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A spiroligomer α-helix mimic that binds HDM2, penetrates human cells and stabilizes HDM2 in cell culture.

Brown ZZ, Akula K, Arzumanyan A, Alleva J, Jackson M, Bichenkov E, Sheffield JB, Feitelson MA, Schafmeister CE - PLoS ONE (2012)

Bottom Line: Two series of spiroligomers were synthesized, one of structural analogs and one of stereochemical analogs, from which we identified compound 1, that binds HDM2 with a Kd value of 400 nM.This is a biological effect that is not seen with the HDM2 ligand nutlin-3a.We propose that compound 1 modulates the levels of HDM2 by stabilizing it to proteolysis, allowing it to accumulate in the absence of a p53/HDM2 feedback loop.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America.

ABSTRACT
We demonstrate functionalized spiroligomers that mimic the HDM2-bound conformation of the p53 activation domain. Spiroligomers are stereochemically defined, functionalized, spirocyclic monomers coupled through pairs of amide bonds to create spiro-ladder oligomers. Two series of spiroligomers were synthesized, one of structural analogs and one of stereochemical analogs, from which we identified compound 1, that binds HDM2 with a Kd value of 400 nM. The spiroligomer 1 penetrates human liver cancer cells through passive diffusion and in a dose-dependent and time-dependent manner increases the levels of HDM2 more than 30-fold in Huh7 cells in which the p53/HDM2 negative feed-back loop is inoperative. This is a biological effect that is not seen with the HDM2 ligand nutlin-3a. We propose that compound 1 modulates the levels of HDM2 by stabilizing it to proteolysis, allowing it to accumulate in the absence of a p53/HDM2 feedback loop.

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The structures of spiroligomers, which explored the use of different functional groups as side-chains on a fixed backbone (all centers have “S” stereochemistry).
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pone-0045948-g003: The structures of spiroligomers, which explored the use of different functional groups as side-chains on a fixed backbone (all centers have “S” stereochemistry).

Mentions: As a first step to creating functionalized spiroligomers that modulate protein function we chose to create spiroligomers that could mimic the HDM2 bound conformation of p53. We have recently described versatile and efficient solution and solid-phase synthetic strategies for synthesizing functionalized spiroligomers [15], [16]. This methodology exploits our recent discovery of a new reaction, called “acyl-transfer coupling” that enables the formation of hindered tertiary amides and diketopiperazines by coupling active esters with unprotected N-alkyl amino acids [30]. To identify functionalized spiroligomers that could mimic the HDM2 bound conformation of p53 we used an in-house developed software package called CANDO [1] that rapidly builds models of millions of spiroligomers and scores them for their ability to display functional groups in desired constellations. CANDO is able to vary back-bone stereochemistry and conformations as well as side-chain conformations to identify spiroligomers that could present functional groups to mimic the presentation of the Cα-Cβ bond vectors of residues Phe19, Trp23 and Leu26 of p53 bound to HDM2 from the X-ray crystal structure [3]. The scoring function used by CANDO in the design of spiroligomers was the least squares fit of the Cα-Cβ bond vectors of these residues superposed onto the bond vectors that we could functionalize on the spiroligomers. CANDO presented several stereoisomers out of 256 possible stereoisomers (eight stereocenters) that modeling suggested could mimic the N-terminal peptide of p53 including the stereoisomer with all (S) stereochemistry (Figure 1, Figure 3). We then synthesized on solid support compounds 3–7 and compounds 1 and 8–12, two series of spiroligomers which explore the effects of varying functional groups on one stereochemically defined backbone (compounds 3–7) and varying stereochemistry with one set of functional groups (compounds 1, 8–12) on the binding to HDM2 [15], [16].


A spiroligomer α-helix mimic that binds HDM2, penetrates human cells and stabilizes HDM2 in cell culture.

Brown ZZ, Akula K, Arzumanyan A, Alleva J, Jackson M, Bichenkov E, Sheffield JB, Feitelson MA, Schafmeister CE - PLoS ONE (2012)

The structures of spiroligomers, which explored the use of different functional groups as side-chains on a fixed backbone (all centers have “S” stereochemistry).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475717&req=5

pone-0045948-g003: The structures of spiroligomers, which explored the use of different functional groups as side-chains on a fixed backbone (all centers have “S” stereochemistry).
Mentions: As a first step to creating functionalized spiroligomers that modulate protein function we chose to create spiroligomers that could mimic the HDM2 bound conformation of p53. We have recently described versatile and efficient solution and solid-phase synthetic strategies for synthesizing functionalized spiroligomers [15], [16]. This methodology exploits our recent discovery of a new reaction, called “acyl-transfer coupling” that enables the formation of hindered tertiary amides and diketopiperazines by coupling active esters with unprotected N-alkyl amino acids [30]. To identify functionalized spiroligomers that could mimic the HDM2 bound conformation of p53 we used an in-house developed software package called CANDO [1] that rapidly builds models of millions of spiroligomers and scores them for their ability to display functional groups in desired constellations. CANDO is able to vary back-bone stereochemistry and conformations as well as side-chain conformations to identify spiroligomers that could present functional groups to mimic the presentation of the Cα-Cβ bond vectors of residues Phe19, Trp23 and Leu26 of p53 bound to HDM2 from the X-ray crystal structure [3]. The scoring function used by CANDO in the design of spiroligomers was the least squares fit of the Cα-Cβ bond vectors of these residues superposed onto the bond vectors that we could functionalize on the spiroligomers. CANDO presented several stereoisomers out of 256 possible stereoisomers (eight stereocenters) that modeling suggested could mimic the N-terminal peptide of p53 including the stereoisomer with all (S) stereochemistry (Figure 1, Figure 3). We then synthesized on solid support compounds 3–7 and compounds 1 and 8–12, two series of spiroligomers which explore the effects of varying functional groups on one stereochemically defined backbone (compounds 3–7) and varying stereochemistry with one set of functional groups (compounds 1, 8–12) on the binding to HDM2 [15], [16].

Bottom Line: Two series of spiroligomers were synthesized, one of structural analogs and one of stereochemical analogs, from which we identified compound 1, that binds HDM2 with a Kd value of 400 nM.This is a biological effect that is not seen with the HDM2 ligand nutlin-3a.We propose that compound 1 modulates the levels of HDM2 by stabilizing it to proteolysis, allowing it to accumulate in the absence of a p53/HDM2 feedback loop.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America.

ABSTRACT
We demonstrate functionalized spiroligomers that mimic the HDM2-bound conformation of the p53 activation domain. Spiroligomers are stereochemically defined, functionalized, spirocyclic monomers coupled through pairs of amide bonds to create spiro-ladder oligomers. Two series of spiroligomers were synthesized, one of structural analogs and one of stereochemical analogs, from which we identified compound 1, that binds HDM2 with a Kd value of 400 nM. The spiroligomer 1 penetrates human liver cancer cells through passive diffusion and in a dose-dependent and time-dependent manner increases the levels of HDM2 more than 30-fold in Huh7 cells in which the p53/HDM2 negative feed-back loop is inoperative. This is a biological effect that is not seen with the HDM2 ligand nutlin-3a. We propose that compound 1 modulates the levels of HDM2 by stabilizing it to proteolysis, allowing it to accumulate in the absence of a p53/HDM2 feedback loop.

Show MeSH
Related in: MedlinePlus