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HIV-1 Integrase Strand Transfer Inhibitorswith Reduced Susceptibility to Drug Resistant Mutant Integrases

View Article: PubMed Central - PubMed

ABSTRACT

HIVintegrase (IN) strand transfer inhibitors (INSTIs) are amongthe newest anti-AIDS drugs; however, mutant forms of IN can conferresistance. We developed noncytotoxic naphthyridine-containing INSTIsthat retain low nanomolar IC50 values against HIV-1 variantsharboring all of the major INSTI-resistant mutations. We found byanalyzing crystal structures of inhibitors bound to the IN from theprototype foamy virus (PFV) that the most successful inhibitors showstriking mimicry of the bound viral DNA prior to 3′-processingand the bound host DNA prior to strand transfer. Using this conceptof “bi-substrate mimicry,” we developed a new broadlyeffective inhibitor that not only mimics aspects of both the boundtarget and viral DNA but also more completely fills the space theywould normally occupy. Maximizing shape complementarity and recapitulatingstructural components encompassing both of the IN DNA substrates couldserve as a guiding principle for the development of new INSTIs.

No MeSH data available.


PFV Intasome crystal structure complexed with 4f.(A) Crystal structure oriented to show the complexed Mg2+ ions (blue spheres) and the semitransparent surface of 4f (orange surface with carbons in cream), 3′P DNA (purple surface),and protein (gray surface) with key protein residues shown (carbonsin light gray). Important binding interactions are indicated. (B)Bound 4f with superimposed pre-3′-processed DNA(carbons in purple; PDB code: 4E7I(25)) and targetDNA (carbons in black; PDB code: 4E7K(25)). Regionswhere the side chain of 4f overlaps with DNA are indicatedby black dashed ovals.
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fig4: PFV Intasome crystal structure complexed with 4f.(A) Crystal structure oriented to show the complexed Mg2+ ions (blue spheres) and the semitransparent surface of 4f (orange surface with carbons in cream), 3′P DNA (purple surface),and protein (gray surface) with key protein residues shown (carbonsin light gray). Important binding interactions are indicated. (B)Bound 4f with superimposed pre-3′-processed DNA(carbons in purple; PDB code: 4E7I(25)) and targetDNA (carbons in black; PDB code: 4E7K(25)). Regionswhere the side chain of 4f overlaps with DNA are indicatedby black dashed ovals.

Mentions: Tovisualize the interactions 4f makes with the active siteof IN, we determined a crystal structure of 4f boundin the active site of the PFV intasome (Figure 4). The structure revealed that one of thesulfonyl oxygens of 4f forms hydrogen bonds with themain chain amide and the phenolic side chain of Tyr212 via bridgingwater molecules, while the other makes close van der Waals contactswith backbone atoms of Gln186 and Gly187 in the β4-α2loop (Figure 4A). Strikingly,the sulfonylphenyl ring is bent back under the plane of the metal-chelatingnaphthyridinone ring system, where it makes an intramolecular π–πstacking interaction (3.3 Å separation) (Figure 4A and B). By superimposing this structurewith the structures of both the uncleaved (pre-3′-P) viralDNA and the target DNA (ST) substrates (PBD codes 4E7I and 4E7K, respectively),25 it is apparent that the sulfonyl group fillsthe envelope formed by the overlap in the positions of both the bounduncleaved viral and the bound target DNAs (Figure 4B). In addition, the position of the sulfonylphenylring is similar to the position of the deoxyribose sugar of the adenosineA–1 in the scissile A-T dinucleotide of the uncleavedviral DNA, while other portions of the 6-side chain are similar tothe position of the deoxyribose sugar of the G–1 guanosine in the target DNA (Figure 4B).


HIV-1 Integrase Strand Transfer Inhibitorswith Reduced Susceptibility to Drug Resistant Mutant Integrases
PFV Intasome crystal structure complexed with 4f.(A) Crystal structure oriented to show the complexed Mg2+ ions (blue spheres) and the semitransparent surface of 4f (orange surface with carbons in cream), 3′P DNA (purple surface),and protein (gray surface) with key protein residues shown (carbonsin light gray). Important binding interactions are indicated. (B)Bound 4f with superimposed pre-3′-processed DNA(carbons in purple; PDB code: 4E7I(25)) and targetDNA (carbons in black; PDB code: 4E7K(25)). Regionswhere the side chain of 4f overlaps with DNA are indicatedby black dashed ovals.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4836387&req=5

fig4: PFV Intasome crystal structure complexed with 4f.(A) Crystal structure oriented to show the complexed Mg2+ ions (blue spheres) and the semitransparent surface of 4f (orange surface with carbons in cream), 3′P DNA (purple surface),and protein (gray surface) with key protein residues shown (carbonsin light gray). Important binding interactions are indicated. (B)Bound 4f with superimposed pre-3′-processed DNA(carbons in purple; PDB code: 4E7I(25)) and targetDNA (carbons in black; PDB code: 4E7K(25)). Regionswhere the side chain of 4f overlaps with DNA are indicatedby black dashed ovals.
Mentions: Tovisualize the interactions 4f makes with the active siteof IN, we determined a crystal structure of 4f boundin the active site of the PFV intasome (Figure 4). The structure revealed that one of thesulfonyl oxygens of 4f forms hydrogen bonds with themain chain amide and the phenolic side chain of Tyr212 via bridgingwater molecules, while the other makes close van der Waals contactswith backbone atoms of Gln186 and Gly187 in the β4-α2loop (Figure 4A). Strikingly,the sulfonylphenyl ring is bent back under the plane of the metal-chelatingnaphthyridinone ring system, where it makes an intramolecular π–πstacking interaction (3.3 Å separation) (Figure 4A and B). By superimposing this structurewith the structures of both the uncleaved (pre-3′-P) viralDNA and the target DNA (ST) substrates (PBD codes 4E7I and 4E7K, respectively),25 it is apparent that the sulfonyl group fillsthe envelope formed by the overlap in the positions of both the bounduncleaved viral and the bound target DNAs (Figure 4B). In addition, the position of the sulfonylphenylring is similar to the position of the deoxyribose sugar of the adenosineA–1 in the scissile A-T dinucleotide of the uncleavedviral DNA, while other portions of the 6-side chain are similar tothe position of the deoxyribose sugar of the G–1 guanosine in the target DNA (Figure 4B).

View Article: PubMed Central - PubMed

ABSTRACT

HIVintegrase (IN) strand transfer inhibitors (INSTIs) are amongthe newest anti-AIDS drugs; however, mutant forms of IN can conferresistance. We developed noncytotoxic naphthyridine-containing INSTIsthat retain low nanomolar IC50 values against HIV-1 variantsharboring all of the major INSTI-resistant mutations. We found byanalyzing crystal structures of inhibitors bound to the IN from theprototype foamy virus (PFV) that the most successful inhibitors showstriking mimicry of the bound viral DNA prior to 3′-processingand the bound host DNA prior to strand transfer. Using this conceptof “bi-substrate mimicry,” we developed a new broadlyeffective inhibitor that not only mimics aspects of both the boundtarget and viral DNA but also more completely fills the space theywould normally occupy. Maximizing shape complementarity and recapitulatingstructural components encompassing both of the IN DNA substrates couldserve as a guiding principle for the development of new INSTIs.

No MeSH data available.