ORCID Profile
0000-0002-9320-4840
Current Organisation
Université de Strasbourg
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Publisher: American Chemical Society (ACS)
Date: 05-09-2012
DOI: 10.1021/CI300196G
Abstract: Selectivity is a key factor in drug development. In this paper, we questioned the Protein Data Bank to better understand the reasons for the promiscuity of bioactive compounds. We assembled a data set of >1000 pairs of three-dimensional structures of complexes between a "drug-like" ligand (as its physicochemical properties overlap that of approved drugs) and two distinct "druggable" protein targets (as their binding sites are likely to accommodate "drug-like" ligands). Studying the similarity between the ligand-binding sites in the different targets revealed that the lack of selectivity of a ligand can be due (i) to the fact that Nature has created the same binding pocket in different proteins, which do not necessarily have otherwise sequence or fold similarity, or (ii) to specific characteristics of the ligand itself. In particular, we demonstrated that many ligands can adapt to different protein environments by changing their conformation, by using different chemical moieties to anchor to different targets, or by adopting unusual extreme binding modes (e.g., only apolar contact between the ligand and the protein, even though polar groups are present on the ligand or at the protein surface). Lastly, we provided new elements in support to the recent studies which suggest that the promiscuity of a ligand might be inferred from its molecular complexity.
Publisher: Georg Thieme Verlag KG
Date: 03-11-2017
Abstract: Recently, we have demonstrated that site comparison methodology using flavonoid biosynthetic enzymes as the query could automatically identify structural features common to different flavonoid-binding proteins, allowing for the identification of flavonoid targets such as protein kinases. With the aim of further validating the hypothesis that biosynthetic enzymes and therapeutic targets can contain a similar natural product imprint, we collected a set of 159 crystallographic structures representing 38 natural product biosynthetic enzymes by searching the Protein Databank. Each enzyme structure was used as a query to screen a repository of approximately 10 000 ligandable sites by active site similarity. We report a full analysis of the screening results and highlight three retrospective ex les where the natural product validates the method, thereby revealing novel structural relationships between natural product biosynthetic enzymes and putative protein targets of the natural product. From a prospective perspective, our work provides a list of up to 64 potential novel targets for 25 well-characterized natural products.
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1NP00026H
Publisher: Elsevier BV
Date: 09-2011
Publisher: Future Science Ltd
Date: 10-2016
Abstract: Aim: We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction. Results: We modified the in-house program SiteAlign to replace generic pharmacophoric descriptors of cavity-lining amino acids by descriptors accounting for solvent exposure. Benchmarking the novel, atom-based, method (SiteAlign2) revealed no global improvement of performance. However, in the rare cases of no sequence or global structure similarities between the compared proteins, SiteAlign2 was more successful if backbone atoms are key determinants of ligand binding. Conclusion: SiteAlign suits the comparison of binding sites for close or distant homologs. SiteAlign2 provides a better insight into the physical model of site similarity between nonhomologs, but at the expense of an increased sensitivity to atomic coordinates.
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C9MD00128J
Abstract: One of chemistry's grand challenges is to find a function for every known metabolite. We explore the opportunity for artificial intelligence to provide rationale interrogation of metabolites to predict their function.
Publisher: American Chemical Society (ACS)
Date: 27-02-2012
DOI: 10.1021/JM201348T
Abstract: Two fluorescent derivatives of the M1 muscarinic selective agonist AC-42 were synthesized by coupling the lissamine rhodamine B fluorophore (in ortho and para positions) to AC42-NH(2). This precursor, prepared according to an original seven-step procedure, was included in the study together with the LRB fluorophore (alone or linked to an alkyl chain). All these compounds are antagonists, but examination of their ability to inhibit or modulate orthosteric [(3)H]NMS binding revealed that para-LRB-AC42 shared several properties with AC-42. Carefully designed experiments allowed para-LRB-AC42 to be used as a FRET tracer on EGFP-fused M1 receptors. Under equilibrium binding conditions, orthosteric ligands, AC-42, and the allosteric modulator gallamine behaved as competitors of para-LRB-AC42 binding whereas other allosteric compounds such as WIN 51,708 and N-desmethylclozapine were noncompetitive inhibitors. Finally, molecular modeling studies focused on putative orthosteric/allosteric bitopic poses for AC-42 and para-LRB-AC42 in a 3D model of the human M1 receptor.
Publisher: Georg Thieme Verlag KG
Date: 26-02-2015
Abstract: Natural products are made by nature through interaction with biosynthetic enzymes. They also exert their effect as drugs by interaction with proteins. To address the question "Do biosynthetic enzymes and therapeutic targets share common mechanisms for the molecular recognition of natural products?", we compared the active site of five flavonoid biosynthetic enzymes to 8077 ligandable binding sites in the Protein Data Bank using two three-dimensional-based methods (SiteAlign and Shaper). Virtual screenings efficiently retrieved known flavonoid targets, in particular protein kinases. A consistent performance obtained for variable site descriptions (presence/absence of water, variable boundaries, or small structural changes) indicated that the methods are robust and thus well suited for the identification of potential target proteins of natural products. Finally, our results suggested that flavonoid binding is not primarily driven by shape, but rather by the recognition of common anchoring points.
Publisher: Elsevier BV
Date: 02-2011
No related grants have been discovered for Esther Kellenberger.