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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment‐Bindung an die Kinase‐Scharnier‐Region: Wenn Ladungsverteilung und lokale p
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‐Verschiebungen etablierte Bioisosterie‐Konzepte fehlleiten. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matthias Oebbeke
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Christof Siefker
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Björn Wagner
- Roche Innovation Center Grenzacherstr. 124 4070 Basel Schweiz
| | - Andreas Heine
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Philipps Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 35032 Marburg Deutschland
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Oebbeke M, Siefker C, Wagner B, Heine A, Klebe G. Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts. Angew Chem Int Ed Engl 2021; 60:252-258. [PMID: 33021032 PMCID: PMC7821265 DOI: 10.1002/anie.202011295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 12/25/2022]
Abstract
Medicinal-chemistry optimization follows strategies replacing functional groups and attaching larger substituents at a promising lead scaffold. Well-established bioisosterism rules are considered, however, it is difficult to estimate whether the introduced modifications really match the required properties at a binding site. The electron density distribution and pKa values are modulated influencing protonation states and bioavailability. Considering the adjacent H-bond donor/acceptor pattern of the hinge binding motif in a kinase, we studied by crystallography a set of fragments to map the required interaction pattern. Unexpectedly, benzoic acid and benzamidine, decorated with the correct substituents, are totally bioisosteric just as carboxamide and phenolic OH. A mono-dentate pyridine nitrogen out-performs bi-dentate functionalities. The importance of correctly designing pKa values of attached functional groups by additional substituents at the parent scaffold is rendered prominent.
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Affiliation(s)
- Matthias Oebbeke
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
| | - Christof Siefker
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
| | - Björn Wagner
- Roche Innovation CenterGrenzacherstr. 1244070BaselSwitzerland
| | - Andreas Heine
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
| | - Gerhard Klebe
- Philipps Universität MarburgInstitut für Pharmazeutische ChemieMarbacher Weg 635032MarburgGermany
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Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low‐Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology University of Tennessee Knoxville TN 37996 USA
- Present address: Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - Pratul K. Agarwal
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - M. Brett Waddell
- Molecular Interaction Analysis Shared Resource St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Tanja Mittag
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Engin H. Serpersu
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
- National Science Foundation Alexandria VA 22314 USA
| | - Matthew J. Cuneo
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
- Oak Ridge National Laboratory Oak Ridge TN 37830 USA
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Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019; 58:16260-16266. [PMID: 31515870 DOI: 10.1002/anie.201908535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Indexed: 01/14/2023]
Abstract
The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-à-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.
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Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Present address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Engin H Serpersu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.,National Science Foundation, Alexandria, VA, 22314, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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