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Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants.

Frey KM, Puleo DE, Spasov KA, Bollini M, Jorgensen WL, Anderson KS - J. Med. Chem. (2015)

Bottom Line: Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket.Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket.Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.

View Article: PubMed Central - PubMed

Affiliation: †Department of Pharmacology, ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8066, United States.

ABSTRACT
The development of novel non-nucleoside inhibitors (NNRTIs) with activity against variants of HIV reverse transcriptase (RT) is crucial for overcoming treatment failure. The NNRTIs bind in an allosteric pocket in RT ∼10 Å away from the active site. Earlier analogues of the catechol diether compound series have picomolar activity against HIV strains with wild-type RT but lose potency against variants with single Y181C and double K103N/Y181C mutations. As guided by structure-based and computational studies, removal of the 5-Cl substitution of compound 1 on the catechol aryl ring system led to a new analogue compound 2 that maintains greater potency against Y181C and K103N/Y181C variants and better solubility (510 μg/mL). Crystal structures were determined for wild-type, Y181C, and K103N/Y181C RT in complex with both compounds 1 and 2 to understand the structural basis for these findings. Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket. Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket. Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.

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Stereo view of superimposedwild-type and mutant RT complexes boundto 1 (pink) and 2 (purple). RT (WT) structuresare illustrated in teal, RT (Y181C) structures are illustrated inlight green, and RT (K103N/Y181C) structures are illustrated in gold.The orientation of compound 1 shifts in the various wild-typeand mutant RT binding pockets; compound 2 maintains thesame conformation.
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fig1: Stereo view of superimposedwild-type and mutant RT complexes boundto 1 (pink) and 2 (purple). RT (WT) structuresare illustrated in teal, RT (Y181C) structures are illustrated inlight green, and RT (K103N/Y181C) structures are illustrated in gold.The orientation of compound 1 shifts in the various wild-typeand mutant RT binding pockets; compound 2 maintains thesame conformation.

Mentions: The omit electron density clearly defines the bindingsite residuesfor all five structures and compounds 1 and 2 (Figure S3). All atom alignments of theinhibitor and binding pockets for wild-type and mutant-inhibitor complexes(Figure 1) reveal the lack of global conformationalchanges imparted by the resistance mutations K103N and Y181C, whichwas also observed in earlier complexes determined for RT (K103N/Y181C):rilpivirine(PDB code: 3BGR), RT (Y181C):nevirapine (PDB code: 1JLB), RT (K103N):rilpivirine (PDB code: 3MEG), and RT(K103N):etravirine(PDB code: 3MED).11,12,15 In addition,Cα backbone traces (Figure S1) androot-mean-square deviations (rmsds) for the alignments (Table S1) reveal that the wild-type and mutantcomplexes are similar and adopt the usual “open” conformationobserved in RT (WT) complexes (Figures 1, S1).12,19,20 Despite the dramatic change in EC50 values, both compounds 1 and 2 retain several van der Waals and hydrophobicinteractions in the RT (Y181C) and RT (K103N/Y181C) binding pockets.Specifically, residues Leu100, Val106, Val108, Val179, Tyr188, Gly190,Phe227, Trp229, Leu234, Pro236, and Tyr188 interact with both compounds,despite the presence of Cys181 or Asn103 mutations (Figure 1). In all complexes, the planar aromatic ring moietiesof compounds 1 and 2 arrange in a similarorientation, which seems influenced by the arrangement of hydrophobicresidues in the binding pocket. Slight changes in rotamer conformationare observed in the mutant pockets most likely as a result of thechanging spatial environment imparted by the K103N and Y181C mutations.Specifically, the absence of Tyr181 creates an opening in the pocketnear Val179, which consequently affects the binding orientation ofcompound 1 (Figure 2, Figure S2). The overall surface area for thisregion is reduced by 41–58 Å2 (Table S2) in the RT (Y181C) and RT (K103N/Y181C)structures as compared with the RT (WT) structures, where Tyr181 ispresent (Table S2).


Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants.

Frey KM, Puleo DE, Spasov KA, Bollini M, Jorgensen WL, Anderson KS - J. Med. Chem. (2015)

Stereo view of superimposedwild-type and mutant RT complexes boundto 1 (pink) and 2 (purple). RT (WT) structuresare illustrated in teal, RT (Y181C) structures are illustrated inlight green, and RT (K103N/Y181C) structures are illustrated in gold.The orientation of compound 1 shifts in the various wild-typeand mutant RT binding pockets; compound 2 maintains thesame conformation.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4378236&req=5

fig1: Stereo view of superimposedwild-type and mutant RT complexes boundto 1 (pink) and 2 (purple). RT (WT) structuresare illustrated in teal, RT (Y181C) structures are illustrated inlight green, and RT (K103N/Y181C) structures are illustrated in gold.The orientation of compound 1 shifts in the various wild-typeand mutant RT binding pockets; compound 2 maintains thesame conformation.
Mentions: The omit electron density clearly defines the bindingsite residuesfor all five structures and compounds 1 and 2 (Figure S3). All atom alignments of theinhibitor and binding pockets for wild-type and mutant-inhibitor complexes(Figure 1) reveal the lack of global conformationalchanges imparted by the resistance mutations K103N and Y181C, whichwas also observed in earlier complexes determined for RT (K103N/Y181C):rilpivirine(PDB code: 3BGR), RT (Y181C):nevirapine (PDB code: 1JLB), RT (K103N):rilpivirine (PDB code: 3MEG), and RT(K103N):etravirine(PDB code: 3MED).11,12,15 In addition,Cα backbone traces (Figure S1) androot-mean-square deviations (rmsds) for the alignments (Table S1) reveal that the wild-type and mutantcomplexes are similar and adopt the usual “open” conformationobserved in RT (WT) complexes (Figures 1, S1).12,19,20 Despite the dramatic change in EC50 values, both compounds 1 and 2 retain several van der Waals and hydrophobicinteractions in the RT (Y181C) and RT (K103N/Y181C) binding pockets.Specifically, residues Leu100, Val106, Val108, Val179, Tyr188, Gly190,Phe227, Trp229, Leu234, Pro236, and Tyr188 interact with both compounds,despite the presence of Cys181 or Asn103 mutations (Figure 1). In all complexes, the planar aromatic ring moietiesof compounds 1 and 2 arrange in a similarorientation, which seems influenced by the arrangement of hydrophobicresidues in the binding pocket. Slight changes in rotamer conformationare observed in the mutant pockets most likely as a result of thechanging spatial environment imparted by the K103N and Y181C mutations.Specifically, the absence of Tyr181 creates an opening in the pocketnear Val179, which consequently affects the binding orientation ofcompound 1 (Figure 2, Figure S2). The overall surface area for thisregion is reduced by 41–58 Å2 (Table S2) in the RT (Y181C) and RT (K103N/Y181C)structures as compared with the RT (WT) structures, where Tyr181 ispresent (Table S2).

Bottom Line: Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket.Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket.Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.

View Article: PubMed Central - PubMed

Affiliation: †Department of Pharmacology, ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8066, United States.

ABSTRACT
The development of novel non-nucleoside inhibitors (NNRTIs) with activity against variants of HIV reverse transcriptase (RT) is crucial for overcoming treatment failure. The NNRTIs bind in an allosteric pocket in RT ∼10 Å away from the active site. Earlier analogues of the catechol diether compound series have picomolar activity against HIV strains with wild-type RT but lose potency against variants with single Y181C and double K103N/Y181C mutations. As guided by structure-based and computational studies, removal of the 5-Cl substitution of compound 1 on the catechol aryl ring system led to a new analogue compound 2 that maintains greater potency against Y181C and K103N/Y181C variants and better solubility (510 μg/mL). Crystal structures were determined for wild-type, Y181C, and K103N/Y181C RT in complex with both compounds 1 and 2 to understand the structural basis for these findings. Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket. Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket. Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.

Show MeSH