5YC0 | pdb_00005yc0

Crystal structure of LP-46/N44

PDB DOI: https://doi.org/10.2210/pdb5YC0/pdb

Classification: VIRAL PROTEIN/INHIBITOR
Organism(s): Human immunodeficiency virus 1
Mutation(s): No

Deposited: 2017-09-05 Released: 2018-02-14
Deposition Author(s): Zhang, X., Wang, X., He, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.256 (Depositor), 0.262 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Exceptional potency and structural basis of a T1249-derived lipopeptide fusion inhibitor against HIV-1, HIV-2, and simian immunodeficiency virus

Zhu, Y., Zhang, X., Ding, X., Chong, H., Cui, S., He, J., Wang, X., He, Y.

(2018) J Biological Chem 293: 5323-5334

PubMed: 29425101 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.RA118.001729
Primary Citation Related Structures:
5YC0

PubMed Abstract:
Enfuvirtide (T20) is the only viral fusion inhibitor approved for clinical use, but it has relatively weak anti-HIV activity and easily induces drug resistance. In succession to T20, T1249 has been designed as a 39-mer peptide composed of amino acid sequences derived from HIV-1, HIV-2, and simian immunodeficiency virus (SIV); however, its development has been suspended due to formulation difficulties. We recently developed a T20-based lipopeptide (LP-40) showing greatly improved pharmaceutical properties. Here, we generated a T1249-based lipopeptide, termed LP-46, by replacing its C-terminal tryptophan-rich sequence with fatty acid. As compared with T20, T1249, and LP-40, the truncated LP-46 (31-mer) had dramatically increased activities in inhibiting a large panel of HIV-1 subtypes, with IC ₅₀ values approaching low picomolar concentrations. Also, LP-46 was an exceptionally potent inhibitor against HIV-2, SIV, and T20-resistant variants, and it displayed obvious synergistic effects with LP-40. Furthermore, we showed that LP-46 had increased helical stability and binding affinity with the target site. The crystal structure of LP-46 in complex with a target surrogate revealed its critical binding motifs underlying the mechanism of action. Interestingly, it was found that the introduced pocket-binding domain in LP-46 did not interact with the gp41 pocket as expected; instead, it adopted a mode similar to that of LP-40. Therefore, our studies have provided an exceptionally potent and broad fusion inhibitor for developing new anti-HIV drugs, which can also serve as a tool to exploit the mechanisms of viral fusion and inhibition.

Organizational Affiliation

From the MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.

Macromolecule Content

Total Structure Weight: 53.59 kDa
Atom Count: 3,846
Modeled Residue Count: 433
Deposited Residue Count: 450
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein	A B C G [auth D] H [auth E] A, B, C, G [auth D], H [auth E], I [auth F]	44	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578 Go to UniProtKB: P04578
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04578
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LP-46	D [auth Q] E [auth W] F [auth P] J [auth H] K [auth I] D [auth Q], E [auth W], F [auth P], J [auth H], K [auth I], L [auth G]	31	Human immunodeficiency virus 1	Mutation(s): 0