Finding the Right Candidate for the Right Position: A Fast NMR-Assisted Combinatorial Method for Optimizing Nucleic Acids Binders.
Development of strong and selective binders from promiscuous lead compounds represents one of the most expensive and time-consuming tasks in drug discovery. We herein present a novel fragment-based combinatorial strategy for the optimization of multivalent polyamine scaffolds as DNA/RNA ligands. Our protocol provides a quick access to a large variety of regioisomer libraries that can be tested for selective recognition by combining microdialysis assays with simple isotope labeling and NMR experiments. To illustrate our approach, 20 small libraries comprising 100 novel kanamycin-B derivatives have been prepared and evaluated for selective binding to the ribosomal decoding A-Site sequence. Contrary to the common view of NMR as a low-throughput technique, we demonstrate that our NMR methodology represents a valuable alternative for the detection and quantification of complex mixtures, even integrated by highly similar or structurally related derivatives, a common situation in the context of a lead optimization process. Furthermore, this study provides valuable clues about the structural requirements for selective A-site recognition.
Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain.
Ester
E
Jiménez-Moreno
Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain.
Laura
L
Montalvillo-Jiménez
Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain.
Andrés G
AG
Santana
Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain.
Ana M
AM
Gómez
Departamento de Química y Centro de Investigación en Síntesis Química, Universidad de La Rioja , 26006 Logroño, La Rioja, Spain.|Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , BIFI-IQFR (CSIC), 50018 Zaragoza, Spain.
Gonzalo
G
Jiménez-Osés
Departamento de Química y Centro de Investigación en Síntesis Química, Universidad de La Rioja , 26006 Logroño, La Rioja, Spain.
Francisco
F
Corzana
Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain.
Agatha
A
Bastida
Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain.|Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio, Bizkaia, Spain.|Basque Foundation for Science, Ikerbasque , 48013 Bilbao, Bizkaia, Spain.
Jesús
J
Jiménez-Barbero
Centro de Investigaciones Biológicas (CIB-CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain.
Francisco Javier
FJ
Cañada
Instituto de Química-Física Rocasolano (IQFR-CSIC) , C/ Serrano 119, 28006 Madrid, Spain.
Irene
I
Gómez-Pinto
Instituto de Química-Física Rocasolano (IQFR-CSIC) , C/ Serrano 119, 28006 Madrid, Spain.
Carlos
C
González
Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3, 28006 Madrid, Spain.
Juan Luis
JL
Asensio
D020650:Combinatorial Chemistry Techniques; D055808:Drug Discovery; D007612:Kanamycin / Q000031:analogs & derivatives / Q000737:chemistry; D017551:Microdialysis; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009696:Nucleic Acids / Q000737:chemistry*; D011789:Quantum Theory; D054852:Small Molecule Libraries / Q000737:chemistry*
D009696:Nucleic Acids; D054852:Small Molecule Libraries; C001495:bekanamycin; D007612:Kanamycin