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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.

Show MeSH
Ethoxy uracil conformation of compounds 1 and 2 in the RT (WT) [teal], RT (Y181C) [lightgreen], and RT(K103N/Y181C) [gold] crystal structures. The sag conformationof compound 1 differs from the aag ofcompound 2. The sag conformation androtation of the uracil in the RT (Y181C):1 and RT (K103N/Y181C):1 causes the loss of hydrogen bonds in the mutant structures.Compound 2 maintains the same aag conformationin all of the structures; two hydrogen bonds with residues Lys103and Pro236 are maintained in the RT (Y181C):2 and RT(K103N/Y181C:2 structures.
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fig4: Ethoxy uracil conformation of compounds 1 and 2 in the RT (WT) [teal], RT (Y181C) [lightgreen], and RT(K103N/Y181C) [gold] crystal structures. The sag conformationof compound 1 differs from the aag ofcompound 2. The sag conformation androtation of the uracil in the RT (Y181C):1 and RT (K103N/Y181C):1 causes the loss of hydrogen bonds in the mutant structures.Compound 2 maintains the same aag conformationin all of the structures; two hydrogen bonds with residues Lys103and Pro236 are maintained in the RT (Y181C):2 and RT(K103N/Y181C:2 structures.

Mentions: Previously, we identified variations in the ethoxyuracil conformation in various structures of RT (WT) in complex withseveral analogues of the catechol diether series, which seem influencedby the C5 substitution on the cyanovinyl aryl ring.20 Crystal structures from the analysis revealed two uniqueconformations of the ethoxy uracil side chain characterized by uniquetorsion angles: syn-anti-gauche (sag) and anti-anti-gauche (aag) conformations.20 Alignments for compounds 1 and 2 in the RT (WT), RT (Y181C), and RT (K103N/Y181C) structuresshow the differences between the ethoxy uracil side chain for the sag and aag conformations (Figure 3). Although the sag conformationseems favorable in the RT (WT):1 structure, as observedby the multiple hydrogen bonds formed between the uracil ring andLys102, Lys103, and Pro236 (Figure 4), it seemsthat this conformation is unfavorable in the RT (Y181C):1 and RT (K103N/Y181C):1 structure complexes. In comparingthe three binding modes of 1 in the structures, in whichthe ethoxy uracil is in the sag conformation, thecompound seems to shift in the RT (Y181C) and RT (K103N/Y181C) complexes.An all atom superposition of the three binding pockets in complexwith 1 (Figure 1A) reveals slightdifferences in binding conformations in which the compound shiftstoward the pocket opening created by the Cys181 mutation in RT (Y181C):1 and RT (K103N/Y181C):1 structures (Figure 2B,C). Observed only in the mutant complexes withcompound 1, the uracil ring rotates ∼40°in the RT (Y181C):1 and RT (K103N/Y181C):1 complexes (Figure 1A, Figure S2A) in which the O2 of the uracil carbonyl in RT (WT)and RT (Y181C)/RT (K103N/Y181C) structures serves as a reference point.Elimination of a π–π stacking interaction betweenTyr181 and the catechol aryl may contribute to the observed shiftof compound 1 in the mutant structures.


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)

Ethoxy uracil conformation of compounds 1 and 2 in the RT (WT) [teal], RT (Y181C) [lightgreen], and RT(K103N/Y181C) [gold] crystal structures. The sag conformationof compound 1 differs from the aag ofcompound 2. The sag conformation androtation of the uracil in the RT (Y181C):1 and RT (K103N/Y181C):1 causes the loss of hydrogen bonds in the mutant structures.Compound 2 maintains the same aag conformationin all of the structures; two hydrogen bonds with residues Lys103and Pro236 are maintained in the RT (Y181C):2 and RT(K103N/Y181C:2 structures.
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Related In: Results  -  Collection

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fig4: Ethoxy uracil conformation of compounds 1 and 2 in the RT (WT) [teal], RT (Y181C) [lightgreen], and RT(K103N/Y181C) [gold] crystal structures. The sag conformationof compound 1 differs from the aag ofcompound 2. The sag conformation androtation of the uracil in the RT (Y181C):1 and RT (K103N/Y181C):1 causes the loss of hydrogen bonds in the mutant structures.Compound 2 maintains the same aag conformationin all of the structures; two hydrogen bonds with residues Lys103and Pro236 are maintained in the RT (Y181C):2 and RT(K103N/Y181C:2 structures.
Mentions: Previously, we identified variations in the ethoxyuracil conformation in various structures of RT (WT) in complex withseveral analogues of the catechol diether series, which seem influencedby the C5 substitution on the cyanovinyl aryl ring.20 Crystal structures from the analysis revealed two uniqueconformations of the ethoxy uracil side chain characterized by uniquetorsion angles: syn-anti-gauche (sag) and anti-anti-gauche (aag) conformations.20 Alignments for compounds 1 and 2 in the RT (WT), RT (Y181C), and RT (K103N/Y181C) structuresshow the differences between the ethoxy uracil side chain for the sag and aag conformations (Figure 3). Although the sag conformationseems favorable in the RT (WT):1 structure, as observedby the multiple hydrogen bonds formed between the uracil ring andLys102, Lys103, and Pro236 (Figure 4), it seemsthat this conformation is unfavorable in the RT (Y181C):1 and RT (K103N/Y181C):1 structure complexes. In comparingthe three binding modes of 1 in the structures, in whichthe ethoxy uracil is in the sag conformation, thecompound seems to shift in the RT (Y181C) and RT (K103N/Y181C) complexes.An all atom superposition of the three binding pockets in complexwith 1 (Figure 1A) reveals slightdifferences in binding conformations in which the compound shiftstoward the pocket opening created by the Cys181 mutation in RT (Y181C):1 and RT (K103N/Y181C):1 structures (Figure 2B,C). Observed only in the mutant complexes withcompound 1, the uracil ring rotates ∼40°in the RT (Y181C):1 and RT (K103N/Y181C):1 complexes (Figure 1A, Figure S2A) in which the O2 of the uracil carbonyl in RT (WT)and RT (Y181C)/RT (K103N/Y181C) structures serves as a reference point.Elimination of a π–π stacking interaction betweenTyr181 and the catechol aryl may contribute to the observed shiftof compound 1 in the mutant structures.

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