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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.


DTG and 4a binding in the active site of the PFV intasome.PFV-bound DTG (cyan with protein ribbon in gray) is shown with Mg2+ ions (solid blue spheres) along with the A-1 and C-2 nucleotidesof 3′-processed viral DNA and the G4 nucleotide of the uncleavedcomplementary strand (PDB code 3S3M). Interacting residues are shown withcontacting carbons shown in cream (corresponding IN residues are indicatedin parentheses). The protein β4−α2 loop is highlightedin orange. Contact residues associated with RAL resistance (Y143Rand G118R) are highlighted in yellow. PFV-bound 4a issuperimposed onto the DTG-bound structure with the ligand carbonsin magenta and the protein ribbon in blue.
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fig2: DTG and 4a binding in the active site of the PFV intasome.PFV-bound DTG (cyan with protein ribbon in gray) is shown with Mg2+ ions (solid blue spheres) along with the A-1 and C-2 nucleotidesof 3′-processed viral DNA and the G4 nucleotide of the uncleavedcomplementary strand (PDB code 3S3M). Interacting residues are shown withcontacting carbons shown in cream (corresponding IN residues are indicatedin parentheses). The protein β4−α2 loop is highlightedin orange. Contact residues associated with RAL resistance (Y143Rand G118R) are highlighted in yellow. PFV-bound 4a issuperimposed onto the DTG-bound structure with the ligand carbonsin magenta and the protein ribbon in blue.

Mentions: The extended tricyclic ring system of DTG permitsits third ring (highlighted in green in Figure 1) to contact the β4-α2 loop inthe active site of IN (highlighted in orange, Figure 2). Maintenance of interactions in this regionhas been suggested to be important for the binding of DTG, as wellas for the binding of other second generation INSTIs.20,29−31 In order to determine the importance of these interactions,we modified 4a by adding substituents at its 6-position(highlighted in green in Figure 1). Our intent was to create hydrogen bonds with theprotein or with bound water molecules proximal to the 6-position.Although there are a variety of constructs that could be used, thework reported herein is focused on simple linear methylene chainsof increasing lengths with terminal hydroxyl groups (compounds 4b–4e, Table 1 and Supporting Information Scheme S1). The in vitro ST inhibitory potencieswere relatively independent of chain length in going from three methylenes(4b, IC50 value = 11 nM) to eight methylenes(4e, IC50 value = 5 nM). The most potent analogue(by a small margin) was 4c with IC50 = 2.7nM; Table 1), whichalso displayed an antiviral inhibitory potency against the Q148H/G140Smutant (4c, EC50 ≃ 7 nM), which wassimilar to that of DTG (Table 2).


HIV-1 Integrase Strand Transfer Inhibitorswith Reduced Susceptibility to Drug Resistant Mutant Integrases
DTG and 4a binding in the active site of the PFV intasome.PFV-bound DTG (cyan with protein ribbon in gray) is shown with Mg2+ ions (solid blue spheres) along with the A-1 and C-2 nucleotidesof 3′-processed viral DNA and the G4 nucleotide of the uncleavedcomplementary strand (PDB code 3S3M). Interacting residues are shown withcontacting carbons shown in cream (corresponding IN residues are indicatedin parentheses). The protein β4−α2 loop is highlightedin orange. Contact residues associated with RAL resistance (Y143Rand G118R) are highlighted in yellow. PFV-bound 4a issuperimposed onto the DTG-bound structure with the ligand carbonsin magenta and the protein ribbon in blue.
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fig2: DTG and 4a binding in the active site of the PFV intasome.PFV-bound DTG (cyan with protein ribbon in gray) is shown with Mg2+ ions (solid blue spheres) along with the A-1 and C-2 nucleotidesof 3′-processed viral DNA and the G4 nucleotide of the uncleavedcomplementary strand (PDB code 3S3M). Interacting residues are shown withcontacting carbons shown in cream (corresponding IN residues are indicatedin parentheses). The protein β4−α2 loop is highlightedin orange. Contact residues associated with RAL resistance (Y143Rand G118R) are highlighted in yellow. PFV-bound 4a issuperimposed onto the DTG-bound structure with the ligand carbonsin magenta and the protein ribbon in blue.
Mentions: The extended tricyclic ring system of DTG permitsits third ring (highlighted in green in Figure 1) to contact the β4-α2 loop inthe active site of IN (highlighted in orange, Figure 2). Maintenance of interactions in this regionhas been suggested to be important for the binding of DTG, as wellas for the binding of other second generation INSTIs.20,29−31 In order to determine the importance of these interactions,we modified 4a by adding substituents at its 6-position(highlighted in green in Figure 1). Our intent was to create hydrogen bonds with theprotein or with bound water molecules proximal to the 6-position.Although there are a variety of constructs that could be used, thework reported herein is focused on simple linear methylene chainsof increasing lengths with terminal hydroxyl groups (compounds 4b–4e, Table 1 and Supporting Information Scheme S1). The in vitro ST inhibitory potencieswere relatively independent of chain length in going from three methylenes(4b, IC50 value = 11 nM) to eight methylenes(4e, IC50 value = 5 nM). The most potent analogue(by a small margin) was 4c with IC50 = 2.7nM; Table 1), whichalso displayed an antiviral inhibitory potency against the Q148H/G140Smutant (4c, EC50 ≃ 7 nM), which wassimilar to that of DTG (Table 2).

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.