The Structural Biology of HIV-1: Mechanistic and Therapeutic Insights

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The Structural Biology of HIV-1: Mechanistic and Therapeutic Insights REVIEWS The structural biology of HIV‑1: mechanistic and therapeutic insights Alan Engelman1 and Peter Cherepanov2 Abstract | Three-dimensional molecular structures can provide detailed information on biological mechanisms and, for cases in which the molecular function affects human health, can significantly aid in the development of therapeutic interventions. For almost 25 years, key components of the lentivirus HIV‑1, including the envelope glycoproteins, the capsid and the replication enzymes reverse transcriptase, integrase and protease, have been scrutinized to near atomic-scale resolution. Moreover, structural analyses of the interactions between viral and host cell components have yielded key insights into the mechanisms of viral entry, chromosomal integration, transcription and egress from cells. Here, we review recent advances in HIV‑1 structural biology, focusing on the molecular mechanisms of viral replication and on the development of new therapeutics. zoonotic Zoonotic HIV‑1 arose through several independent trans‑ had on our understanding of viral growth and on the Pertaining to a disease: an missions of simian immunodeficiency viruses during the development of new antiretroviral therapies. infection that can transfer past century1–3. Today, HIV‑1, along with its less wide‑ between animals and humans. spread cousin HIV‑2, infects more than 30 million peo‑ Viral entry CD4+ T cells ple worldwide. Both viruses belong to the Retroviridae, a The HIV‑1 envelope spikes comprise trimers of non- A subpopulation of T cells that viral family that has left numerous scars of ancient infec‑ covalently linked heterodimers consisting of the surface express the CD4 receptor. tions in mammalian genomes; indeed, derelict retroviral glycoprotein gp120 and the transmembrane glyco­protein These cells aid in immune sequences constitute as much as 8% of our ‘own’ DNA4. gp41 (REFS 7–9). When triggered, these spikes initiate a responses and are therefore The evolutionary success of this family is in contrast to cascade of conformational changes that culminates in also referred to as T helper cells. its deceptive simplicity: HIV‑1 can persistently infect fusion between the viral and host cell membranes and humans by subverting the innate and adaptive immune release of the viral core into the cytoplasm. HIV‑1 pri‑ systems, despite encoding only 15 mature proteins. marily infects CD4+ T cells and macrophages. An initial Viral replication at the cellular level proceeds through interaction between gp120 and the surface receptor CD4 a series of steps that starts when a virus productively induces the formation of a bridging sheet between the engages cell surface receptors and ends when nascent inner and outer domains of the gp120 monomer, expos‑ particles mature into infectious virions (FIG. 1). During ing the binding site for a second cell surface molecule, this process, HIV‑1 exploits a myriad of cellular factors typically CC-chemokine receptor 5 (CCR5)10–12 (FIG. 1, to replicate, whereas host restriction factors fight to sup‑ step 1). Engagement of this co-receptor leads to inser‑ press this replication5,6. The mainstream highly active tion of the fusion peptide, located at the amino termi‑ 1Department of Cancer antiretroviral therapy (HAART) drug cocktails that nus of gp41, into the cell membrane. This event triggers Immunology and AIDS, are primarily used to target the reverse transcriptase significant rearrangements of the trimerized amino- Dana-Farber Cancer Institute, (RT) and protease (PR) enzymes potently suppress viral and carboxy‑terminal heptad repeat sequences within Boston, Massachusetts 02215, loads and transmission rates, but complications can arise gp41, the formation of a six-helix hairpin structure USA. 2Cancer Research UK London from compound toxicity and the emergence of resistant and the apposition and fusion of the viral and host cell 13–15 Research Institute, Clare Hall strains (BOX 1). Advances in structural biology can aid membranes (FIG. 1, step 2). Laboratories, South Mimms, the development of next-generation compounds that are Initial cryo-electron tomography studies provided cru‑ Hertfordshire EN6 3LD, UK. active against previously exploited targets, and can also cial glimpses of the HIV‑1 envelope and its associated e-mails: alan_engelman@ help define new drug targets and boost the effectiveness conformational flexibility7,8, although the low-resolution dfci.harvard.edu; peter.cherepanov@ of vaccination strategies. This Review proceeds step‑ models that were generated left many key aspects of 9,16,17 cancer.org.uk wise through the HIV‑1 replication cycle, highlighting the native structure unresolved . Higher-resolution doi:10.1038/nrmicro2747 the impact that major structural biology advances have crystallographic studies using engineered HIV‑1 NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 279 © 2012 Macmillan Publishers Limited. All rights reserved REVIEWS 13 Maturation 1 Attachment Tetherin Protease inhibitors 12 Release Fusion inhibitors Env Accessory viral proteins Vif Gag 11 CD4 Vpu Rev Gag Pol Budding CCR5 inhibitors Tat Assembly 9 ALIX, 10 Translation ESCRT-I, ESCRT-III AAA CCR5 PIC AAA 2 5 Gag Pol Gag 9 Fusion APOBEC3G Nuclear import Translation SAMHD1 8 TRIM5 NRTIs, Nuclear AAA export NNRTIs CRM1 AAA INSTIs AAA Uncoating AAA AAA 6 3 AAA 4 Integration Reverse LEDGF transcription AAA 7 Transcription RNA Pol II P-TEFb 5ʹ LTR 3ʹ LTR Nucleus Figure 1 | Schematic overview of the HIV‑1 replication cycle. Those host proteins that have a role in the replication Nature Reviews | Microbiology cycle and are discussed in the text are indicated. The infection begins when the envelope (Env) glycoprotein spikes engage the receptor CD4 and the membrane-spanning co‑receptor CC-chemokine receptor 5 (CCR5) (step 1), leading to fusion of the viral and cellular membranes and entry of the viral particle into the cell (step 2). Partial core shell uncoating (step 3) facilitates reverse transcription (step 4), which in turn yields the pre-integration complex (PIC). Following import into the cell nucleus (step 5), PIC-associated integrase orchestrates the formation of the integrated provirus, aided by the host chromatin-binding protein lens epithelium-derived growth factor (LEDGF) (step 6). Proviral transcription (step 7), mediated by host RNA polymerase II (RNA Pol II ) and positive transcription elongation factor b (P-TEFb), yields viral mRNAs of different sizes, the larger of which require energy-dependent export to leave the nucleus via host protein CRM1 (step 8). mRNAs serve as templates for protein production (step 9), and genome-length RNA is incorporated into viral particles with protein components (step 10). Viral-particle budding (step 11) and release (step 12) from the cell is mediated by ESCRT (endosomal sorting complex required for transport) complexes and ALIX and is accompanied or soon followed by protease-mediated maturation (step 13) to create an infectious viral particle. Each step in the HIV‑1 life cycle is a potential target for antiviral intervention165; the sites of action of clinical inhibitors (white boxes) and cellular restriction factors (blue boxes) are indicated. INSTI, integrase strand transfer inhibitor; LTR, long terminal repeat; NNRTI, non-nucleoside reverse transcriptase inhibitor; NRTI, nucleoside reverse transcriptase inhibitor. glycoprotein constructs have been instrumental in devel‑ However, several groups recently described patient- oping entry inhibitors and elucidating the mechanistic derived gp120‑reactive antibodies with broad HIV‑1 basis of virus neutralization by antibodies. Recent stud‑ neutralization activity20–24. One group in particu‑ ies have highlighted the striking flexibility of the core lar took a structure-based approach to stabilize the gp120 structure, which allows extreme conformational CD4‑bound conformation of gp120 using disulphide changes following CD4 engagement without destabiliz‑ bonds, and redesigned its surface to mask positions ing the interaction with gp41 (REFS 12,18). CD4 binds that are exterior to the CD4-binding site21,22. Using one gp120 at a depression formed between the inner and such construct as bait and peripheral mononuclear cells Cryo-electron tomography A technique in which a outer domains, where the CD4 residue Phe43 partially from patients with AIDS, they isolated B cell clones 10 specimen, embedded in fills a hydrophobic cavity (FIG. 2a). Small molecules that produced antibodies with remarkably broad neu‑ vitreous ice, is imaged from designed to bind and extend further into this pocket tralizing activity. Structural characterization of these multiple angles using electron display antiviral activity; thus, increasing the affinity of antibodies revealed that, when bound to gp120, the microscopy. The resulting such molecules for gp120 might lead to the development heavy chains of the immunoglobulins mimic CD4 images are then combined 19 (FIG. 2a,b) to reconstruct the of clinically useful inhibitors . , with their epitopes almost precisely over‑ three-dimensional structure Most antibodies directed against gp120 are strain lapping the primary CD4‑binding site on gp120 of the specimen. specific and, moreover, fail to neutralize the virus. (REFS 22,25). These results define the structural basis 280 | APRIL 2012 | VOLUME 10 www.nature.com/reviews/micro © 2012 Macmillan Publishers Limited. All rights reserved REVIEWS Box 1 | a Highly active antiretroviral therapy CD4 (D1) Approximately 30 different drugs targeting four different steps in the
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