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Vaas S, Zimmermann MO, Klett T, Boeckler FM. Synthesis of Amino Acids Bearing Halodifluoromethyl Moieties and Their Application to p53-Derived Peptides Binding to Mdm2/Mdm4. Drug Des Devel Ther 2023; 17:1247-1274. [PMID: 37128274 PMCID: PMC10148652 DOI: 10.2147/dddt.s406703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/01/2023] [Indexed: 05/03/2023] Open
Abstract
Introduction Therapeutic peptides are a significant class of drugs in the treatment of a wide range of diseases. To enhance their properties, such as stability or binding affinity, they are usually chemically modified. This includes, among other techniques, cyclization of the peptide chain by bridging, modifications to the backbone, and incorporation of unnatural amino acids. One approach previously established, is the use of halogenated aromatic amino acids. In principle, they are thereby enabled to form halogen bonds (XB). In this study, we focus on the -R-CF2X moiety (R = O, NHCO; X = Cl, Br) as an uncommon halogen bond donor. These groups enable more spatial variability in protein-protein interactions. The chosen approach via Fmoc-protected building blocks allows for the incorporation of these modified amino acids in peptides using solid-phase peptide synthesis. Results and Discussion Using a competitive fluorescence polarization assay to monitor binding to Mdm4, we demonstrate that a p53-derived peptide with Lys24Nle(εNHCOCF2X) exhibits an improved inhibition constant Ki compared to the unmodified peptide. Decreasing Ki values observed with the increasing XB capacity of the halogen atoms (F ≪ Cl < Br) indicates the formation of a halogen bond. By reducing the side chain length of Nle(εNHCOCF2X) to Abu(γNHCOCF2X) as control experiments and through quantum mechanical calculations, we suggest that the observed affinity enhancement is related to halogen bond-induced intramolecular stabilization of the α-helical binding mode of the peptide or a direct interaction with His54 in human Mdm4.
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Affiliation(s)
- Sebastian Vaas
- Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Laboratory for Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Tübingen, 72076, Germany
| | - Markus O Zimmermann
- Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Laboratory for Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Tübingen, 72076, Germany
| | - Theresa Klett
- Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Laboratory for Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Laboratory for Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Tübingen, 72076, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Correspondence: Frank M Boeckler, Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8 (Haus B), Tübingen, D-72076, Germany, Tel +49 7071 29 74567, Fax +49 7071 29 5637, Email
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Stahlecker J, Klett T, Schwer M, Jaag S, Dammann M, Ernst LN, Braun MB, Zimmermann MO, Kramer M, Lämmerhofer M, Stehle T, Coles M, Boeckler FM. Revisiting a challenging p53 binding site: a diversity-optimized HEFLib reveals diverse binding modes in T-p53C-Y220C. RSC Med Chem 2022; 13:1575-1586. [PMID: 36561072 PMCID: PMC9749929 DOI: 10.1039/d2md00246a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
The cellular tumor antigen p53 is a key component in cell cycle control. The mutation Y220C heavily destabilizes the protein thermally but yields a druggable crevice. We have screened the diversity-optimized halogen-enriched fragment library against T-p53C-Y220C with STD-NMR and DSF to identify hits, which we validated by 1H,15N-HSQC NMR. We could identify four hits binding in the Y220C cleft, one hit binding covalently and four hits binding to an uncharacterized binding site. Compound 1151 could be crystallized showing a flip of C220 and thus opening subsite 3. Additionally, 4482 was identified to alkylate cysteines. Data shows that the diversity-optimized HEFLib leads to multiple diverse hits. The identified scaffolds can be used to further optimize interactions with T-p53C-Y220C and increase thermal stability.
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Affiliation(s)
- Jason Stahlecker
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Theresa Klett
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Martin Schwer
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Simon Jaag
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Marcel Dammann
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Larissa N Ernst
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Michael B Braun
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 34 72076 Tübingen Germany
| | - Markus O Zimmermann
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Markus Kramer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 34 72076 Tübingen Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen Max-Planck-Ring 5 72076 Tübingen Germany
| | - Frank M Boeckler
- Lab for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen Sand 14 72076 Tübingen Germany
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Luo J, Dai H, Zeng C, Wu D, Cao M. A Theoretical Study of the Halogen Bond between Heteronuclear Halogen and Benzene. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228078. [PMID: 36432179 PMCID: PMC9692316 DOI: 10.3390/molecules27228078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied using density functional theory. The structures of the complexes between heteronuclear halogen and benzene have Cs symmetry. The interaction energies of the complexes between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene range from -27.80 to -37.18 kJ/mol, increasing with the increases in the polarity between the atoms of X and D, and are proportional to the angles of a between the Z axis and the covalent bond of heteronuclear halogen. The electron density (ρ) and corresponding Laplacian (∇2ρ) values indicate that the interaction of the heteronuclear halogen and benzene is a typical long-range weak interaction similar to a hydrogen bond. Independent gradient model analysis suggests that the van der Waals is the main interaction between the complexes of heteronuclear halogen and benzene. Symmetry-adapted perturbation theory analysis suggests that the electrostatic interaction is the dominant part in the complexes of C6H6⋯ClF, C6H6⋯ICl, C6H6⋯BrF and C6H6⋯IF, and the dispersion interaction is the main part in the complexes of C6H6⋯BrCl, C6H6⋯IBr.
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Dammann M, Stahlecker J, Zimmermann MO, Klett T, Rotzinger K, Kramer M, Coles M, Stehle T, Boeckler FM. Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes. J Med Chem 2022; 65:14539-14552. [DOI: 10.1021/acs.jmedchem.2c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel Dammann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Jason Stahlecker
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Markus O. Zimmermann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Kilian Rotzinger
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Markus Kramer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
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5
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Dammann M, Kramer M, Zimmermann MO, Boeckler FM. Quadruple Target Evaluation of Diversity-Optimized Halogen-Enriched Fragments (HEFLibs) Reveals Substantial Ligand Efficiency for AP2-Associated Protein Kinase 1 (AAK1). Front Chem 2022; 9:815567. [PMID: 35186897 PMCID: PMC8847695 DOI: 10.3389/fchem.2021.815567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Fragment-based drug discovery is one of the most utilized approaches for the identification of novel weakly binding ligands, by efficiently covering a wide chemical space with rather few compounds and by allowing more diverse binding modes to be found. This approach has led to various clinical candidates and approved drugs. Halogen bonding, on the other hand, has gained traction in molecular design and lead optimization, but could offer additional benefits in early drug discovery. Screening halogen-enriched fragments (HEFLibs) could alleviate problems associated with the late introduction of such a highly geometry dependent interaction. Usually, the binding mode is then already dominated by other strong interactions. Due to the fewer competing interactions in fragments, the halogen bond should more often act as an anchor point for the binding mode. Previously, we proposed a fragment library with a focus on diverse binding modes that involve halogens for gaining initial affinity and selectivity. Herein, we demonstrate the applicability of these HEFLibs with a small set of diverse enzymes: the histone-lysine N-methyltransferase DOT1L, the indoleamine 2,3-dioxygenase 1 (IDO1), the AP2-associated protein kinase 1 (AAK1), and the calcium/calmodulin-dependent protein kinase type 1G (CAMK1G). We were able to identify various binding fragments via STD-NMR. Using ITC to verify these initial hits, we determined affinities for many of these fragments. The best binding fragments exhibit affinities in the one-digit micromolar range and ligand efficiencies up to 0.83 for AAK1. A small set of analogs was used to study structure-affinity relationships and hereby analyze the specific importance of each polar interaction. This data clearly suggests that the halogen bond is the most important interaction of fragment 9595 with AAK1.
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Affiliation(s)
- Marcel Dammann
- Lab for Molecular Design and Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Markus Kramer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Markus O. Zimmermann
- Lab for Molecular Design and Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Frank M. Boeckler
- Lab for Molecular Design and Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, Germany
- *Correspondence: Frank M. Boeckler,
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6
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Walloch P, Henke B, Häuer S, Bergmann B, Spielmann T, Beitz E. Introduction of Scaffold Nitrogen Atoms Renders Inhibitors of the Malarial l-Lactate Transporter, PfFNT, Effective against the Gly107Ser Resistance Mutation. J Med Chem 2020; 63:9731-9741. [DOI: 10.1021/acs.jmedchem.0c00852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Philipp Walloch
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Björn Henke
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Susan Häuer
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Bärbel Bergmann
- Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Tobias Spielmann
- Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
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7
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Hayakawa D, Sawada N, Watanabe Y, Gouda H. A molecular interaction field describing nonconventional intermolecular interactions and its application to protein–ligand interaction prediction. J Mol Graph Model 2020; 96:107515. [DOI: 10.1016/j.jmgm.2019.107515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
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8
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Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
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Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
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9
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Lange A, Heidrich J, Zimmermann MO, Exner TE, Boeckler FM. Scaffold Effects on Halogen Bonding Strength. J Chem Inf Model 2019; 59:885-894. [DOI: 10.1021/acs.jcim.8b00621] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Andreas Lange
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Johannes Heidrich
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Markus O. Zimmermann
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Thomas E. Exner
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- Center for Bioinformatics Tuebingen (ZBIT), Eberhard Karls University Tuebingen, Sand 1, 72076 Tuebingen, Germany
| | - Frank M. Boeckler
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- Center for Bioinformatics Tuebingen (ZBIT), Eberhard Karls University Tuebingen, Sand 1, 72076 Tuebingen, Germany
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10
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Nunes R, Vila-Viçosa D, Machuqueiro M, Costa PJ. Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field. J Chem Theory Comput 2018; 14:5383-5392. [PMID: 30215528 DOI: 10.1021/acs.jctc.8b00278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodine corresponding to Rmin provides a good qualitative description of XBs in MD simulations, supporting the compatibility of our approach with the GROMOS 54A7 force field.
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Affiliation(s)
- Rafael Nunes
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal.,Centro de Química Estrutural, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Paulo J Costa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
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11
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Yang X, Yang F, Wu RZ, Yan CX, Zhou DG, Zhou PP, Yao X. Linear σ-hole⋯C O⋯σ-hole intermolecular interactions between carbon monoxide and dihalogen molecules XY (X, Y = Cl, Br). J Mol Graph Model 2017; 76:419-428. [DOI: 10.1016/j.jmgm.2017.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022]
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12
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Zhang Q, Xu Z, Shi J, Zhu W. Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. J Chem Inf Model 2017. [DOI: 10.1021/acs.jcim.7b00235] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Qian Zhang
- Department
of Computer Science and Technology, East China Normal University, Shanghai 200241, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin du Foriest, B-1420 Braine-l′Alleud, Belgium
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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13
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Petrelli R, Scortichini M, Kachler S, Boccella S, Cerchia C, Torquati I, Del Bello F, Salvemini D, Novellino E, Luongo L, Maione S, Jacobson KA, Lavecchia A, Klotz KN, Cappellacci L. Exploring the Role of N 6-Substituents in Potent Dual Acting 5'-C-Ethyltetrazolyladenosine Derivatives: Synthesis, Binding, Functional Assays, and Antinociceptive Effects in Mice ∇. J Med Chem 2017; 60:4327-4341. [PMID: 28447789 DOI: 10.1021/acs.jmedchem.7b00291] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structural determinants of affinity of N6-substituted-5'-C-(ethyltetrazol-2-yl)adenosine and 2-chloroadenosine derivatives at adenosine receptor (AR) subtypes were studied with binding and molecular modeling. Small N6-cycloalkyl and 3-halobenzyl groups furnished potent dual acting A1AR agonists and A3AR antagonists. 4 was the most potent dual acting human (h) A1AR agonist (Ki = 0.45 nM) and A3AR antagonist (Ki = 0.31 nM) and highly selective versus A2A; 11 and 26 were most potent at both h and rat (r) A3AR. All N6-substituted-5'-C-(ethyltetrazol-2-yl)adenosine derivatives proved to be antagonists at hA3AR but agonists at the rA3AR. Analgesia of 11, 22, and 26 was evaluated in the mouse formalin test (A3AR antagonist blocked and A3AR agonist strongly potentiated). N6-Methyl-5'-C-(ethyltetrazol-2-yl)adenosine (22) was most potent, inhibiting both phases, as observed combining A1AR and A3AR agonists. This study demonstrated for the first time the advantages of a single molecule activating two AR pathways both leading to benefit in this acute pain model.
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Affiliation(s)
- Riccardo Petrelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino , Via S. Agostino 1, 62032 Camerino, Italy
| | - Mirko Scortichini
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino , Via S. Agostino 1, 62032 Camerino, Italy
| | - Sonja Kachler
- Institut für Pharmakologie and Toxikologie, Universität Würzburg , D-97078 Würzburg, Germany
| | - Serena Boccella
- Section of Pharmacology "L. Donatelli", Department of Experimental Medicine, University of Campania "L. Vanvitelli" , 80138 Naples, Italy
| | - Carmen Cerchia
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II , 80131 Naples, Italy
| | - Ilaria Torquati
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino , Via S. Agostino 1, 62032 Camerino, Italy
| | - Fabio Del Bello
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino , Via S. Agostino 1, 62032 Camerino, Italy
| | - Daniela Salvemini
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
| | - Ettore Novellino
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II , 80131 Naples, Italy
| | - Livio Luongo
- Section of Pharmacology "L. Donatelli", Department of Experimental Medicine, University of Campania "L. Vanvitelli" , 80138 Naples, Italy
| | - Sabatino Maione
- Section of Pharmacology "L. Donatelli", Department of Experimental Medicine, University of Campania "L. Vanvitelli" , 80138 Naples, Italy
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Antonio Lavecchia
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II , 80131 Naples, Italy
| | - Karl-Norbert Klotz
- Institut für Pharmakologie and Toxikologie, Universität Würzburg , D-97078 Würzburg, Germany
| | - Loredana Cappellacci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino , Via S. Agostino 1, 62032 Camerino, Italy
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14
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Zhang Q, Xu Z, Zhu W. The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design. J Chem Inf Model 2016; 57:22-26. [DOI: 10.1021/acs.jcim.6b00628] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Qian Zhang
- Department
of Computer Science and Technology, East China Normal University, Shanghai 200241, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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15
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Zimmermann MO, Lange A, Zahn S, Exner TE, Boeckler FM. Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine. J Chem Inf Model 2016; 56:1373-83. [DOI: 10.1021/acs.jcim.6b00075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Markus O. Zimmermann
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Andreas Lange
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Stefan Zahn
- Physikalisch-Chemisches
Institut, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring
17, 35392 Gießen, Germany
| | - Thomas E. Exner
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
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16
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Zimmermann MO, Boeckler FM. Targeting the protein backbone with aryl halides: systematic comparison of halogen bonding and π⋯π interactions using N-methylacetamide. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00499c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Systematic plane scans reveal a seamless transition from σ-hole interactions with the carbonyl oxygen to interactions with the amide π-electrons at increasing distances.
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Affiliation(s)
- M. O. Zimmermann
- Department of Pharmaceutical and Medicinal Chemistry
- Institute of Pharmaceutical Sciences
- Eberhard Karls Universität Tübingen
- 72076 Tübingen
- Germany
| | - F. M. Boeckler
- Department of Pharmaceutical and Medicinal Chemistry
- Institute of Pharmaceutical Sciences
- Eberhard Karls Universität Tübingen
- 72076 Tübingen
- Germany
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17
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Adasme-Carreño F, Muñoz-Gutierrez C, Alzate-Morales JH. Halogen bonding in drug-like molecules: a computational and systematic study of the substituent effect. RSC Adv 2016. [DOI: 10.1039/c6ra14837a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Systematic study of the effect of fourteen chemical groups at the ortho, para and meta positions of NMA⋯halobenzene complexes showed a significant influence on halogen bonding, and also non-additive effects. A comprehensive description is reported.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
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18
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Wilcken R, Zimmermann MO, Bauer MR, Rutherford TJ, Fersht AR, Joerger AC, Boeckler FM. Experimental and Theoretical Evaluation of the Ethynyl Moiety as a Halogen Bioisostere. ACS Chem Biol 2015; 10:2725-32. [PMID: 26378745 PMCID: PMC4836799 DOI: 10.1021/acschembio.5b00515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Bioisosteric replacements
are widely used in medicinal chemistry
to improve physicochemical and ADME properties of molecules while
retaining or improving affinity. Here, using the p53 cancer mutant
Y220C as a test case, we investigate both computationally and experimentally
whether an ethynyl moiety is a suitable bioisostere to replace iodine
in ligands that form halogen bonds with the protein backbone. This
bioisosteric transformation is synthetically feasible via Sonogashira
cross-coupling. In our test case of a particularly strong halogen
bond, replacement of the iodine with an ethynyl group resulted in
a 13-fold affinity loss. High-resolution crystal structures of the
two analogues in complex with the p53-Y220C mutant enabled us to correlate
the different affinities with particular features of the binding site
and subtle changes in ligand binding mode. In addition, using QM calculations
and analyzing the PDB, we provide general guidelines for identifying
cases where such a transformation is likely to improve ligand recognition.
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Affiliation(s)
- Rainer Wilcken
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Markus O. Zimmermann
- Molecular
Design and Pharmaceutical Biophysics, Department of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Matthias R. Bauer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Trevor J. Rutherford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alan R. Fersht
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Andreas C. Joerger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Frank M. Boeckler
- Molecular
Design and Pharmaceutical Biophysics, Department of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
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19
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Lange A, Günther M, Büttner FM, Zimmermann MO, Heidrich J, Hennig S, Zahn S, Schall C, Sievers-Engler A, Ansideri F, Koch P, Laemmerhofer M, Stehle T, Laufer SA, Boeckler FM. Targeting the Gatekeeper MET146 of C-Jun N-Terminal Kinase 3 Induces a Bivalent Halogen/Chalcogen Bond. J Am Chem Soc 2015; 137:14640-52. [DOI: 10.1021/jacs.5b07090] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Andreas Lange
- Molecular
Design and Pharmaceutical Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Marcel Günther
- Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Felix Michael Büttner
- Interfaculty
Institute of Biochemistry, Eberhard Karls Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Markus O. Zimmermann
- Molecular
Design and Pharmaceutical Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Johannes Heidrich
- Molecular
Design and Pharmaceutical Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Susanne Hennig
- Molecular
Design and Pharmaceutical Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan Zahn
- Institute
of Physical Chemistry, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring
17, 35392 Gießen, Germany
| | - Christoph Schall
- Interfaculty
Institute of Biochemistry, Eberhard Karls Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Adrian Sievers-Engler
- Pharmaceutical
(Bio)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Francesco Ansideri
- Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Pierre Koch
- Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Laemmerhofer
- Pharmaceutical
(Bio)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Thilo Stehle
- Interfaculty
Institute of Biochemistry, Eberhard Karls Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
- Department
of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Stefan A. Laufer
- Pharmaceutical
and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Molecular
Design and Pharmaceutical Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
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20
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Zimmermann MO, Lange A, Boeckler FM. Evaluating the potential of halogen bonding in molecular design: automated scaffold decoration using the new scoring function XBScore. J Chem Inf Model 2015; 55:687-99. [PMID: 25654403 DOI: 10.1021/ci5007118] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a QM-derived empirical scoring function for the interaction between aromatic halogenated ligands and the carbonyl oxygen atom of the protein backbone. Applying this scoring function, we developed an algorithm that evaluates the potential of protein-bound ligands to form favorable halogen-bonding contacts upon scaffold decoration with chlorine, bromine, or iodine. Full recovery of all existing halogen bonds in the PDB involving the protein backbone was achieved with our protocol. Interestingly, the potential for introducing halogen bonds through scaffold decoration of unsubstituted aromatic carbon atoms appears to easily match the number of previously known halogen bonds. Our approach can thus be used as a blueprint for integration of halogen bonding into general empirical scoring functions, which at present ignore this interaction. Most importantly, we were able to identify a substantial number of protein-ligand complexes where the benefits and challenges of introducing a halogen bond by molecular design can be studied experimentally.
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Affiliation(s)
- Markus O Zimmermann
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Lange
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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21
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Ren J, He Y, Chen W, Chen T, Wang G, Wang Z, Xu Z, Luo X, Zhu W, Jiang H, Shen J, Xu Y. Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors. J Med Chem 2014; 57:3588-93. [PMID: 24702184 DOI: 10.1021/jm5002315] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reveal that binding strength of the halogen bonding between chlorine, bromine, and iodine of inhibitor and the protein is -1.57, -3.09, and -5.59 kJ/mol, respectively. The halogens interact with the designed residue Y612 and an unexpected buried water molecule.
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Affiliation(s)
- Jing Ren
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS) , 555 Zuchongzhi Road, Shanghai 201203, China
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22
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Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery. Future Med Chem 2014; 6:617-39. [DOI: 10.4155/fmc.14.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Halogen bonding has recently experienced a renaissance, gaining increased recognition as a useful molecular interaction in the life sciences. Halogen bonds are favorable, fairly directional interactions between an electropositive region on the halogen (the σ-hole) and a number of different nucleophilic interaction partners. Some aspects of halogen bonding are not yet understood well enough to take full advantage of its potential in drug discovery. We describe and present the concept of halogen-enriched fragment libraries. These libraries consist of unique chemical probes, facilitating the identification of favorable halogen bonds by sharing the advantages of classical fragment-based screening. Besides providing insights into the nature and applicability of halogen bonding, halogen-enriched fragment libraries provide smart starting points for hit-to-lead evolution.
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