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Fanfrlík J, Brynda J, Kugler M, Lepšík M, Pospíšilová K, Holub J, Hnyk D, Nekvinda J, Grüner B, Řezáčová P. B-H⋯π and C-H⋯π interactions in protein-ligand complexes: carbonic anhydrase II inhibition by carborane sulfonamides. Phys Chem Chem Phys 2023; 25:1728-1733. [PMID: 36594655 DOI: 10.1039/d2cp04673c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Among non-covalent interactions, B-H⋯π and C-H⋯π hydrogen bonding is rather weak and less studied. Nevertheless, since both can affect the energetics of protein-ligand binding, their understanding is an important prerequisite for reliable predictions of affinities. Through a combination of high-resolution X-ray crystallography and quantum-chemical calculations on carbonic anhydrase II/carborane-based inhibitor systems, this paper provides the first example of B-H⋯π hydrogen bonding in a protein-ligand complex. It shows that the B-H⋯π interaction is stabilized by dispersion, followed by electrostatics. Furthermore, it demonstrates that the similar C-H⋯π interaction is twice as strong, with a slightly smaller contribution of dispersion and a slightly higher contribution of electrostatics. Such a detailed insight will facilitate the rational design of future protein ligands, controlling these types of non-covalent interactions.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Klára Pospíšilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jan Nekvinda
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
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Freindorf M, McCutcheon M, Beiranvand N, Kraka E. Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010263. [PMID: 36615456 PMCID: PMC9822382 DOI: 10.3390/molecules28010263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms-in-Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode-mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal-like structures makes them interesting for potential hydrogen storage applications.
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