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Roth FA, Schmidts V, Thiele CM. TITANIA: Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds. J Org Chem 2021; 86:15387-15402. [PMID: 34677977 DOI: 10.1021/acs.joc.1c01926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) become increasingly important as additional NMR parameters in the structure elucidation of organic compounds but are usually used in fitting procedures to discriminate between (computed) structures that are in accordance with RDCs and others that can be ruled out. Thus, the determination of configurations requires prior structural information. The direct use of RDCs as restraints to construct structures based on RDCs has only recently begun also in organic compounds. No protocol has been published though that uses the vector and dynamics information available in multialignment data sets directly for the joint determination of conformation and configuration of organic compounds. This is proposed in the current study. We show that by employing these data, even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. The requirements in terms of the number of RDCs and alignment media necessary are discussed in detail.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
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2
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Horst R, Farley KA, Kormos BL, Withka JM. NMR spectroscopy: the swiss army knife of drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:509-519. [PMID: 32617727 DOI: 10.1007/s10858-020-00330-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool within drug discovery over the last two decades. While traditionally being used by medicinal chemists for small molecule structure elucidation, it can also be a valuable tool for the identification of small molecules that bind to drug targets, for the characterization of target-ligand interactions and for hit-to-lead optimization. Here, we describe how NMR spectroscopy is integrated into the Pfizer drug discovery pipeline and how we utilize this approach to identify and validate initial hits and generate leads.
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Affiliation(s)
- Reto Horst
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA.
| | - Kathleen A Farley
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Bethany L Kormos
- Medicinal Sciences, Pfizer, 610 Main St., Cambridge, MA, 02139, USA
| | - Jane M Withka
- Medicinal Sciences, Pfizer, 610 Main St., Cambridge, MA, 02139, USA
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3
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Farley KA, Che Y, Navarro-Vázquez A, Limberakis C, Anderson D, Yan J, Shapiro M, Shanmugasundaram V, Gil RR. Cyclic Peptide Design Guided by Residual Dipolar Couplings, J-Couplings, and Intramolecular Hydrogen Bond Analysis. J Org Chem 2019; 84:4803-4813. [PMID: 30605335 DOI: 10.1021/acs.joc.8b02811] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyclic peptides have long tantalized drug designers with their potential ability to combine the best attributes of antibodies and small molecules. An ideal cyclic peptide drug candidate would be able to recognize a protein surface like an antibody while achieving the oral bioavailability of a small molecule. It has been hypothesized that such cyclic peptides balance permeability and solubility using their solvent-dependent conformational flexibility. Herein we report a conformational deconvolution NMR methodology that combines residual dipolar couplings, J-couplings, and intramolecular hydrogen bond analysis along with conformational analysis using molecular dynamics simulations and density functional theory calculations for studying cyclic peptide conformations in both low-dielectric solvent (chloroform) and high-dielectric solvent (DMSO) to experimentally study the solvent-dependent conformational change hypothesis. Taken together, the combined experimental and computational approaches can illuminate conformational ensembles of cyclic peptides in solution and help identify design opportunities for better permeability.
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Affiliation(s)
- Kathleen A Farley
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Ye Che
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, CCEN , Universidade Federal de Pernambuco , Cidade Universitária, Recife , PE 50740-560 , Brazil
| | - Chris Limberakis
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Dennis Anderson
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Jiangli Yan
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Michael Shapiro
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Veerabahu Shanmugasundaram
- Medicinal Sciences, Pfizer Worldwide R&D , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Roberto R Gil
- Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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4
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Li GW, Liu H, Qiu F, Wang XJ, Lei XX. Residual Dipolar Couplings in Structure Determination of Natural Products. NATURAL PRODUCTS AND BIOPROSPECTING 2018; 8:279-295. [PMID: 29943349 PMCID: PMC6102172 DOI: 10.1007/s13659-018-0174-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/14/2018] [Indexed: 05/16/2023]
Abstract
The determination of natural products stereochemistry remains a formidable task. Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for determination of the stereochemistry of organic molecule in solution. This review will provide a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized. This review provides a short introduction on RDCs-based methodology for the structural elucidation of natural products. Special attention is given to the current availability of alignment media in organic solvents. The applications of RDCs for structural analysis of some examples of natural products were discussed and summarized.
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Affiliation(s)
- Gao-Wei Li
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Han Liu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Feng Qiu
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China
| | - Xiao-Juan Wang
- College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, People's Republic of China
| | - Xin-Xiang Lei
- School of Pharmaceutical Sciences, South Central University for Nationalities, Wuhan, 430074, People's Republic of China.
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5
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Rigling C, Ebert MO. RDC-enhanced structure calculation of a β-heptapeptide in methanol. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:655-661. [PMID: 27976817 DOI: 10.1002/mrc.4569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/06/2016] [Accepted: 12/12/2016] [Indexed: 05/28/2023]
Abstract
Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β-peptide with proteinogenic side chains in methanol. 1 DCH , 1 DNH , and 2 DHH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long-range definition in the backbone of the resulting 314 -helix and uncovers side-chain mobility. Experimental side-chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three-state model. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Carla Rigling
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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6
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Jędrzejczak K, Hrynczyszyn P, Szczesio M, Artym J, Jastrząbek T, Kocięba M, Główka M, Huben K, Kochanowska I, Zimecki M, Zabrocki J, Jankowski S, Kolesińska B. Synthesis and biological activity of cyclolinopeptide A analogues modified with γ 4-bis(homo-phenylalanine). Bioorg Med Chem 2017; 25:4265-4276. [PMID: 28662964 DOI: 10.1016/j.bmc.2017.05.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 05/28/2017] [Accepted: 05/30/2017] [Indexed: 01/19/2023]
Abstract
Cyclolinopeptide A (CLA), an immunosuppressive nonapeptide derived from linen seeds, was modified with S or R-γ4-bis(homo-phenylalanine) in positions 3 or 4, or both 3 and 4. These modifications changed the flexibility of new analogues and distribution of intramolecular hydrogen bonds. Analogues 11 c(Pro1-Pro2-Phe3-S-γ4-hhPhe4-Leu5-Ile6-Ile7-Leu8-Val9), 13 c(Pro1-Pro2-S-γ4-hhPhe3-R-γ4-hhPhe4-Leu5-Ile6-Ile7-Leu8-Val9) and 15 c(Pro1-Pro2-R-γ4-hhPhe3-Phe4-Leu5-Ile6-Ile7-Leu8-Val9) existed as a mixture of stable cis/trans isomers of Pro-Pro peptide bond. The comparison of the relative spatial orientations in crystal state of the two carbonyl groups, neighboring γ-amino acids, revealed conformational similarities to α-peptides. The addition of two -CH2- groups in γ-amino acids led to a more rigid conformation, although a more flexible one was expected. A significant difference in the relative orientation of the carbonyl groups was found for cyclic γ-peptides with a dominance of an antiparallel arrangement. As carbonyl groups may be engaged in the interactions with plausible receptors through hydrogen bonds, a similar biological activity of the modified peptides was expected. Our biological studies showed that certain cyclic, but not the corresponding linear peptides, lowered the viability of peripheral blood mononuclear cells (PBMC) at 100μg/mL concentration. The proliferation of PBMC induced by phytohemagglutinin A (PHA) was strongly inhibited by cyclic peptides only, in a dose-dependant manner. On the other hand, lipopolysaccharide (LPS)-induced tumor necrosis factor alpha (TNF-α) production in whole blood cell cultures was inhibited by both linear and cyclic peptides. Peptide 15 c(Pro1-Pro2-R-γ4-hhPhe3-Phe4-Leu5-Ile6-Ile7-Leu8-Val9) blocked the expression of caspase-3, inhibited the expression of caspases-8 and -9 in 24h culture of Jurkat cells, and caused DNA fragmentation in these cells, as an indicator of apoptosis. Thus, we revealed a new mechanism of immunosuppressive action of a nonapeptide.
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Affiliation(s)
- Karol Jędrzejczak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland.
| | - Paweł Hrynczyszyn
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Jolanta Artym
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wrocław, Poland
| | - Tomasz Jastrząbek
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Maja Kocięba
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wrocław, Poland
| | - Marek Główka
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Krzysztof Huben
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Iwona Kochanowska
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wrocław, Poland
| | - Michał Zimecki
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wrocław, Poland
| | - Janusz Zabrocki
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Stefan Jankowski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Beata Kolesińska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
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Fredersdorf M, Kurz M, Bauer A, Ebert MO, Rigling C, Lannes L, Thiele CM. Conformational Analysis of an Antibacterial Cyclodepsipeptide Active against Mycobacterium tuberculosis
by a Combined ROE and RDC Analysis. Chemistry 2017; 23:5729-5735. [DOI: 10.1002/chem.201605143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Maic Fredersdorf
- Sanofi-Aventis GmbH; Department of Chemistry; Industriepark Hoechst 65926 Frankfurt am Main Germany
- Technische Universität Darmstadt; Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Michael Kurz
- Sanofi-Aventis GmbH; Department of Chemistry; Industriepark Hoechst 65926 Frankfurt am Main Germany
| | - Armin Bauer
- Sanofi-Aventis GmbH; Department of Chemistry; Industriepark Hoechst 65926 Frankfurt am Main Germany
| | - Marc-Olivier Ebert
- ETH Zürich; Laboratorium für Organische Chemie, D-CHAB; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Carla Rigling
- ETH Zürich; Laboratorium für Organische Chemie, D-CHAB; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Laurie Lannes
- Present address: Center for Biomolecular Magnetic Resonance; BMRZ); Institute of Organic Chemistry and Chemical Biology; Johann Wolfgang Goethe Universität Frankfurt; Max-von-Laue-Straße 7 60438 Frankfurt Germany
| | - Christina Marie Thiele
- Technische Universität Darmstadt; Clemens-Schöpf-Institut für Organische Chemie und Biochemie; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
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8
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Chitanda JM, Zhu J, Mausberg P, Burnett PGG, Reaney MJT. [1–9-NαC]-Linusorb B3 (cyclolinopeptide A) acetonitrile disolvate. IUCRDATA 2016. [DOI: 10.1107/s2414314616017065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The title compound, C57H85N9O9·2C2H3N [systematic name:cyclo-(prolyl-prolyl-phenylalanyl-phenylalanyl-leucyl-isoleucyl-isoleucylleucyl-valyl) acetonitrile disolvate; synonym: cyclolinopeptide acetonitrile disolvate], is a polypeptide with nine amino acids,viz.NαC-(Pro1–Pro2–Phe3–Phe4–Leu5–Ile6–Ile7–Leu8–Val9). It was extracted from flaxseed oil and crystallized from acetonitrile as a disolvate. In the title molecule, there are four intramolecular N—H...O hydrogen bonds. One of the two acetonitrile molecules is hydrogen bonded to Phe3viaan N—H...N hydrogen bond, while the second acetonitrile molecule is located at the other side of the peptide ring and is linked to the title molecule by a C—H...N hydrogen bond. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming chains along thea-axis direction. The chains are linked by C—H...O hydrogen bonds, forming undulating layers parallel to theacplane.
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9
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Jędrzejczak K, Hrynczyszyn P, Artym J, Kocięba M, Zimecki M, Zabrocki J, Jankowski S. Synthesis and biological activity of cyclolinopeptide A analogues modified with γ(3)-bis(homophenylalanine). Eur J Med Chem 2014; 86:515-27. [PMID: 25203781 DOI: 10.1016/j.ejmech.2014.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 01/01/2023]
Abstract
Cyclolinopeptide A, naturally occurring immunomodulatory nonapeptide, was modified with S or R-γ(3)-bis(homophenylalanine) in positions 3 or 4, or both 3 and 4. The replacement of one or both Phe residues by γ(3)-hhPhe led to decrease of their conformational flexibility in the analogues in comparison to CLA. All cyclic peptides, except 11, exist as isomers with the cis Pro-Pro peptide bond. Cyclic peptide 11 with single modification S-γ(3)-hhPhe(4) exists as a mixture of two isomers and the major isomer (89%) contains all peptide bonds of the trans geometry. The peptides were subjected to several immunological tests in vitro and in vivo. Linear peptides 1-8, precursors of CLA analogues 9-16, were not toxic against human peripheral blood mononuclear cells (PBMC) but cyclic analogues showed dose-dependent toxicity with exception of peptide 11. Linear peptides did not inhibit mitogen-induced PBMC proliferation whereas cyclic ones inhibited the proliferation in a dose-dependent manner. The actions of linear and cyclic peptides with regard to lipopolysaccharide (LPS) -induced tumour necrosis factor alpha (TNF α) production in whole human blood cultures were differential but particularly suppressive in the case of linear compound 6. Therefore, for in vivo tests compounds 6 and 11 were selected. The compounds showed comparable, suppressive actions in induction and effector phases of delayed type hypersensitivity as well as in the carrageenan-induced foot pad edema in mouse models. In summary, linear peptide 6 and cyclic peptide 11 are attractive as potential immune suppressor drugs.
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Affiliation(s)
- Karol Jędrzejczak
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland
| | - Paweł Hrynczyszyn
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland
| | - Jolanta Artym
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Maja Kocięba
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Michał Zimecki
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Janusz Zabrocki
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland; Peptaderm Ltd., Rydygiera 8, 01-793 Warsaw, Poland
| | - Stefan Jankowski
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland.
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