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Experimental and Theoretical Evaluation of the Ethynyl Moiety as a Halogen Bioisostere.

Wilcken R, Zimmermann MO, Bauer MR, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM - ACS Chem. Biol. (2015)

Bottom Line: This bioisosteric transformation is synthetically feasible via Sonogashira cross-coupling.High-resolution crystal structures of the two analogues in complex with the p53-Y220C mutant enabled us to correlate the different affinities with particular features of the binding site and subtle changes in ligand binding mode.In addition, using QM calculations and analyzing the PDB, we provide general guidelines for identifying cases where such a transformation is likely to improve ligand recognition.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

ABSTRACT
Bioisosteric replacements are widely used in medicinal chemistry to improve physicochemical and ADME properties of molecules while retaining or improving affinity. Here, using the p53 cancer mutant Y220C as a test case, we investigate both computationally and experimentally whether an ethynyl moiety is a suitable bioisostere to replace iodine in ligands that form halogen bonds with the protein backbone. This bioisosteric transformation is synthetically feasible via Sonogashira cross-coupling. In our test case of a particularly strong halogen bond, replacement of the iodine with an ethynyl group resulted in a 13-fold affinity loss. High-resolution crystal structures of the two analogues in complex with the p53-Y220C mutant enabled us to correlate the different affinities with particular features of the binding site and subtle changes in ligand binding mode. In addition, using QM calculations and analyzing the PDB, we provide general guidelines for identifying cases where such a transformation is likely to improve ligand recognition.

No MeSH data available.


Related in: MedlinePlus

Optimized binding sites of PK5176 (2) andPK5211 (3). (a) Binding site of 2 with twostructuralwaters comprising 343 atoms. (b) Binding site of 3 withtwo structural waters comprising 345 atoms.
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fig4: Optimized binding sites of PK5176 (2) andPK5211 (3). (a) Binding site of 2 with twostructuralwaters comprising 343 atoms. (b) Binding site of 3 withtwo structural waters comprising 345 atoms.

Mentions: For feasibilitypurposes, the binding sites of 2 and 3 inboth chain A and B of the asymmetric unit were reduced to residueswithin 5 Å of the respective ligands, including two structuralwater molecules (Figure 4). The C- and N-termini of the selected amino acids were saturatedwith a methyl group. For residues with alternative conformations (Pro150,Glu221, and Thr230), the conformation with the highest occupancy inthe crystal structure was used. The protein was prepared at standardsettings with MOE2012.10.26 After addinghydrogen atoms, the binding sites comprised 343 atoms for both chainsof the p53-Y220C-2 structure (PDB ID: 4AGP) and 345 atoms forboth chains of p53-Y220C-3 (PDB ID: 5A7B), spanning residues144–156, 219–224, and 228–231. Keeping the coordinatesof all heavy atoms frozen, the positions of the hydrogen atoms wereoptimized at the TPSS-D3/def2-SV(P) level. Subsequently, the ligands’complex formation energies were calculated. Using the optimized bindingsite of chain A of 4AGP as a reference (set to ΔΔE = 0.0 kcal/mol),the complex formation energy of chain B only differed by ΔΔE = +0.1 kcal/mol. In contrast, the complex formation energyof 3 is considerably disfavored with ΔΔE = +5.0 kcal/mol (chain A of 5A7B) and +5.3 kcal/mol (chain B of 5A7B), which is in agreementwith the biophysical studies shown to favor 2 over 3. TPSS-D3/def2-SV(P) was chosen for this initial energy assessmentbecause of previous favorable experience with its performance combinedwith Grimme’s dispersion correction (-D) in a systematic studyon halogen bonds in small model systems.27,28 We additionally decided to forego the use of the computationallymore demanding triple-ζ basis sets in favor of modeling thefull binding site enclosing the ligand to capture all key protein–ligandinteractions.


Experimental and Theoretical Evaluation of the Ethynyl Moiety as a Halogen Bioisostere.

Wilcken R, Zimmermann MO, Bauer MR, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM - ACS Chem. Biol. (2015)

Optimized binding sites of PK5176 (2) andPK5211 (3). (a) Binding site of 2 with twostructuralwaters comprising 343 atoms. (b) Binding site of 3 withtwo structural waters comprising 345 atoms.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4836799&req=5

fig4: Optimized binding sites of PK5176 (2) andPK5211 (3). (a) Binding site of 2 with twostructuralwaters comprising 343 atoms. (b) Binding site of 3 withtwo structural waters comprising 345 atoms.
Mentions: For feasibilitypurposes, the binding sites of 2 and 3 inboth chain A and B of the asymmetric unit were reduced to residueswithin 5 Å of the respective ligands, including two structuralwater molecules (Figure 4). The C- and N-termini of the selected amino acids were saturatedwith a methyl group. For residues with alternative conformations (Pro150,Glu221, and Thr230), the conformation with the highest occupancy inthe crystal structure was used. The protein was prepared at standardsettings with MOE2012.10.26 After addinghydrogen atoms, the binding sites comprised 343 atoms for both chainsof the p53-Y220C-2 structure (PDB ID: 4AGP) and 345 atoms forboth chains of p53-Y220C-3 (PDB ID: 5A7B), spanning residues144–156, 219–224, and 228–231. Keeping the coordinatesof all heavy atoms frozen, the positions of the hydrogen atoms wereoptimized at the TPSS-D3/def2-SV(P) level. Subsequently, the ligands’complex formation energies were calculated. Using the optimized bindingsite of chain A of 4AGP as a reference (set to ΔΔE = 0.0 kcal/mol),the complex formation energy of chain B only differed by ΔΔE = +0.1 kcal/mol. In contrast, the complex formation energyof 3 is considerably disfavored with ΔΔE = +5.0 kcal/mol (chain A of 5A7B) and +5.3 kcal/mol (chain B of 5A7B), which is in agreementwith the biophysical studies shown to favor 2 over 3. TPSS-D3/def2-SV(P) was chosen for this initial energy assessmentbecause of previous favorable experience with its performance combinedwith Grimme’s dispersion correction (-D) in a systematic studyon halogen bonds in small model systems.27,28 We additionally decided to forego the use of the computationallymore demanding triple-ζ basis sets in favor of modeling thefull binding site enclosing the ligand to capture all key protein–ligandinteractions.

Bottom Line: This bioisosteric transformation is synthetically feasible via Sonogashira cross-coupling.High-resolution crystal structures of the two analogues in complex with the p53-Y220C mutant enabled us to correlate the different affinities with particular features of the binding site and subtle changes in ligand binding mode.In addition, using QM calculations and analyzing the PDB, we provide general guidelines for identifying cases where such a transformation is likely to improve ligand recognition.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

ABSTRACT
Bioisosteric replacements are widely used in medicinal chemistry to improve physicochemical and ADME properties of molecules while retaining or improving affinity. Here, using the p53 cancer mutant Y220C as a test case, we investigate both computationally and experimentally whether an ethynyl moiety is a suitable bioisostere to replace iodine in ligands that form halogen bonds with the protein backbone. This bioisosteric transformation is synthetically feasible via Sonogashira cross-coupling. In our test case of a particularly strong halogen bond, replacement of the iodine with an ethynyl group resulted in a 13-fold affinity loss. High-resolution crystal structures of the two analogues in complex with the p53-Y220C mutant enabled us to correlate the different affinities with particular features of the binding site and subtle changes in ligand binding mode. In addition, using QM calculations and analyzing the PDB, we provide general guidelines for identifying cases where such a transformation is likely to improve ligand recognition.

No MeSH data available.


Related in: MedlinePlus