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Silva Elipe MV, Ndukwe IE, Murray JI. Cryogen-free 400-MHz nuclear magnetic resonance spectrometer as a versatile tool for pharmaceutical process analytical technology. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:512-534. [PMID: 38369696 DOI: 10.1002/mrc.5434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
The discovery of new ceramic materials containing Ba-La-Cu oxides in 1986 that exhibited superconducting properties at high temperatures in the range of 35 K or higher, recognized with the Nobel Prize in Physics in 1987, opened a new world of opportunities for nuclear magnetic resonance (NMRs) and magnetic resonance imaging (MRIs) to move away from liquid cryogens. This discovery expands the application of high temperature superconducting (HTS) materials to fields beyond the chemical and medical industries, including electrical power grids, energy, and aerospace. The prototype 400-MHz cryofree HTS NMR spectrometer installed at Amgen's chemistry laboratory has been vital for a variety of applications such as structure analysis, reaction monitoring, and CASE-3D studies with RDCs. The spectrometer has been integrated with Amgen's chemistry and analytical workflows, providing pipeline project support in tandem with other Kinetic Analysis Platform technologies. The 400-MHz cryofree HTS NMR spectrometer, as the name implies, does not require liquid cryogens refills and has smaller footprint that facilitates installation into a chemistry laboratory fume hood, sharing the hood with a process chemistry reactor. Our evaluation of its performance for structural analysis with CASE-3D protocol and for reaction monitoring of Amgen's pipeline chemistry was successful. We envision that the HTS magnets would become part of the standard NMR and MRI spectrometers in the future. We believe that while the technology is being developed, there is room for all magnet options, including HTS, low temperature superconducting (LTS) magnets, and low field benchtop NMRs with permanent magnets, where utilization will be dependent on application type and costs.
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Affiliation(s)
| | - Ikenna Edward Ndukwe
- Department of Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, California, USA
| | - James I Murray
- Pivotal and Commercial Drug Substance Technologies, Process Development, Amgen Inc., Thousand Oaks, California, USA
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2
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Garnsey MR, Smith AC, Polivkova J, Arons AL, Bai G, Blakemore C, Boehm M, Buzon LM, Campion SN, Cerny M, Chang SC, Coffman K, Farley KA, Fonseca KR, Ford KK, Garren J, Kong JX, Koos MRM, Kung DW, Lian Y, Li MM, Li Q, Martinez-Alsina LA, O'Connor R, Ogilvie K, Omoto K, Raymer B, Reese MR, Ryder T, Samp L, Stevens KA, Widlicka DW, Yang Q, Zhu K, Fortin JP, Sammons MF. Discovery of the Potent and Selective MC4R Antagonist PF-07258669 for the Potential Treatment of Appetite Loss. J Med Chem 2023; 66:3195-3211. [PMID: 36802610 DOI: 10.1021/acs.jmedchem.2c02012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The melanocortin-4 receptor (MC4R) is a centrally expressed, class A GPCR that plays a key role in the regulation of appetite and food intake. Deficiencies in MC4R signaling result in hyperphagia and increased body mass in humans. Antagonism of MC4R signaling has the potential to mitigate decreased appetite and body weight loss in the setting of anorexia or cachexia due to underlying disease. Herein, we report on the identification of a series of orally bioavailable, small-molecule MC4R antagonists using a focused hit identification effort and the optimization of these antagonists to provide clinical candidate 23. Introduction of a spirocyclic conformational constraint allowed for simultaneous optimization of MC4R potency and ADME attributes while avoiding the production of hERG active metabolites observed in early series leads. Compound 23 is a potent and selective MC4R antagonist with robust efficacy in an aged rat model of cachexia and has progressed into clinical trials.
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Affiliation(s)
| | - Aaron C Smith
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Jana Polivkova
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Autumn L Arons
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Guoyun Bai
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | - Markus Boehm
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Leanne M Buzon
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Sarah N Campion
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Matthew Cerny
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Shiao-Chi Chang
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Karen Coffman
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | - Kari R Fonseca
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Kristen K Ford
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Jeonifer Garren
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Jimmy X Kong
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Martin R M Koos
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Daniel W Kung
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Yajing Lian
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Monica M Li
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Qifang Li
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | | | - Kevin Ogilvie
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Kiyoyuki Omoto
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Brian Raymer
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Matthew R Reese
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Tim Ryder
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | - Lacey Samp
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
| | | | | | - Qingyi Yang
- Pfizer, Incorporated, Cambridge, Massachusetts 02139, United States
| | - Kaicheng Zhu
- Pfizer, Incorporated, Groton, Connecticut 06340, United States
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3
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Venturi L, Bua E, Caputo G, Mileo V. Residual Dipolar Coupling Based Conformational Analysis Allows the Configurational Assessment of Steroids with up to Eight Stereocenters. Chempluschem 2023; 88:e202200391. [PMID: 36811319 DOI: 10.1002/cplu.202200391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Residual dipolar couplings (RDCs) induced by anisotropic media have been proved as a powerful tool for the structure elucidation of organic molecules in solution in nuclear magnetic resonance (NMR) based analysis. The value of dipolar couplings to solve complex conformational and configurational problems represents indeed an appealing analytical tool for the pharmaceutical industry particularly focusing on the stereochemistry characterization of NCEs since the early phase of the drug development process. In our work, RDCs were used for the conformational and configurational study of synthetic steroids with multiple stereocenters - prednisone and beclomethasone dipropionate (BDP) -. For both molecules the correct relative configuration was identified among all the possible diastereoisomers (32 and 128 respectively) arising from the compounds stereogenic carbons. Only for prednisone the use of additional experimental data (i. e. rOes) was necessary to resolve the right stereochemical structure.
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Affiliation(s)
- Luca Venturi
- Preclinical Analytics and Early Formulations Department, Chiesi Farmaceutici Spa, Largo Belloli 11/A, 43123, Parma, PR, Italy
| | - Emanuela Bua
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, PR, Italy
| | - Giulia Caputo
- Pharmacy Department, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini, 66100, Chieti, CH, Italy
| | - Valentina Mileo
- Preclinical Analytics and Early Formulations Department, Chiesi Farmaceutici Spa, Largo Belloli 11/A, 43123, Parma, PR, Italy
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Saunders GJ, Yudin AK. Property‐Driven Development of Passively Permeable Macrocyclic Scaffolds Using Heterocycles**. Angew Chem Int Ed Engl 2022; 61:e202206866. [DOI: 10.1002/anie.202206866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Indexed: 12/18/2022]
Affiliation(s)
- George J. Saunders
- Davenport Research Laboratories University of Toronto 80 St. George St Toronto Ontario, M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories University of Toronto 80 St. George St Toronto Ontario, M5S 3H6 Canada
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5
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Saunders GJ, Yudin AK. Property‐Driven Development of Passively Permeable Macrocyclic Scaffolds using Heterocycles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- George J. Saunders
- University of Toronto - St George Campus: University of Toronto Chemistry 80 St George St M5S3H6 Toronto CANADA
| | - Andrei K. Yudin
- University of Toronto Department of Chemistry 80 St. George Street M5S 3H6 Toronto CANADA
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6
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil-Silva LF, Gil RR. Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021; 60:26314-26319. [PMID: 34609778 DOI: 10.1002/anie.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/07/2022]
Abstract
Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.
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Affiliation(s)
- Kathleen A Farley
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Martin R M Koos
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Ye Che
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Reto Horst
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Chris Limberakis
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Justin Bellenger
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | - Ricardo Lira
- Medicinal Sciences, Pfizer, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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7
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Farley KA, Koos MRM, Che Y, Horst R, Limberakis C, Bellenger J, Lira R, Gil‐Silva LF, Gil RR. Cross‐Linked Poly‐4‐Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
| | - Ye Che
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Reto Horst
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Chris Limberakis
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Justin Bellenger
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | - Ricardo Lira
- Medicinal Sciences Pfizer Eastern Point Road Groton CT 06340 USA
| | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University 4400 Fifth Avenue Pittsburgh PA 15213 USA
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8
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Peintner S, Erdélyi M. Pushing the Limits of Characterising a Weak Halogen Bond in Solution. Chemistry 2021; 28:e202103559. [PMID: 34807488 PMCID: PMC9300211 DOI: 10.1002/chem.202103559] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 01/06/2023]
Abstract
Detection and characterisation of very weak, non-covalent interactions in solution is inherently challenging. Low affinity, short complex lifetime and a constant battle against entropy brings even the most sensitive spectroscopic methods to their knees. Herein we introduce a strategy for the accurate experimental description of weak chemical forces in solution. Its scope is demonstrated by the detailed geometric and thermodynamic characterisation of the weak halogen bond of a non-fluorinated aryl iodide and an ether oxygen (0.6 kJ mol-1 ). Our approach makes use of the entropic advantage of studying a weak force intramolecularly, embedded into a cooperatively folding system, and of the combined use of NOE- and RDC-based ensemble analyses to accurately describe the orientation of the donor and acceptor sites. Thermodynamic constants (ΔG, ΔH and ΔS), describing the specific interaction, were derived from variable temperature chemical shift analysis. We present a methodology for the experimental investigation of remarkably weak halogen bonds and other related weak forces in solution, paving the way for their improved understanding and strategic use in chemistry and biology.
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Affiliation(s)
- Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, SE-751, 23, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, SE-751, 23, Uppsala, Sweden
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9
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Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
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10
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Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool. Mar Drugs 2021; 19:md19060311. [PMID: 34072121 PMCID: PMC8229464 DOI: 10.3390/md19060311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.
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11
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de Melo Sousa CM, Giordani RB, de Almeida WAM, Griesinger C, Gil RR, Navarro-Vázquez A, Hallwass F. Effect of the solvent on the conformation of monocrotaline as determined by isotropic and anisotropic NMR parameters. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:561-568. [PMID: 31715029 DOI: 10.1002/mrc.4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
The conformation in solution of monocrotaline, a pyrrolizidine alkaloid presenting an eleven-membered macrocyclic diester ring, has been investigated using a combination of isotropic and anisotropic nuclear magnetic resonance parameters measured in four solvents of different polarity (D2 O, DMSO-d6 , CDCl3 , and C6 D6 ). Anisotropic nuclear magnetic resonance parameters were measured in different alignment media, based on their compatibility with the solvent of interest: cromoglycate liquid crystal solution was used for D2 O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl3 and C6 D6 , and a poly (hydroxyethyl methacrylate) gel for DMSO-d6 . Whereas the pyrrolizidine ring shows an E6 exo-puckered conformation in all of the solvents, the macrocyclic eleven-membered ring adopts different populations of syn-parallel and anti-parallel relative orientation of the carbonyl groups according to the polarity of the solvent.
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Affiliation(s)
- Cleyton Marcos de Melo Sousa
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- Instituto Federal de Pernambuco, Caruaru, Pernambuco, Brazil
| | - Raquel Brandt Giordani
- Laboratório de Farmacognosia, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Christian Griesinger
- Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Armando Navarro-Vázquez
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Fernando Hallwass
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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12
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Moritsugu K, Takeuchi K, Kamiya N, Higo J, Yasumatsu I, Fukunishi Y, Fukuda I. Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation. J Chem Inf Model 2021; 61:1921-1930. [PMID: 33835817 DOI: 10.1021/acs.jcim.0c01427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantifying the cell permeability of cyclic peptides is crucial for their rational drug design. However, the reasons remain unclear why a minor chemical modification, such as the difference between Ras inhibitors cyclorasin 9A5 and 9A54, can substantially change a peptide's permeability. To address this question, we performed enhanced sampling simulations of these two 11-mer peptides using the coupled Nosé-Hoover equation (cNH) we recently developed. The present cNH simulations realized temperature fluctuations over a wide range (240-600 K) in a dynamic manner, allowing structural samplings that were well validated by nuclear Overhauser effect measurements. The derived structural ensembles were comprehensively analyzed by all-atom structural clustering, mapping the derived clusters onto principal components (PCs) that characterize the cyclic structure, and calculating cluster-dependent geometric and chemical properties. The planar-open conformation was dominant in aqueous solvent, owing to inclusion of the Trp side chain in the main-chain ring, while the compact-closed conformation, which favors cell permeation due to its compactness and high polarity, was also accessible. Conformation-dependent cell permeability was observed in one of the derived PCs, demonstrating that decreased cell permeability in 9A54 is due to the high free energy barrier separating the two conformations. The origin of the change in free energy surface was determined to be loss of flexibility in the modified residues 2-3, resulting from the increased bulkiness of their side chains. The derived molecular mechanism of cell permeability highlights the significance of complete structural dynamics surveys for accelerating drug development with cyclic peptides.
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Affiliation(s)
- Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Isao Yasumatsu
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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13
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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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14
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Dal Poggetto G, Soares JV, Tormena CF. Selective Nuclear Magnetic Resonance Experiments for Sign-Sensitive Determination of Heteronuclear Couplings: Expanding the Analysis of Crude Reaction Mixtures. Anal Chem 2020; 92:14047-14053. [PMID: 32924438 PMCID: PMC7660590 DOI: 10.1021/acs.analchem.0c02976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
State-of-the-art nuclear magnetic resonance (NMR) selective experiments are capable of directly analyzing crude reaction mixtures. A new experiment named HD-HAPPY-FESTA yields ultrahigh-resolution total correlation subspectra, which are suitable for sign-sensitive determination of heteronuclear couplings, as demonstrated here by measuring the sign and magnitude for proton-fluorine couplings (JHF) from major and minor isomer products of a two-step reaction without any purification. Proton-fluorine couplings ranging from 51.5 to -2.6 Hz could be measured using HD-HAPPY-FESTA, with the smallest measured magnitude of 0.8 Hz. Experimental JHF values were used to identify the two fluoroketone intermediates and the four fluoroalcohol products. Results were rationalized and compared with the density functional theory (DFT) calculations. Experimental data were further compared with the couplings reported in the literature, where pure samples were analyzed.
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Affiliation(s)
- Guilherme Dal Poggetto
- Institute of Chemistry, University of Campinas (UNICAMP), PO BOX 6154, Campinas, São Paulo CEP 13083-970, Brazil
| | - João Vitor Soares
- Institute of Chemistry, University of Campinas (UNICAMP), PO BOX 6154, Campinas, São Paulo CEP 13083-970, Brazil
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas (UNICAMP), PO BOX 6154, Campinas, São Paulo CEP 13083-970, Brazil
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Richaud AD, Roche SP. Structure-Property Relationship Study of N-(Hydroxy)Peptides for the Design of Self-Assembled Parallel β-Sheets. J Org Chem 2020; 85:12329-12342. [PMID: 32881524 DOI: 10.1021/acs.joc.0c01441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The design of novel and functional biomimetic foldamers remains a major challenge in creating mimics of native protein structures. Herein, we report the stabilization of a remarkably short β-sheet by incorporating N-(hydroxy)glycine (Hyg) residues into the backbone of peptides. These peptide-peptoid hybrids form unique parallel β-sheet structures by self-assembly upon hydrogenation. Our spectroscopic and crystallographic data suggest that the local conformational perturbations induced by N-(hydroxy)amides are outweighed by a network of strong interstrand hydrogen bonds.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States.,Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33458, United States
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16
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Qin S, Jiang Y, Sun H, Liu H, Zhang A, Lei X. Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Si‐Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Yan Jiang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Section of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Han Liu
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ai‐Qing Zhang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Xinxiang Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
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17
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Qin S, Jiang Y, Sun H, Liu H, Zhang A, Lei X. Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid‐Crystalline‐Based Medium. Angew Chem Int Ed Engl 2020; 59:17097-17103. [DOI: 10.1002/anie.202007243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Si‐Yong Qin
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Yan Jiang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Han Sun
- Section of Structural Biology Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) 13125 Berlin Germany
| | - Han Liu
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
| | - Ai‐Qing Zhang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
| | - Xinxiang Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science South-Central University for Nationalities Wuhan 430074 China
- School of Pharmaceutical Sciences South-Central University for Nationalities Wuhan 430074 China
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18
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Koos MRM, Navarro‐Vázquez A, Anklin C, Gil RR. Computer‐Assisted 3D Structure Elucidation (CASE‐3D): The Structural Value of
2
J
CH
in Addition to
3
J
CH
Coupling Constants. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
| | | | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
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19
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Koos MRM, Navarro‐Vázquez A, Anklin C, Gil RR. Computer‐Assisted 3D Structure Elucidation (CASE‐3D): The Structural Value of
2
J
CH
in Addition to
3
J
CH
Coupling Constants. Angew Chem Int Ed Engl 2020; 59:3938-3941. [DOI: 10.1002/anie.201915103] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
| | | | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
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20
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Efimov S, Zgadzay Y, Darwish S, Klochkov V. Conformational Variability of Cyclosporin C Dissolved in Dimethylformamide. BIONANOSCIENCE 2019. [DOI: 10.1007/s12668-019-00641-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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