1
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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2
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Peluso P, Mamane V, Spissu Y, Casu G, Dessì A, Dallocchio R, Sechi B, Palmieri G, Rozzo C. Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines. ChemMedChem 2024; 19:e202300662. [PMID: 38489502 DOI: 10.1002/cmdc.202300662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR CNRS 7177, Centre National de la Recherche Scientifique (CNRS), 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Ylenia Spissu
- Istituto di Scienze delle Produzioni Alimentari ISPA-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Giuseppina Casu
- Istituto di Ricerca Genetica e Biomedica IRGB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Barbara Sechi
- Istituto di Chimica Biomolecolare ICB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Giuseppe Palmieri
- Istituto di Ricerca Genetica e Biomedica IRGB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
| | - Carla Rozzo
- Istituto di Ricerca Genetica e Biomedica IRGB-CNR, Consiglio Nazionale delle Ricerche (CNR), Traversa La Crucca, 3, Li Punti, 07100, Sassari, Italy
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3
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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4
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Ong HW, de Silva C, Avalani K, Kwarcinski F, Mansfield CR, Chirgwin M, Truong A, Derbyshire ER, Zutshi R, Drewry DH. Characterization of 2,4-Dianilinopyrimidines Against Five P. falciparum Kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. ACS Med Chem Lett 2023; 14:1774-1784. [PMID: 38116430 PMCID: PMC10726455 DOI: 10.1021/acsmedchemlett.3c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Plasmodium kinases are increasingly recognized as potential novel antiplasmodial targets for the treatment of malaria, but only a small subset of these kinases have had structure-activity relationship (SAR) campaigns reported. Herein we report the discovery of CZC-54252 (1) as an inhibitor of five P. falciparum kinases PfARK1, PfARK3, PfNEK3, PfPK9, and PfPKB. 39 analogues were evaluated against all five kinases to establish SAR at three regions of the kinase active site. Nanomolar inhibitors of each kinase were discovered. We identified common and divergent SAR trends across all five kinases, highlighting substituents in each region that improve potency and selectivity for each kinase. Potent analogues were evaluated against the P. falciparum blood stage. Eight submicromolar inhibitors were discovered, of which 37 demonstrated potent antiplasmodial activity (EC50 = 0.16 μM). Our results provide an understanding of features needed to inhibit each individual kinase and lay groundwork for future optimization efforts toward novel antimalarials.
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Affiliation(s)
- Han Wee Ong
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chandi de Silva
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Krisha Avalani
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Frank Kwarcinski
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Christopher R. Mansfield
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
| | - Michael Chirgwin
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Anna Truong
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Reena Zutshi
- Luceome
Biotechnologies, LLC, 1665 East 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - David H. Drewry
- Structural
Genomics Consortium and Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger
Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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5
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Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [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: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
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Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
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6
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Vaas S, Zimmermann MO, Schollmeyer D, Stahlecker J, Engelhardt MU, Rheinganz J, Drotleff B, Olfert M, Lämmerhofer M, Kramer M, Stehle T, Boeckler FM. Principles and Applications of CF 2X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery. J Med Chem 2023; 66:10202-10225. [PMID: 37487500 PMCID: PMC10424184 DOI: 10.1021/acs.jmedchem.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 07/26/2023]
Abstract
As an orthogonal principle to the established (hetero)aryl halides, we herein highlight the usefulness of CF2X (X = Cl, Br, or I) moieties. Using tool compounds bearing CF2X moieties, we study their chemical/metabolic stability and their logP/solubility, as well as the role of XB in their small molecular crystal structures. Employing QM techniques, we analyze the observed interactions, provide insights into the conformational flexibilities and preferences in the potential interaction space. For their application in molecular design, we characterize their XB donor capacities and its interaction strength dependent on geometric parameters. Implementation of CF2X acetamides into our HEFLibs and biophysical evaluation (STD-NMR/ITC), followed by X-ray analysis, reveals a highly interesting binding mode for fragment 23 in JNK3, featuring an XB of CF2Br toward the P-loop, as well as chalcogen bonds. We suggest that underexplored chemical space combined with unconventional binding modes provides excellent opportunities for patentable chemotypes for therapeutic intervention.
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Affiliation(s)
- Sebastian Vaas
- Laboratory
for Molecular Design & Pharmaceutical Biophysics, Institute of
Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Markus O. Zimmermann
- Laboratory
for Molecular Design & Pharmaceutical Biophysics, Institute of
Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Dieter Schollmeyer
- Department
of Chemistry, Johannes Gutenberg-Universität
Mainz, 55099 Mainz, Germany
| | - Jason Stahlecker
- Laboratory
for Molecular Design & Pharmaceutical Biophysics, Institute of
Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Marc U. Engelhardt
- Laboratory
for Molecular Design & Pharmaceutical Biophysics, Institute of
Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Janosch Rheinganz
- Laboratory
for Molecular Design & Pharmaceutical Biophysics, Institute of
Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Bernhard Drotleff
- Pharmaceutical
(Bio)Analysis, Institute of Pharmaceutical Sciences, Department of
Pharmacy and Biochemistry, Eberhard Karls
Universität Tübingen, 72076 Tübingen, Germany
| | - Matthias Olfert
- Pharmaceutical
(Bio)Analysis, Institute of Pharmaceutical Sciences, Department of
Pharmacy and Biochemistry, Eberhard Karls
Universität Tübingen, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Pharmaceutical
(Bio)Analysis, Institute of Pharmaceutical Sciences, Department of
Pharmacy and Biochemistry, Eberhard Karls
Universität Tübingen, 72076 Tübingen, Germany
| | - Markus Kramer
- Institute
of Organic Chemistry, Eberhard Karls Universität
Tübingen, 72076 Tübingen, Germany
| | - Thilo Stehle
- Interfaculty
Institute of Biochemistry, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design & Pharmaceutical Biophysics, Institute of
Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Institute
for Bioinformatics and Medical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
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7
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Ito A, Asato M, Asami Y, Fukuda K, Yamasaki R, Okamoto I. Synthesis and Conformational Analysis of N-Aromatic Acetamides Bearing Thiophene: Effect of Intramolecular Chalcogen-Chalcogen Interaction on Amide Conformational Stability. J Org Chem 2023. [PMID: 37154822 DOI: 10.1021/acs.joc.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The conformations of aromatic amides bearing an N-(2-thienyl) or N-(3-thienyl) group were investigated in solution and in the crystal state. NMR spectral data indicate that the conformational preferences of these amides in solution are dependent not only on the relative π-electron densities of the N-aromatic moieties, but also on the three-dimensional relationship between carbonyl oxygen and the N-aromatic moieties. A comparison of the conformational preferences of N-(2-thienyl)amides and N-(3-thienyl)amides revealed that the Z-conformers of N-(2-thienyl)acetamides are stabilized by 1,5-type intramolecular S···O═C interactions between amide carbonyl and thiophene sulfur. The crystal structures of these compounds were similar to the solution structures. The stabilization energy due to 1,5-type intramolecular S···O═C interaction in N-aryl-N-(2-thienyl)acetamides and N-methyl-N-(2-thienyl)acetamide was estimated to be ca. 0.74 and 0.93 kcal/mol, respectively.
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Affiliation(s)
- Ai Ito
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Marino Asato
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yuki Asami
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Kazuo Fukuda
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Ryu Yamasaki
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Iwao Okamoto
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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8
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Geng H, Chen F, Zhao Y, Guo B, Tang L, Yang YY. Protecting-Group-Free Synthesis of Meridianin A-G and Derivatives and Its Antibiofilm Evaluation. J Org Chem 2023; 88:3927-3934. [PMID: 36815756 DOI: 10.1021/acs.joc.2c02837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Herein, a protecting-group-free protocol was developed to realize a time and step economy diversification of the Meridianin alkaloid. A broad range of substituents are tolerated to deliver the products in moderate to high yields, and the first synthesis of Meridianin B was achieved. The simplicity of this protocol enables the rapid construction of a Meridianin derivative library for antibiofilm evaluation. Preliminary results reveal that Meridianin derivatives were capable of inhibiting the Acinetobacter baumannii biofilm and lowering the antibiotic MIC synergistically.
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Affiliation(s)
- Huidan Geng
- School of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, 550014 Guiyang, P. R. China
| | - Fei Chen
- School of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, 550014 Guiyang, P. R. China
| | - Yonglong Zhao
- School of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, 550014 Guiyang, P. R. China
| | - Bing Guo
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550004 Guiyang, P. R. China
| | - Lei Tang
- School of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, 550014 Guiyang, P. R. China
| | - Yuan-Yong Yang
- School of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, 550014 Guiyang, P. R. China
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9
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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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10
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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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11
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Galal KA, Truong A, Kwarcinski F, de Silva C, Avalani K, Havener TM, Chirgwin ME, Merten E, Ong HW, Willis C, Abdelwaly A, Helal MA, Derbyshire ER, Zutshi R, Drewry DH. Identification of Novel 2,4,5-Trisubstituted Pyrimidines as Potent Dual Inhibitors of Plasmodial PfGSK3/ PfPK6 with Activity against Blood Stage Parasites In Vitro. J Med Chem 2022; 65:13172-13197. [PMID: 36166733 PMCID: PMC9574854 DOI: 10.1021/acs.jmedchem.2c00996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Essential plasmodial kinases PfGSK3
and PfPK6 are considered novel drug targets to combat
rising
resistance to traditional antimalarial therapy. Herein, we report
the discovery of IKK16 as a dual PfGSK3/PfPK6 inhibitor active against blood stage Pf3D7 parasites. To establish structure–activity relationships
for PfPK6 and PfGSK3, 52 analogues
were synthesized and assessed for the inhibition of PfGSK3 and PfPK6, with potent inhibitors further assessed
for activity against blood and liver stage parasites. This culminated
in the discovery of dual PfGSK3/PfPK6 inhibitors 23d (PfGSK3/PfPK6 IC50 = 172/11 nM) and 23e (PfGSK3/PfPK6 IC50 = 97/8 nM)
with antiplasmodial activity (23dPf3D7 EC50 = 552 ± 37 nM and 23ePf3D7 EC50 = 1400 ± 13 nM). However, both
compounds exhibited significant promiscuity when tested in a panel
of human kinase targets. Our results demonstrate that dual PfPK6/PfGSK3 inhibitors with antiplasmodial
activity can be identified and can set the stage for further optimization
efforts.
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Affiliation(s)
- Kareem A Galal
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Anna Truong
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Frank Kwarcinski
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Chandi de Silva
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Krisha Avalani
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Tammy M Havener
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michael E Chirgwin
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Eric Merten
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Han Wee Ong
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Caleb Willis
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - Ahmad Abdelwaly
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza 12587, Egypt
| | - Mohamed A Helal
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza 12587, Egypt.,Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
| | - Reena Zutshi
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, Arizona 85719, United States
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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12
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Jackson JJ, Shibuya GM, Ravishankar B, Adusumilli L, Bradford D, Brockstedt DG, Bucher C, Bui M, Cho C, Colas C, Cutler G, Dukes A, Han X, Hu DX, Jacobson S, Kassner PD, Katibah GE, Ko MYM, Kolhatkar U, Leger PR, Ma A, Marshall L, Maung J, Ng AA, Okano A, Pookot D, Poon D, Ramana C, Reilly MK, Robles O, Schwarz JB, Shakhmin AA, Shunatona HP, Sreenivasan R, Tivitmahaisoon P, Xu M, Zaw T, Wustrow DJ, Zibinsky M. Potent GCN2 Inhibitor Capable of Reversing MDSC-Driven T Cell Suppression Demonstrates In Vivo Efficacy as a Single Agent and in Combination with Anti-Angiogenesis Therapy. J Med Chem 2022; 65:12895-12924. [PMID: 36127295 DOI: 10.1021/acs.jmedchem.2c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
General control nonderepressible 2 (GCN2) protein kinase is a cellular stress sensor within the tumor microenvironment (TME), whose signaling cascade has been proposed to contribute to immune escape in tumors. Herein, we report the discovery of cell-potent GCN2 inhibitors with excellent selectivity against its closely related Integrated Stress Response (ISR) family members heme-regulated inhibitor kinase (HRI), protein kinase R (PKR), and (PKR)-like endoplasmic reticulum kinase (PERK), as well as good kinome-wide selectivity and favorable PK. In mice, compound 39 engages GCN2 at levels ≥80% with an oral dose of 15 mg/kg BID. We also demonstrate the ability of compound 39 to alleviate MDSC-related T cell suppression and restore T cell proliferation, similar to the effect seen in MDSCs from GCN2 knockout mice. In the LL2 syngeneic mouse model, compound 39 demonstrates significant tumor growth inhibition (TGI) as a single agent. Furthermore, TGI mediated by anti-VEGFR was enhanced by treatment with compound 39 demonstrating the complementarity of these two mechanisms.
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Affiliation(s)
- Jeffrey J Jackson
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Grant M Shibuya
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Buvana Ravishankar
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Lavanya Adusumilli
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Delia Bradford
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Dirk G Brockstedt
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Cyril Bucher
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Minna Bui
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Cynthia Cho
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Christoph Colas
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Gene Cutler
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Adrian Dukes
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Xinping Han
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Dennis X Hu
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Scott Jacobson
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Paul D Kassner
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - George E Katibah
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Michelle Yoo Min Ko
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Urvi Kolhatkar
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Paul R Leger
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Anqi Ma
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Lisa Marshall
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Jack Maung
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Andrew A Ng
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Akinori Okano
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Deepa Pookot
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Daniel Poon
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Chandru Ramana
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Maureen K Reilly
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Omar Robles
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Jacob B Schwarz
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Anton A Shakhmin
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Hunter P Shunatona
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Raashi Sreenivasan
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | | | - Mengshu Xu
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Thant Zaw
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - David J Wustrow
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
| | - Mikhail Zibinsky
- RAPT Therapeutics, 561 Eccles Avenue, South San Francisco, California94080, United States
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13
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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14
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Young J, Garikipati N, Durrant JD. BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript. J Chem Inf Model 2022; 62:753-760. [PMID: 35129332 PMCID: PMC8889568 DOI: 10.1021/acs.jcim.1c01461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
BINding ANAlyzer
(BINANA) is an algorithm for identifying and characterizing
receptor/ligand interactions and other factors that contribute to
binding. We recently updated BINANA to make the algorithm more accessible
to a broader audience. We have also ported the Python3 codebase to
JavaScript, thus enabling BINANA analysis in the web browser. As proof
of principle, we created a web-browser application so students and
chemical-biology researchers can quickly visualize receptor/ligand
complexes and their unique binding interactions.
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Affiliation(s)
- Jade Young
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Neerja Garikipati
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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15
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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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16
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Bata N, Chaikuad A, Bakas NA, Limpert AS, Lambert LJ, Sheffler DJ, Berger LM, Liu G, Yuan C, Wang L, Peng Y, Dong J, Celeridad M, Layng F, Knapp S, Cosford NDP. Inhibitors of the Hippo Pathway Kinases STK3/MST2 and STK4/MST1 Have Utility for the Treatment of Acute Myeloid Leukemia. J Med Chem 2022; 65:1352-1369. [PMID: 34807584 PMCID: PMC10149138 DOI: 10.1021/acs.jmedchem.1c00804] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Serine/threonine-protein kinases 3 and 4 (STK3 and STK4, respectively) are key components of the Hippo signaling pathway, which regulates cell proliferation and death and provides a potential therapeutic target for acute myeloid leukemia (AML). Herein, we report the structure-based design of a series of pyrrolopyrimidine derivatives as STK3 and STK4 inhibitors. In an initial screen, the compounds exhibited low nanomolar potency against both STK3 and STK4. Crystallization of compound 6 with STK4 revealed two-point hinge binding in the ATP-binding pocket. Further characterization and analysis demonstrated that compound 20 (SBP-3264) specifically inhibited the Hippo signaling pathway in cultured mammalian cells and possessed favorable pharmacokinetic and pharmacodynamic properties in mice. We show that genetic knockdown and pharmacological inhibition of STK3 and STK4 suppress the proliferation of AML cells in vitro. Thus, SBP-3264 is a valuable chemical probe for understanding the roles of STK3 and STK4 in AML and is a promising candidate for further advancement as a potential therapy.
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Affiliation(s)
- Nicole Bata
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Apirat Chaikuad
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Nicole A Bakas
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Allison S Limpert
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lester J Lambert
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Douglas J Sheffler
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lena M Berger
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Guoxiong Liu
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Cunxiang Yuan
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Li Wang
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Yi Peng
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Jing Dong
- Chemistry Department, Viva Biotech Ltd., 581 Shen Kuo Road, Shanghai 201203, China
| | - Maria Celeridad
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Fabiana Layng
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Stefan Knapp
- Buchmann Institute for Molecular Life Sciences, Structural Genomics Consortium, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Max von Lauestrasse 9, Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany.,Translational cancer network DKTK site Frankfurt/Mainz and Frankfurt Cancer Institute (FCI), Johann Wolfgang Goethe-University, D-60438 Frankfurt am Main, Germany
| | - Nicholas D P Cosford
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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17
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Piña MDLN, Frontera A, Bauza A. Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study. ACS Chem Biol 2021; 16:1701-1708. [PMID: 34427431 PMCID: PMC8525861 DOI: 10.1021/acschembio.1c00417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
In this study, we provide experimental
(Protein Data Bank (PDB)
inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence
of the involvement of charge assisted chalcogen bonding (ChB) interactions
in the recognition and folding mechanisms of S-adenosylmethionine
(SAM) riboswitches. Concretely, an initial PDB search revealed several
examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine
(EEM) molecules and uracil (U) bases belonging to RNA take place.
While these interactions are usually described as a merely Coulombic
attraction between the positively charged S/Se group and RNA, theoretical
calculations indicated that the σ holes of S and Se are involved.
Moreover, computational models shed light on the strength and directionality
properties of the interaction, which was also further characterized
from a charge-density perspective using Bader’s “Atoms
in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot)
visual index, and Natural Bonding Orbital (NBO) analyses. As far as
our knowledge extends, this is the first time that ChBs in SAM–RNA
complexes have been systematically analyzed, and we believe the results
might be useful for scientists working in the field of RNA engineering
and chemical biology as well as to increase the visibility of the
interaction among the biological community.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauza
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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18
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Assessing reversible and irreversible binding effects of kinase covalent inhibitors through ADP-Glo assays. STAR Protoc 2021; 2:100717. [PMID: 34401783 PMCID: PMC8353353 DOI: 10.1016/j.xpro.2021.100717] [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] [Indexed: 12/02/2022] Open
Abstract
Typical enzymatic inhibition assays often demonstrate improved potency for kinase covalent inhibitors compared to reversible inhibitors. This can primarily be attributed to the irreversible mode of action and could affect the evaluations of the ATP-competitive nature of covalent inhibitors, hindering optimization of these compounds. Here, we describe a version of ADP-Glo assay, in which modification of inhibitor incubation time in the presence or absence of ATP enables a quick assessment of relative reversible and irreversible effects of kinase covalent inhibitors. For complete details on the use and execution of this protocol, please refer to Schröder et al. (2020). Simple enzymatic assays for quick assessment of kinase covalent inhibitors Modification of incubation time allows probing ATP-competitive nature of inhibitors The assays enable the evaluation of relative reversible and irreversible effects
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19
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Fernández Riveras JA, Frontera A, Bauzá A. Selenium chalcogen bonds are involved in protein-carbohydrate recognition: a combined PDB and theoretical study. Phys Chem Chem Phys 2021; 23:17656-17662. [PMID: 34373871 DOI: 10.1039/d1cp01929e] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this manuscript the ability of selenium carbohydrates to undergo chalcogen bonding (ChB) interactions with protein residues has been studied at the RI-MP2/def2-TZVP level of theory. An inspection of the Protein Data Bank (PDB) revealed SeA (A = O, C and S) intermolecular contacts involving Se-pyranose ligands and ASP, TYR, SER and MET residues. Theoretical models were built to analyse the strength and directionality of the interaction together with "Atoms in Molecules" (AIM), Natural Bonding Orbital (NBO) and Non Covalent Interactions plot (NCIplot) analyses, which further assisted in the characterization of the ChBs described herein. We expect that the results from this study will be useful to expand the current knowledge regarding biological ChBs as well as to increase the visibility of the interaction among the carbohydrate chemistry community.
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Affiliation(s)
- Jose A Fernández Riveras
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma (Baleares) 07122, Spain.
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20
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Frontera A, Bauzá A. Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases. Org Biomol Chem 2021; 19:6858-6864. [PMID: 34319314 DOI: 10.1039/d1ob01212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.
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Affiliation(s)
- Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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21
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study. J Comput Chem 2021; 42:688-698. [PMID: 33543482 PMCID: PMC7986859 DOI: 10.1002/jcc.26489] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/27/2022]
Abstract
We have performed a hierarchical ab initio benchmark and DFT performance study of D2 Ch•••A- chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all-electron relativistically contracted variants of Karlsruhe basis sets (ZORA-def2-SVP, ZORA-def2-TZVPP, ZORA-def2-QZVPP) with and without diffuse functions. The highest-level ZORA-CCSD(T)/ma-ZORA-def2-QZVPP counterpoise-corrected complexation energies (ΔECPC ) are converged within 1.1-3.4 kcal mol-1 and 1.5-3.1 kcal mol-1 with respect to the method and basis set, respectively. Next, we used the ZORA-CCSD(T)/ma-ZORA-def2-QZVPP (ΔECPC ) as reference data for analyzing the performance of 13 different ZORA-relativistic DFT approaches in combination with the Slater-type QZ4P basis set. We find that the three-best performing functionals are M06-2X, B3LYP, and M06, with mean absolute errors (MAE) of 4.1, 4.2, and 4.3 kcal mol-1 , respectively. The MAE for BLYP-D3(BJ) and PBE amount to 8.5 and 9.3 kcal mol-1 , respectively.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Institute for Molecules and MaterialsRadboud University NijmegenNijmegenNetherlands
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22
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de Azevedo Santos L, van der Lubbe SCC, Hamlin TA, Ramalho TC, Matthias Bickelhaupt F. A Quantitative Molecular Orbital Perspective of the Chalcogen Bond. ChemistryOpen 2021; 10:391-401. [PMID: 33594829 PMCID: PMC8015733 DOI: 10.1002/open.202000323] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
| | - Stephanie C. C. van der Lubbe
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Teodorico C. Ramalho
- Department of Chemistry Institute of Natural SciencesFederal University of LavrasCEP 37200-900Lavras-MGBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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23
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Liu N, Li Q, McDowell SAC. Reliable Comparison of Pnicogen, Chalcogen, and Halogen Bonds in Complexes of 6-OXF 2-Fulvene (X = As, Sb, Se, Te, Be, I) With Three Electron Donors. Front Chem 2020; 8:608486. [PMID: 33425859 PMCID: PMC7793776 DOI: 10.3389/fchem.2020.608486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/27/2020] [Indexed: 01/03/2023] Open
Abstract
The pnicogen, chalcogen, and halogen bonds between 6-OXF2-fulvene (X = As, Sb, Se, Te, Br, and I) and three nitrogen-containing bases (FCN, HCN, and NH3) are compared. For each nitrogen base, the halogen bond is strongest, followed by the pnicogen bond, and the chalcogen bond is weakest. For each type of bond, the binding increases in the FCN < HCN < NH3 pattern. Both FCN and HCN engage in a bond with comparable strengths and the interaction energies of most bonds are < -6 kcal/mol. However, the strongest base NH3 forms a much more stable complex, particularly for the halogen bond with the interaction energy going up to -18 kcal/mol. For the same type of interaction, its strength increases as the mass of the central X atom increases. These bonds are different in strength, but all of them are dominated by the electrostatic interaction, with the polarization contribution important for the stronger interaction. The presence of these bonds changes the geometries of 6-OXF2-fulvene, particularly for the halogen bond formed by NH3, where the F-X-F arrangement is almost vertical to the fulvene ring.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, China
| | - Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
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24
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Duong MTH, Lee JH, Ahn HC. C-Jun N-terminal kinase inhibitors: Structural insight into kinase-inhibitor complexes. Comput Struct Biotechnol J 2020; 18:1440-1457. [PMID: 32637042 PMCID: PMC7327381 DOI: 10.1016/j.csbj.2020.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 12/12/2022] Open
Abstract
The activation of c-Jun N-terminal kinases (JNKs) plays an important role in physiological processes including neuronal function, immune activity, and development, and thus, JNKs have been a therapeutic target for various diseases such as neurodegenerative diseases, inflammation, and cancer. Efforts to develop JNK-specific inhibitors have been ongoing for several decades. In this process, the structures of JNK in complex with various inhibitors have contributed greatly to the design of novel compounds and to the elucidation of structure-activity relationships. Almost 100 JNK structures with various compounds have been determined. Here we summarize the information gained from these structures and classify the inhibitors into several groups based on the binding mode. These groups include inhibitors in the open conformation and closed conformation of the gatekeeper residue, non-ATP site binders, peptides, covalent inhibitors, and type II kinase inhibitors. Through this work, deep insight into the interaction of inhibitors with JNKs can be gained and this will be helpful for developing novel, potent, and selective inhibitors.
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Affiliation(s)
- Men Thi Hoai Duong
- Department of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi 10326, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, South Korea
| | - Hee-Chul Ahn
- Department of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi 10326, South Korea
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25
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, 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
- University of Chinese Academy of Sciences, Beijing 100049, 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
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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26
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Kumar V, Xu Y, Bryce DL. Double Chalcogen Bonds: Crystal Engineering Stratagems via Diffraction and Multinuclear Solid-State Magnetic Resonance Spectroscopy. Chemistry 2020; 26:3275-3286. [PMID: 31794082 DOI: 10.1002/chem.201904795] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Indexed: 12/22/2022]
Abstract
Group 16 chalcogens potentially provide Lewis-acidic σ-holes, which are able to form attractive supramolecular interactions with electron rich partners through chalcogen bonds. Here, a multifaceted experimental and computational study of a large series of novel chalcogen-bonded cocrystals, prepared using the principles of crystal engineering, is presented. Single-crystal X-ray diffraction studies reveal that dicyanoselenadiazole and dicyanotelluradiazole derivatives work as promising supramolecular synthons with the ability to form double chalcogen bonds with a wide range of electron donors including halides and oxygen- and nitrogen-containing heterocycles. Extensive 77 Se and 125 Te solid-state nuclear magnetic resonance spectroscopic investigations of cocrystals establish correlations between the NMR parameters of selenium and tellurium and the local chalcogen bonding geometry. The relationships between the electronic environment of the chalcogen bond and the 77 Se and 125 Te chemical shift tensors were elucidated through a natural localized molecular orbital density functional theory analysis. This systematic study of chalcogen-bond-based crystal engineering lays the foundations for the preparation of the various multicomponent systems and establishes solid-state NMR protocols to detect these interactions in powdered materials.
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Affiliation(s)
- Vijith Kumar
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
| | - Yijue Xu
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, K1N 6N5, Canada
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27
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Kumar V, Xu Y, Leroy C, Bryce DL. Direct investigation of chalcogen bonds by multinuclear solid-state magnetic resonance and vibrational spectroscopy. Phys Chem Chem Phys 2020; 22:3817-3824. [DOI: 10.1039/c9cp06267j] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a multifaceted experimental and computational study of three self-complementary chalcogen-bond donors as well as a series of seven chalcogen bonded cocrystals.
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Affiliation(s)
- Vijith Kumar
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- 10 Marie Curie Private
- Ottawa
- Canada
| | - Yijue Xu
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- 10 Marie Curie Private
- Ottawa
- Canada
| | - César Leroy
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- 10 Marie Curie Private
- Ottawa
- Canada
| | - David L. Bryce
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- 10 Marie Curie Private
- Ottawa
- Canada
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28
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Previtali V, Sánchez-Sanz G, Trujillo C. Theoretical Investigation of Cyano-Chalcogen Dimers and Their Importance in Molecular Recognition. Chemphyschem 2019; 20:3186-3194. [PMID: 31608563 DOI: 10.1002/cphc.201900899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Indexed: 11/10/2022]
Abstract
In this manuscript the different noncovalent interactions established between (HYCN)2 dimers (Y=S, Se and Te) have been studied at the MP2 and CCSD(T) level of theory. Several homodimers have been taken into account, highlighting the capacity of these compounds to act both as electron donor and acceptor. The main properties studied were geometries, binding energy (Eb ), and molecular electrostatic potential (MEP). Given the wide application of chalcogen bonds, and more specifically of cyano-chalcogen moieties in molecular recognition, natural bond orbital (NBO), "atoms-in-molecules" (AIM), and electron density shift (EDS) analysis were also used to analyse the different noncovalent interactions upon complexation. The presence of hydrogen, chalcogen and dipole-dipole interactions was confirmed and their implications on molecular recognition were analysed.
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Affiliation(s)
- Viola Previtali
- Center for Nanomedicine & Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby, DK, Denmark
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublini, 152-160 Pearse Street, Dublin 2, Ireland
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29
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Insights into the c-Jun N-terminal kinase 3 (JNK3) inhibitors: CoMFA, CoMSIA analyses and molecular docking studies. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02416-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Tuffaha GO, Hatmal MM, Taha MO. Discovery of new JNK3 inhibitory chemotypes via QSAR-Guided selection of docking-based pharmacophores and comparison with other structure-based pharmacophore modeling methods. J Mol Graph Model 2019; 91:30-51. [PMID: 31158642 DOI: 10.1016/j.jmgm.2019.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022]
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31
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Wang Y, Fu Q, Zhou Y, Du Y, Huang N. Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions. J Chem Inf Model 2019; 59:3136-3143. [PMID: 31187992 DOI: 10.1021/acs.jcim.9b00128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Halogen bond interaction between a protein electronegative atom and a ligand halogen atom is increasingly attracting attention in the field of structure-based drug design. Nevertheless, gaps in understanding make it desirable to better examine the role of forces governing the formation of favorable halogen bond interactions, and the development of effective and efficient computational approaches to "design in" favorable halogen bond interactions in lead optimization process are warranted. Here, we analyzed the binding-site water properties of crystal structures with characterized halogen bond interactions between ligand halogen atoms and protein backbone carbonyl groups and, thus, found that halogen atoms involved in halogen bond interactions frequently replace calculated binding-site waters upon ligand binding. Moreover, we observed that the preferential directionality of halogen bond interactions aligns well with the orientations of these replaced waters, and these replaced waters exhibited differential energetic characteristics as compared to waters that are displaced by halogen atoms that do not form halogen bond interactions. Our discovery that replacement of calculated binding-site waters contributes to the formation of favorable halogen bond interactions suggests a practical approach for rational drug design utilizing halogen bond interactions with protein backbone carbonyl groups.
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Affiliation(s)
- Yuanxun Wang
- School of Pharmaceutical Science & Technology , Tianjin University , Tianjin 300072 , China.,National Institute of Biological Sciences , Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park , Beijing 102206 , China
| | - Qiuyu Fu
- National Institute of Biological Sciences , Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park , Beijing 102206 , China.,College of Biological Sciences , China Agricultural University , Beijing 100193 , China
| | - Yu Zhou
- National Institute of Biological Sciences , Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park , Beijing 102206 , China
| | - Yunfei Du
- School of Pharmaceutical Science & Technology , Tianjin University , Tianjin 300072 , China
| | - Niu Huang
- National Institute of Biological Sciences , Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park , Beijing 102206 , China.,Tsinghua Institute of Multidisciplinary Biomedical Research , Tsinghua University , Beijing 102206 , China
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32
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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: 29] [Impact Index Per Article: 5.8] [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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33
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Pisa R, Cupido T, Kapoor TM. Designing Allele-Specific Inhibitors of Spastin, a Microtubule-Severing AAA Protein. J Am Chem Soc 2019; 141:5602-5606. [PMID: 30875216 DOI: 10.1021/jacs.8b13257] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The bump-hole approach is a powerful chemical biology strategy to specifically probe the functions of closely related proteins. However, for many protein families, such as the ATPases associated with diverse cellular activities (AAA), we lack structural data for inhibitor-protein complexes to design allele-specific chemical probes. Here we report the X-ray structure of a pyrazolylaminoquinazoline-based inhibitor bound to spastin, a microtubule-severing AAA protein, and characterize the residues involved in inhibitor binding. We show that an inhibitor analogue with a single-atom hydrogen-to-fluorine modification can selectively target a spastin allele with an engineered cysteine mutation in its active site. We also report an X-ray structure of the fluoro analogue bound to the spastin mutant. Furthermore, analyses of other mutant alleles suggest how the stereoelectronics of the fluorine-cysteine interaction, rather than sterics alone, contribute to the inhibitor-allele selectivity. This approach could be used to design allele-specific probes for studying cellular functions of spastin isoforms. Our data also suggest how tuning stereoelectronics can lead to specific inhibitor-allele pairs for the AAA superfamily.
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Affiliation(s)
- Rudolf Pisa
- Laboratory of Chemistry and Cell Biology , The Rockefeller University , New York , New York 10065 , United States
| | - Tommaso Cupido
- Laboratory of Chemistry and Cell Biology , The Rockefeller University , New York , New York 10065 , United States
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology , The Rockefeller University , New York , New York 10065 , United States
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34
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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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35
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Gholivand K, Tizhoush SK, Kozakiewicz A, Eskandari K, Farshadfar K. Copper( i) complexes of functionalized sulfur-containing ligands: structural and theoretical insights into chalcogen bonding. CrystEngComm 2019. [DOI: 10.1039/c8ce02006j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four new copper(i) thiocyanate complexes were studied using geometrical parameters and the lump–hole approach for justification of the strength and nature of chalcogen bonding.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry
- Faculty of Science
- Tarbiat Modares University
- Tehran
- Iran
| | - Samaneh K. Tizhoush
- Department of Chemistry
- Faculty of Science
- Tarbiat Modares University
- Tehran
- Iran
| | - Anna Kozakiewicz
- Faculty of Chemistry
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
- Poland
| | - Kiamars Eskandari
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | - Kaveh Farshadfar
- Department of Chemistry
- Faculty of Science
- Tarbiat Modares University
- Tehran
- Iran
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36
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Zhu Z, Wang G, Xu Z, Chen Z, Wang J, Shi J, Zhu W. Halogen bonding in differently charged complexes: basic profile, essential interaction terms and intrinsic σ-hole. Phys Chem Chem Phys 2019; 21:15106-15119. [PMID: 31241121 DOI: 10.1039/c9cp01379b] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Studies on halogen bonds (XB) between organohalogens and their acceptors in crystal structures revealed that the XB donor and acceptor could be differently charged, making it difficult to understand the nature of the interaction, especially the negatively charged donor's electrophilicity and positively charged acceptor's nucleophilicity. In this paper, 9 XB systems mimicking all possibly charged halogen bonding interactions were designed and explored computationally. The results revealed that all XBs could be stable, with binding energies after removing background interaction as strong as -1.2, -3.4, and -8.3 kcal mol-1 for Cl, Br, and I involved XBs respectively. Orbital and dispersion interactions are found to be always attractive while unidirectional intermolecular electron transfer from a XB acceptor to a XB donor occurs in all XB complexes. These observations could be attributed to the intrinsic σ-hole of the XB donor and the intrinsic electronic properties of the XB acceptor regardless of their charge states. Intramolecular charge redistribution inside both the donor and the acceptor is found to be system-dependent but always leads to a more stable XB. Accordingly, this study demonstrates that the orbital-based origin of halogen bonds could successfully interpret the complicated behaviour of differently charged XB complexes, while electrostatic interaction may dramatically change the overall bonding strength. The results should further promote the application of halogens in all related areas.
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Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guimin Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, 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. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiye Shi
- 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. and University of Chinese Academy of Sciences, Beijing 100049, China and Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao, 266237, China
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37
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Ams MR, Trapp N, Schwab A, Milić JV, Diederich F. Chalcogen Bonding "2S-2N Squares" versus Competing Interactions: Exploring the Recognition Properties of Sulfur. Chemistry 2018; 25:323-333. [PMID: 30600860 DOI: 10.1002/chem.201804261] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Indexed: 12/25/2022]
Abstract
Chalcogen bonding (CB) is the focus of increased attention for its applications in medicinal chemistry, materials science, and crystal engineering. However, the origin of sulfur's recognition properties remains controversial, and experimental evidence for supporting theories is still emerging. Here, a comprehensive evaluation of sulfur CB interactions is presented by investigating 2,1,3-benzothiadiazole X-ray crystallographic structures gathered from the Cambridge Structure Database (CSD), Protein Data Bank (PDB), and own laboratory findings. Through the systematic analysis of substituent effects on a subset library of over thirty benzothiadiazole derivatives, the competing interactions have been categorized into four main classes, namely 2S-2N CB square, halogen bonding (XB), S⋅⋅⋅S, and hydrogen-bonding (HB). A geometric model is employed to characterize the 2S-2N CB square motifs and discuss the role of electrostatic, dipole, and orbital contributions toward the interaction.
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Affiliation(s)
- Mark R Ams
- Department of Chemistry, Allegheny College, Meadville, PA, 16335, USA
| | - Nils Trapp
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | - Anatol Schwab
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | - Jovana V Milić
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | - François Diederich
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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Riwar L, Trapp N, Root K, Zenobi R, Diederich F. Supramolekulare Kapseln: starke und schwache Chalkogenbrücken im Vergleich. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812095] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Leslie‐Joana Riwar
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Nils Trapp
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Katharina Root
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Renato Zenobi
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - François Diederich
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
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Riwar L, Trapp N, Root K, Zenobi R, Diederich F. Supramolecular Capsules: Strong versus Weak Chalcogen Bonding. Angew Chem Int Ed Engl 2018; 57:17259-17264. [DOI: 10.1002/anie.201812095] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Leslie‐Joana Riwar
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Katharina Root
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Renato Zenobi
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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40
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Ernst C, Heidrich J, Sessler C, Sindlinger J, Schwarzer D, Koch P, Boeckler FM. Switching Between Bicyclic and Linear Peptides - The Sulfhydryl-Specific Linker TPSMB Enables Reversible Cyclization of Peptides. Front Chem 2018; 6:484. [PMID: 30386769 PMCID: PMC6198510 DOI: 10.3389/fchem.2018.00484] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/24/2018] [Indexed: 11/13/2022] Open
Abstract
Phage display-selected bicyclic peptides have already shown their great potential for the development as bioactive modulators of therapeutic targets. They can provide enhanced proteolytic stability and improved membrane permeability. Molecular design of new linker molecules has led to a variety of new synthetic approaches for the generation of chemically constrained cyclic peptides. This diversity can be useful for the development of novel peptide-based therapeutic, diagnostic, and scientific tools. Herein, we introduce 1,3,5-tris((pyridin-2-yldisulfanyl)methyl)benzene (TPSMB) as a planar, trivalent, sulfhydryl-specific linker that facilitates reversible cyclization and linearization via disulfide bond formation and cleavage of bicyclic peptides of the format CXnCXnC, where X is any proteinogenic amino acid except cysteine. The rapid and highly sulfhydryl-specific reaction of TPSMB under physiological conditions is demonstrated by selecting bicyclic peptide binders against c-Jun N-terminal kinase 3 (JNK3) as a model target. While model peptides remain stably cyclized for several hours in presence of typical blood levels of glutathione in vitro, high cytosolic concentrations of glutathione linearize these peptides completely within 1 h. We propose that reversible linkers can be useful tools for several technical applications where target affinity depends on the bicyclic structure of the peptide.
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Affiliation(s)
- Christoph Ernst
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Johannes Heidrich
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Catharina Sessler
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Julia Sindlinger
- Department of Pharmacy and Biochemistry, Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Department of Pharmacy and Biochemistry, Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Pierre Koch
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Frank M. Boeckler
- Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
- Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Tübingen, Germany
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41
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Exploring Halogen Bonds in 5-Hydroxytryptamine 2B Receptor-Ligand Interactions. ACS Med Chem Lett 2018; 9:1019-1024. [PMID: 30344910 DOI: 10.1021/acsmedchemlett.8b00300] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023] Open
Abstract
Here, we predicted the potential halogen bonding interaction between compound 2 and the 5-hydroxytryptamine 2B (5-HT2B) receptor and systematically assessed this interaction via structure-activity relationship analysis and molecular dynamics simulations. A physics-based computational protocol was then developed to further explore the opportunity of "designing in" halogen bonding interactions in structure-based ligand design for the 5-HT2B receptor, which not only facilitated the identification of previously uncharacterized halogen bonds in known 5-HT2B ligands but also enabled the rational design of halogen bonding interactions for the optimization of 5-HT2B ligands. As a proof-of-concept, a series of halogen-substituted analogues of doxepin was synthesized and evaluated, which showed improved in vitro and in vivo potency.
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42
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Kurczab R, Canale V, Satała G, Zajdel P, Bojarski AJ. Amino Acid Hot Spots of Halogen Bonding: A Combined Theoretical and Experimental Case Study of the 5-HT 7 Receptor. J Med Chem 2018; 61:8717-8733. [PMID: 30188719 DOI: 10.1021/acs.jmedchem.8b00828] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A computational approach combining a structure-activity relationship library of halogenated and the corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was used to search for amino acids frequently targeted by halogen bonding (hot spots) in a 5-HT7R as a case study. The procedure identified two sets of hot spots, extracellular (D2.65, T2.64, and E7.35) and transmembrane (C3.36, T5.39, and S5.42), which were further verified by a synthesized library of halogenated arylsulfonamide derivatives of (aryloxy)ethylpiperidines. It was found that a halogen bond formed between T5.39 and a bromine atom at 3-position of the aryloxy fragment caused the most remarkable, 35-fold increase in binding affinity for 5-HT7R when compared to the nonhalogenated analog. The proposed paradigm of halogen bonding hot spots was additionally verified on D4 dopamine receptor showing that it can be used in rational drug design/optimization for any protein target.
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Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| | - Vittorio Canale
- Department of Medicinal Chemistry , Jagiellonian University Medical College , 9 Medyczna Street , 30-688 Krakow , Poland
| | - Grzegorz Satała
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| | - Paweł Zajdel
- Department of Medicinal Chemistry , Jagiellonian University Medical College , 9 Medyczna Street , 30-688 Krakow , Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
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43
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Jiang L, Zhang X, Zhou Y, Chen Y, Luo Z, Li J, Yuan C, Huang M. Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases. RSC Adv 2018; 8:28189-28197. [PMID: 35542712 PMCID: PMC9083945 DOI: 10.1039/c8ra03145b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinase-type plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the high-resolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases. These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.
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Affiliation(s)
| | - Xu Zhang
- Center for Life Science, School of Life Sciences, Yunnan University Kunming 650021 China
| | - Yang Zhou
- College of Chemistry, Fuzhou University Fuzhou 350116 China
| | - Yayu Chen
- College of Chemistry, Fuzhou University Fuzhou 350116 China
| | - Zhipu Luo
- Synchrotron Radiation Research Section, NCI, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Jinyu Li
- College of Chemistry, Fuzhou University Fuzhou 350116 China
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University Fuzhou 350116 China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University Fuzhou 350116 China
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44
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Ajani H, Jansa J, Köprülüoğlu C, Hobza P, Kryštof V, Lyčka A, Lepsik M. Imidazo[1,2-c
]pyrimidin-5(6H
)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring. J Mol Recognit 2018; 31:e2720. [DOI: 10.1002/jmr.2720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Josef Jansa
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Department of Organic Chemistry, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry; Palacký University; Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University and Institute of Experimental Botany; Olomouc Czech Republic
| | - Antonín Lyčka
- Research Institute for Organic Syntheses (VUOS); Pardubice-Rybitví Czech Republic
- Faculty of Science; University of Hradec Králové; Hradec Králové Czech Republic
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Wang H, Liu J, Wang W. Intermolecular and very strong intramolecular C–Se⋯O/N chalcogen bonds in nitrophenyl selenocyanate crystals. Phys Chem Chem Phys 2018; 20:5227-5234. [DOI: 10.1039/c7cp08215k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Different bonding strengths of C–Se⋯O/N chalcogen bonds involved in polymorphic o-NSC (1a/1b) and monomorphic p-NSC (2) result in different thermal properties.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, College of Chemistry & Material Science, Shanxi Normal University
- Linfen
- People's Republic of China
| | - Ju Liu
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, College of Chemistry & Material Science, Shanxi Normal University
- Linfen
- People's Republic of China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University
- Luoyang 471934
- People's Republic of China
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46
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Pinheiro PDSM, Rodrigues DA, Alves MA, Tinoco LW, Ferreira GB, de Sant’Anna CMR, Fraga CAM. Theoretical and experimental characterization of 1,4-N⋯S σ-hole intramolecular interactions in bioactive N-acylhydrazone derivatives. NEW J CHEM 2018. [DOI: 10.1039/c7nj03543h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Sigma-hole (σ-hole) bonds are interactions that are gaining special attention in medicinal chemistry.
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Affiliation(s)
- Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Marina Amaral Alves
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Luzineide Wanderley Tinoco
- Programa de Pós-Graduação em Farmacologia e Química Medicinal
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- 21941-902
- Rio de Janeiro
| | - Glaucio Braga Ferreira
- Programa de Pós-Graduação em Química
- Instituto de Química
- Universidade Federal Fluminense
- Niterói
- Rio de Janeiro
| | - Carlos Mauricio Rabello de Sant’Anna
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio)
- Instituto de Ciências Biomédicas
- Universidade Federal do Rio de Janeiro
- PO Box 68023
- Rio de Janeiro
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47
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Koch P, Ansideri F. 2-Alkylsulfanyl-4(5)-aryl-5(4)-heteroarylimidazoles: An Overview on Synthetic Strategies and Biological Activity. Arch Pharm (Weinheim) 2017; 350. [PMID: 29143361 DOI: 10.1002/ardp.201700258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 12/14/2022]
Abstract
2-Alkylsulfanyl-4(5)-aryl-5(4)-heteroarylimidazoles represent an important class of ATP-competitive protein kinase inhibitors, offering the possibility of multiple interactions with different regions of the target enzyme. The necessity of exploring the effects of diverse chemical decorations around the imidazole core prompted the design of several synthetic routes aimed at achieving both efficiency and flexibility. Additionally, the optimization of established protocols and the extensive use of transition metal-catalyzed cross-coupling reactions have been broadening the spectrum of preparative methodologies within the last decade. This review summarizes the progress in the development of synthetic strategies leading to 2-alkylsulfanyl-4(5)-aryl-5(4)-heteroarylimidazoles and 1-alkyl-2-alkylsulfanyl-4(5)-aryl-5(4)-heteroarylimidazoles and offers a glance at the biological activities of this class of compounds.
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Affiliation(s)
- Pierre Koch
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Francesco Ansideri
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany
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48
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Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization. Molecules 2017; 22:molecules22101634. [PMID: 28961202 PMCID: PMC6151534 DOI: 10.3390/molecules22101634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/16/2022] Open
Abstract
Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.
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Mitchell MO. Discovering protein-ligand chalcogen bonding in the protein data bank using endocyclic sulfur-containing heterocycles as ligand search subsets. J Mol Model 2017; 23:287. [PMID: 28942498 DOI: 10.1007/s00894-017-3452-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/05/2017] [Indexed: 01/27/2023]
Abstract
The chalcogen bond, the noncovalent, electrostatic attraction between covalently bonded atoms in group 16 and Lewis bases, is present in protein-ligand interactions based on X-ray structures deposited in the Protein Data Bank (PDB). Discovering protein-ligand chalcogen bonding in the PDB employed a strategy that focused on searching the database for protein complexes of five-membered, heterocyclic ligands containing endocyclic sulfur with endo electron-withdrawing groups (isothiazoles; thiazoles; 1,2,3-, 1,2.4-, 1,2,5-, 1,3,4-thiadiazoles) and thiophenes with exo electron-withdrawing groups, e.g., 2-chloro, 2-bromo, 2-amino, 2-alkylthio. Out of 930 ligands investigated, 33 or 3.5% have protein-ligand S---O interactions of which 31 are chalcogen bonds and two appear to be S---HO hydrogen bonds. The bond angles for some of the chalcogen bonds found in the PDB are less than 90°, and an electrostatic model is proposed to explain this phenomenon.
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Affiliation(s)
- Miguel O Mitchell
- American Institutes for Research, 1000 Thomas Jefferson St. NW, Washington, DC, 20007-3835, USA.
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Yan XC, Robertson MJ, Tirado-Rives J, Jorgensen WL. Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization. J Phys Chem B 2017. [PMID: 28627890 DOI: 10.1021/acs.jpcb.7b04233] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The atomic point-charge model used in most molecular mechanics force fields does not represent well the electronic anisotropy that is featured in many directional noncovalent interactions. Sulfur participates in several types of such interactions with its lone pairs and σ-holes. The current study develops a new model, via the addition of off-atom charged sites, for a variety of sulfur compounds in the OPLS-AA and OPLS/CM5 force fields to address the lack of charge anisotropy. Parameter optimization is carried out to reproduce liquid-state properties, torsional and noncovalent energetics from reliable quantum mechanical calculations, and electrostatic potentials. Significant improvements are obtained for computed free energies of hydration, reducing the mean unsigned errors from ca. 1.4 to 0.4-0.7 kcal/mol. Enhanced accuracy in directionality and energetics is also obtained for molecular complexes with sulfur-containing hydrogen and halogen bonds. Moreover, the new model reproduces the unusual conformational preferences of sulfur-containing compounds with 1,4-intramolecular chalcogen bonds. Transferability of the new force field parameters to cysteine and methionine is verified via molecular dynamic simulations of blocked dipeptides. The study demonstrates the effectiveness of using off-atom charge sites to address electronic anisotropy, and provides a parametrization methodology that can be applied to other systems.
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Affiliation(s)
- Xin Cindy Yan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Michael J Robertson
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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