and develop a capsid-targeting drug that could complement existing antiretroviral therapies.

Over the next ten years, Gilead scientists iteratively designed, modified, and tested thousands of capsid-binding compounds to optimize drug potency, stability, and bioavailability (some of these compounds are shown in the "Exploring the Structure" section below). The final result was a drug called lenacapavir, a first-in-class capsid inhibitor that was approved for treatment of multidrug-resistant HIV in 2022, and for pre-exposure prophylaxis (PrEP) in 2025. Lenacapavir's remarkably high potency and long half-life in the body allows for twice-yearly injectable dosing that dramatically improves adherence compared with daily oral antiretroviral regimens.

As shown in the illustration on the right, lenacapavir binds to the interface between two adjacent CA subunits (pdb_00006v2f). Studies have shown that lenacapavir is able to disrupt different stages of the HIV life cycle, most notably impacting viral import into the nucleus and subsequent integration of viral DNA into the host genome, as well as the assembly and maturation of newly formed viruses.

Cracking the capsid

Structural studies have provided new insights into lenacapavir's unique mechanism of action. Using electron cryotomography, researchers found that treatment of intact HIV capsids with lenacapavir causes capsids to rupture, with ruptures occurring first in areas of the capsid with the highest level of curvature. The walls of lenacapavir-treated capsids were observed to flatten during early time points and fragment over the course of the experiment. This process is shown in the animation on the left, created by Rachel Torrez in collaboration with Owen Pornillos (University of Utah). The animation was created using pdb_00009pry and pdb_00009y7j and their corresponding models in the EM Data Bank, EMD-71816 and EMD-72657.

Closer investigation into neighboring hexamers in targeted capsids revealed that lenacapavir binding induces a small and destabilizing rotational change between two hexamers. These changes occur at sites distal from the original lenacapavir binding site, demonstrating that the drug acts allosterically. Researchers hypothesize that lenacapavir binding induces mechanical strain on the capsid lattice, and as more lenacapavir molecules bind, the strain builds until capsid breakage occurs, disrupting viral replication. Premature rupture of the capsid has a secondary effect that likely leads to activation of the innate immune response and contributes to viral elimination.

Exploring the Structure

The development of lenacapavir

Scientists at Gilead Sciences tested numerous compounds enroute to discovering lenacapavir. Take a closer look at a few of the compounds that were synthesized and structurally characterized that helped to optimize lenacapavir's chemical structure. Shown in the JSmol interactive are compound 6 (pdb_00009pgs), compound 12 (pdb_00009pgt), compound 24 (pdb_00009pgv), compound 40 (pdb_00009pgu), and lenacapavir (pdb_00006v2f).

Topics for Further Discussion

  1. Explore other HIV and AIDS-related content on PDB-101.
  2. Take a closer look at the structure of the HIV capsid and build a paper model.
  3. Take a look at an illustration of a cell infected with HIV.
  4. Watch an animation that describes how different classes of anti-retroviral therapies work.

References

  1. pdb_00006v2f: Link JO, Rhee MS, Tse WC, Zheng J, Somoza JR, Rowe W, Begley R, Chiu A, Mulato A, Hansen D, Singer E, Tsai LK, Bam RA, Chou CH, Canales E, Brizgys G, Zhang JR, Li J, Graupe M, Morganelli P, Liu Q, Wu Q, Halcomb RL, Saito RD, Schroeder SD, Lazerwith SE, Bondy S, Jin D, Hung M, Novikov N, Liu X, VillaseƱor AG, Cannizzaro CE, Hu EY, Anderson RL, Appleby TC, Lu B, Mwangi J, Liclican A, Niedziela-Majka A, Papalia GA, Wong MH, Leavitt SA, Xu Y, Koditek D, Stepan GJ, Yu H, Pagratis N, Clancy S, Ahmadyar S, Cai TZ, Sellers S, Wolckenhauer SA, Ling J, Callebaut C, Margot N, Ram RR, Liu YP, Hyland R, Sinclair GI, Ruane PJ, Crofoot GE, McDonald CK, Brainard DM, Lad L, Swaminathan S, Sundquist WI, Sakowicz R, Chester AE, Lee WE, Daar ES, Yant SR, Cihlar T. Clinical targeting of HIV capsid protein with a long-acting small molecule. Nature. 2020 Aug;584(7822):614-618.
  2. pdb_00009pry, pdb_00009y7j: Dos Santos NFB, Lewis JA, Hansen M, Pereira MJB, Christensen DE, Sundquist WI, Ganser-Pornillos BK, Pornillos O. Lenacapavir allosterically remodels the HIV-1 capsid. bioRxiv [Preprint]. 2026 Jan 5:2026.01.05.697065.
  3. pdb_00009pgs, pdb_00009pgt, pdb_00009pgu, pdb_00009pgv: Canales E, Tse W, Schroeder SD, Chou CH, Liu Q, Zhang J, Lazerwith SE, Morganelli P, Saito RD, Brizgys G, Li J, Wu Q, Graupe M, Halcomb RL, Desai M, Cannizzaro C, Hu E, Perry JK, VillaseƱor AG, Somoza JR, Ferrao RD, Swaminathan S, Zheng J, Lu B, Mwangi J, Wang K, Subramanian R, Smith BJ, Rhodes G, Rowe W, Sauer D, Lad L, Papalia GA, Clancy S, Stepan GJ, Yu H, Sakowicz R, Shi B, Carr G, Bam RA, Tsai LK, Singer E, Hansen D, Mulato A, Yant SR, Cihlar T, Link JO. Discovery of Lenacapavir: First-in-Class Twice-Yearly Capsid Inhibitor for HIV-1 Treatment and Pre-exposure Prophylaxis. J Med Chem. 2025 Oct 23;68(20):21072-21094.
  4. von Schwedler UK, Stray KM, Garrus JE, Sundquist WI. Functional surfaces of the human immunodeficiency virus type 1 capsid protein. J Virol. 2003 May;77(9):5439-50.
  5. Pornillos O, Ganser-Pornillos BK, Kelly BN, Hua Y, Whitby FG, Stout CD, Sundquist WI, Hill CP, Yeager M. X-ray structures of the hexameric building block of the HIV capsid. Cell. 2009 Jun 26;137(7):1282-92. doi: 10.1016/j.cell.2009.04.063. Epub 2009 Jun 11. PMID: 19523676; PMCID: PMC2840706.
  6. Bester SM, Wei G, Zhao H, Adu-Ampratwum D, Iqbal N, Courouble VV, Francis AC, Annamalai AS, Singh PK, Shkriabai N, Van Blerkom P, Morrison J, Poeschla EM, Engelman AN, Melikyan GB, Griffin PR, Fuchs JR, Asturias FJ, Kvaratskhelia M. Structural and mechanistic bases for a potent HIV-1 capsid inhibitor. Science. 2020 Oct 16;370(6514):360-364.

March 2026, Janet Iwasa

http://doi.org/10.2210/rcsb_pdb/mom_2026_3
About Molecule of the Month
The Molecule of the Month series presents short accounts on selected topics from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. The series is currently created by Janet Iwasa (University of Utah).