1
|
Harwood LA, Xiong Z, Christensen KE, Wang R, Wong LL, Robertson J. Selective P450 BM3 Hydroxylation of Cyclobutylamine and Bicyclo[1.1.1]pentylamine Derivatives: Underpinning Synthetic Chemistry for Drug Discovery. J Am Chem Soc 2023; 145:27767-27773. [PMID: 38051939 PMCID: PMC10740007 DOI: 10.1021/jacs.3c10542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Achieving single-step syntheses of a set of related compounds divergently and selectively from a common starting material affords substantial efficiency gains when compared with preparing those same compounds by multiple individual syntheses. In order for this approach to be realized, complementary reagent systems must be available; here, a panel of engineered P450BM3 enzymes is shown to fulfill this remit in the selective C-H hydroxylation of cyclobutylamine derivatives at chemically unactivated sites. The oxidations can proceed with high regioselectivity and stereoselectivity, producing valuable bifunctional intermediates for synthesis and applications in fragment-based drug discovery. The process also applies to bicyclo[1.1.1]pentyl (BCP) amine derivatives to achieve the first direct enantioselective functionalization of the bridging methylenes and open a short and efficient route to chiral BCP bioisosteres for medicinal chemistry. The combination of substrate, enzyme, and reaction engineering provides a powerful general platform for small-molecule elaboration and diversification.
Collapse
Affiliation(s)
- Lucy A. Harwood
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ziyue Xiong
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
| | - Kirsten E. Christensen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ruiyao Wang
- Wisdom
Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool
University, Suzhou Industrial
Park, Suzhou, Jiangsu, 215123, P. R. China
| | - Luet L. Wong
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K.
| | - Jeremy Robertson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
| |
Collapse
|
2
|
Reyna-Luna J, Soriano-Agueda L, Vera CJ, Franco-Pérez M. Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn 2+, Cu 2+, and VO 2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models. J Comput Aided Mol Des 2023:10.1007/s10822-023-00506-4. [PMID: 37245168 DOI: 10.1007/s10822-023-00506-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
We present a computational strategy based on thermodynamic cycles to predict and describe the chemical equilibrium between the 3d-transition metal ions Zn2+, Cu2+, and VO2+ and the widely used antineoplastic drug doxorubicin. Our method involves benchmarking a theoretical protocol to compute gas-phase quantities using DLPNO Coupled-Cluster calculations as reference, followed by estimating solvation contributions to the reaction Gibbs free energies using both explicit partial (micro)solvation steps for charged solutes and neutral coordination complexes, as well as a continuum solvation procedure for all solutes involved in the complexation process. We rationalized the stability of these doxorubicin-metal complexes by inspecting quantities obtained from the topology of their electron densities, particularly the bond critical points and non-covalent interaction index. Our approach allowed us to identify representative species in solution phase, infer the most likely complexation process for each case, and identify key intramolecular interactions involved in the stability of these compounds. To the best of our knowledge, this is the first study reporting thermodynamic constants for the complexation of doxorubicin with transition metal ions. Unlike other methods, our procedure is computationally affordable for medium-sized systems and provides valuable insights even with limited experimental data. Furthermore, it can be extended to describe the complexation process between 3d-transition metal ions and other bioactive ligands.
Collapse
Affiliation(s)
- Julieta Reyna-Luna
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Ciudad de Mexico, México
| | - Luis Soriano-Agueda
- Donostia International Physics Center (DIPC), 20018, Donostia, Euskadi, Spain
| | - Christiaan Jardinez Vera
- Laboratorio de Modelado y Simulación Computacional en Nanomedicina, Escuela Superior de Apan, Universidad Autónoma del Estado de Hidalgo, Carretera Apan-Calpulalpan S/N, Colonia, 43920, Chimalpa Tlalayote, Hgo, México
| | - Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Ciudad de Mexico, México.
| |
Collapse
|
3
|
Flanagan KJ, Paradiz Dominguez M, Melissari Z, Eckhardt HG, Williams RM, Gibbons D, Prior C, Locke GM, Meindl A, Ryan AA, Senge MO. Structural effects of meso-halogenation on porphyrins. Beilstein J Org Chem 2021; 17:1149-1170. [PMID: 34093881 PMCID: PMC8144917 DOI: 10.3762/bjoc.17.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
The use of halogens in the crystal engineering of supramolecular porphyrin assemblies has been a topic of strong interest over the past decades. With this in mind we have characterized a series of direct meso-halogenated porphyrins using single crystal X-ray crystallography. This is accompanied by a detailed conformational analysis of all deposited meso-halogenated porphyrins in the CSD. In this study we have used the Hirshfeld fingerprint plots together with normal-coordinate structural decomposition and determined crystal structures to elucidate the conformation, present intermolecular interactions, and compare respective contacts within the crystalline architectures. Additionally, we have used density functional theory calculations to determine the structure of several halogenated porphyrins. This contrasts conformational analysis with existing X-ray structures and gives a method to characterize samples that are difficult to crystallize. By using the methods outlined above we were able to deduce the impact a meso halogen has on a porphyrin, for example, meso-halogenation is dependent on the type of alternate substituents present when forming supramolecular assemblies. Furthermore, we have designed a method to predict the conformation of halogenated porphyrins, without need of crystallization, using DFT calculations with a high degree of accuracy.
Collapse
Affiliation(s)
- Keith J Flanagan
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Maximilian Paradiz Dominguez
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Zoi Melissari
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Hans-Georg Eckhardt
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - René M Williams
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Dáire Gibbons
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Caroline Prior
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Gemma M Locke
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Alina Meindl
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Aoife A Ryan
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Mathias O Senge
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, 152–160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| |
Collapse
|