A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition.

Abstract:

:A DNA-encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5-bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a Kd value of 6 nm, while compounds with the same substituents on an equidistant but flexible l-lysine scaffold showed 140-fold lower affinity. A 18 nm tankyrase-1 binder featured l-lysine as linking moiety, while molecules based on d-Lysine or (2S,4S)-amino-l-proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.

journal_name

ChemMedChem

journal_title

ChemMedChem

authors

Favalli N,Biendl S,Hartmann M,Piazzi J,Sladojevich F,Gräslund S,Brown PJ,Näreoja K,Schüler H,Scheuermann J,Franzini R,Neri D

doi

10.1002/cmdc.201800193

subject

Has Abstract

pub_date

2018-07-06 00:00:00

pages

1303-1307

issue

13

eissn

1860-7179

issn

1860-7187

journal_volume

13

pub_type

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