1
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Wieske LHE, Peintner S, Erdélyi M. Ensemble determination by NMR data deconvolution. Nat Rev Chem 2023:10.1038/s41570-023-00494-x. [PMID: 37169885 DOI: 10.1038/s41570-023-00494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.
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Affiliation(s)
| | - Stefan Peintner
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
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2
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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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3
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Wang S, Krummenacher K, Landrum GA, Sellers BD, Di Lello P, Robinson SJ, Martin B, Holden JK, Tom JYK, Murthy AC, Popovych N, Riniker S. Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. J Chem Inf Model 2022; 62:472-485. [PMID: 35029985 DOI: 10.1021/acs.jcim.1c01165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear magnetic resonance (NMR) data from NOESY (nuclear Overhauser enhancement spectroscopy) and ROESY (rotating frame Overhauser enhancement spectroscopy) experiments can easily be combined with distance geometry (DG) based conformer generators by modifying the molecular distance bounds matrix. In this work, we extend the modern DG based conformer generator ETKDG, which has been shown to reproduce experimental crystal structures from small molecules to large macrocycles well, to include NOE-derived interproton distances. In noeETKDG, the experimentally derived interproton distances are incorporated into the distance bounds matrix as loose upper (or lower) bounds to generate large conformer sets. Various subselection techniques can subsequently be applied to yield a conformer bundle that best reproduces the NOE data. The approach is benchmarked using a set of 24 (mostly) cyclic peptides for which NOE-derived distances as well as reference solution structures obtained by other software are available. With respect to other packages currently available, the advantages of noeETKDG are its speed and that no prior force-field parametrization is required, which is especially useful for peptides with unnatural amino acids. The resulting conformer bundles can be further processed with the use of structural refinement techniques to improve the modeling of the intramolecular nonbonded interactions. The noeETKDG code is released as a fully open-source software package available at www.github.com/rinikerlab/customETKDG.
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Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Kajo Krummenacher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gregory A Landrum
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin D Sellers
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Paola Di Lello
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah J Robinson
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bryan Martin
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeffrey K Holden
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Jeffrey Y K Tom
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Anastasia C Murthy
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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4
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Balazs A, Davies N, Longmire D, Packer M, Chiarparin E. Nuclear magnetic resonance free ligand conformations and atomic resolution dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:489-498. [PMID: 37904764 PMCID: PMC10539760 DOI: 10.5194/mr-2-489-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/28/2021] [Indexed: 11/01/2023]
Abstract
Knowledge of free ligand conformational preferences (energy minima) and conformational dynamics (rotational energy barriers) of small molecules in solution can guide drug design hypotheses and help rank ideas to bias syntheses towards more active compounds. Visualization of conformational exchange dynamics around torsion angles, by replica exchange with solute tempering molecular dynamics (REST-MD), gives results in agreement with high-resolution 1 H nuclear magnetic resonance (NMR) spectra and complements free ligand conformational analyses. Rotational energy barriers around individual bonds are comparable between calculated and experimental values, making the in-silico method relevant to ranking prospective design ideas in drug discovery programs, particularly across a series of analogs. Prioritizing design ideas, based on calculations and analysis of measurements across a series, efficiently guides rational discovery towards the "right molecules" for effective medicines.
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Affiliation(s)
- Amber Y. S. Balazs
- Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Nichola L. Davies
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United
Kingdom
| | - David Longmire
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United
Kingdom
| | - Martin J. Packer
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United
Kingdom
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5
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Begnini F, Poongavanam V, Atilaw Y, Erdelyi M, Schiesser S, Kihlberg J. Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies. ACS Med Chem Lett 2021; 12:983-990. [PMID: 34136079 PMCID: PMC8201747 DOI: 10.1021/acsmedchemlett.1c00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
![]()
Conformation-dependent 3D descriptors
have been shown to provide
better predictions of the physicochemical properties of macrocycles
than 2D descriptors. However, the computational identification of
relevant conformations for macrocycles is nontrivial. Herein, we report
that the Caco-2 cell permeability difference between a pair of diastereomeric
macrocycles correlated with their solvent accessible 3D polar surface
area and radius of gyration. The descriptors were calculated from
the macrocycles’ solution-phase conformational ensembles and
independently from ensembles obtained by conformational sampling.
Calculation of the two descriptors for three other stereo- and regioisomeric
macrocycles also allowed the correct ranking of their cell permeability.
Methods for conformational sampling may thus allow ranking of passive
permeability for moderately flexible macrocycles, thereby contributing
to the prioritization of macrocycles for synthesis in lead optimization.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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6
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Ge Y, Zhang S, Erdelyi M, Voelz VA. Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2. J Chem Inf Model 2021; 61:2353-2367. [PMID: 33905247 PMCID: PMC9960209 DOI: 10.1021/acs.jcim.1c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding mechanisms of protein folding and binding is crucial to designing their molecular function. Molecular dynamics (MD) simulations and Markov state model (MSM) approaches provide a powerful way to understand complex conformational change that occurs over long time scales. Such dynamics are important for the design of therapeutic peptidomimetic ligands, whose affinity and binding mechanism are dictated by a combination of folding and binding. To examine the role of preorganization in peptide binding to protein targets, we performed massively parallel explicit-solvent MD simulations of cyclic β-hairpin ligands designed to mimic the p53 transactivation domain and competitively bind mouse double minute 2 homologue (MDM2). Disrupting the MDM2-p53 interaction is a therapeutic strategy to prevent degradation of the p53 tumor suppressor in cancer cells. MSM analysis of over 3 ms of aggregate trajectory data enabled us to build a detailed mechanistic model of coupled folding and binding of four cyclic peptides which we compare to experimental binding affinities and rates. The results show a striking relationship between the relative preorganization of each ligand in solution and its affinity for MDM2. Specifically, changes in peptide conformational populations predicted by the MSMs suggest that entropy loss upon binding is the main factor influencing affinity. The MSMs also enable detailed examination of non-native interactions which lead to misfolded states and comparison of structural ensembles with experimental NMR measurements. In contrast to an MSM study of p53 transactivation domain (TAD) binding to MDM2, MSMs of cyclic β-hairpin binding show a conformational selection mechanism. Finally, we make progress toward predicting accurate off rates of cyclic peptides using multiensemble Markov models (MEMMs) constructed from unbiased and biased simulated trajectories.
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Affiliation(s)
- Yunui Ge
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
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7
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Nazarski RB. Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Bogaerts J, Atilaw Y, Peintner S, Aerts R, Kihlberg J, Johannessen C, Erdélyi M. Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution. RSC Adv 2021; 11:4200-4208. [PMID: 35424346 PMCID: PMC8694311 DOI: 10.1039/d0ra10167b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the conformational preferences of free ligands in solution is often necessary to rationalize structure-activity relationships in drug discovery. Herein, we examine the conformational behavior of an epimeric pair of side-chain stapled peptides that inhibit the FAD dependent amine oxidase lysine specific demethylase 1 (LSD1). The peptides differ only at a single stereocenter, but display a major difference in binding affinity. Their Raman optical activity (ROA) spectra are most likely dominated by the C-terminus, obscuring the analysis of the epimeric macrocycle. By employing NMR spectroscopy, we show a difference in conformational behavior between the two compounds and that the LSD1 bound conformation of the most potent compound is present to a measurable extent in aqueous solution. In addition, we illustrate that Molecular Dynamics (MD) simulations produce ensembles that include the most important solution conformations, but that it remains problematic to identify relevant conformations with no a priori knowledge from the large conformational pool. Furthermore, this work highlights the importance of understanding the scope and limitations of the available techniques for conducting conformational analyses. It also emphasizes the importance of conformational selection of a flexible ligand in molecular recognition.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | - Roy Aerts
- Department of Chemistry, University of Antwerp 2020 Antwerp Belgium
| | - Jan Kihlberg
- 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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Daranas AH, Sarotti AM. Are Computational Methods Useful for Structure Elucidation of Large and Flexible Molecules? Belizentrin as a Case Study. Org Lett 2020; 23:503-507. [PMID: 33382270 DOI: 10.1021/acs.orglett.0c04016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantum mechanical NMR methods are progressively becoming decisive in structure elucidation. However, problems arise using low-level calculations for complex molecules, whereas methods using higher levels of theory are not practical for large molecules. This report outlines a synergistic effort employing computationally inexpensive quantum mechanical NMR calculations with conformer selection incorporating 3JHH values as a way to solve the structure of large, complex, and highly flexible molecules using readily available computational resources with belizentrin as a case study.
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Affiliation(s)
- Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), La Laguna 38206, Tenerife, Spain
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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10
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Poongavanam V, Atilaw Y, Ye S, Wieske LHE, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Predicting the Permeability of Macrocycles from Conformational Sampling - Limitations of Molecular Flexibility. J Pharm Sci 2020; 110:301-313. [PMID: 33129836 DOI: 10.1016/j.xphs.2020.10.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Macrocycles constitute superior ligands for targets that have flat binding sites but often require long synthetic routes, emphasizing the need for property prediction prior to synthesis. We have investigated the scope and limitations of machine learning classification models and of regression models for predicting the cell permeability of a set of denovo-designed, drug-like macrocycles. 2D-Based classification models, which are fast to calculate, discriminated between macrocycles that had low-medium and high permeability and may be used as virtual filters in early drug discovery projects. Importantly, stereo- and regioisomer were correctly classified. QSPR studies of two small sets of comparator drugs suggested that use of 3D descriptors, calculated from biologically relevant conformations, would allow development of more precise regression models for late phase drug projects. However, a 3D permeability model could only be developed for a rigid series of macrocycles. Comparison of NMR based conformational analysis with in silico conformational sampling indicated that this shortcoming originates from the inability of the molecular mechanics force field to identify the relevant conformations for flexible macrocycles. We speculate that a Kier flexibility index of ≤10 constitutes a current upper limit for reasonably accurate 3D prediction of macrocycle cell permeability.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sofie Ye
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
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11
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Danelius E, Poongavanam V, Peintner S, Wieske LHE, Erdélyi M, Kihlberg J. Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs. Chemistry 2020; 26:5231-5244. [DOI: 10.1002/chem.201905599] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Emma Danelius
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
| | | | - Stefan Peintner
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
| | | | - Máté Erdélyi
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
| | - Jan Kihlberg
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
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12
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Peng C, Atilaw Y, Wang J, Xu Z, Poongavanam V, Shi J, Kihlberg J, Zhu W, Erdélyi M. Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study. ACS OMEGA 2019; 4:22245-22250. [PMID: 31891108 PMCID: PMC6933765 DOI: 10.1021/acsomega.9b03797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 05/02/2023]
Abstract
The replica exchange molecular dynamics (REMD) simulation is demonstrated to readily predict the conformations of the macrocyclic drug lorlatinib, as validated by solution NMR studies. In aqueous solution, lorlatinib adopts a conformer identical to its target bound structure. This conformer is stabilized by an extensive hydrogen bond network to the solvents. In chloroform, lorlatinib populates two conformers with the second one being less polar, which may contribute to lorlatinib's ability to cross cell membranes.
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Affiliation(s)
- Cheng Peng
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yoseph Atilaw
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jinan Wang
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhijian Xu
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | | | - Jiye Shi
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jan Kihlberg
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Weiliang Zhu
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- E-mail: (W.Z.)
| | - Máté Erdélyi
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- E-mail: (M.E.)
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13
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Danelius E, Ohm RG, Ahsanullah, Mulumba M, Ong H, Chemtob S, Erdelyi M, Lubell WD. Dynamic Chirality in the Mechanism of Action of Allosteric CD36 Modulators of Macrophage-Driven Inflammation. J Med Chem 2019; 62:11071-11079. [DOI: 10.1021/acs.jmedchem.9b00918] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Emma Danelius
- Department of Pediatrics, Centre Hospitalier Universitaire (CHU) Sainte—Justine Research Center, Montréal H3T 1C5, Québec, Canada
| | | | | | | | | | - Sylvain Chemtob
- Department of Pediatrics, Centre Hospitalier Universitaire (CHU) Sainte—Justine Research Center, Montréal H3T 1C5, Québec, Canada
| | - Mate Erdelyi
- Department of Chemistry—BMC, Uppsala University, Husargatan 3, Uppsala SE-752 37, Sweden
- The Swedish NMR Centre, Medicinaregatan 5, Gothenburg SE-413 90, Sweden
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14
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Appavoo SD, Huh S, Diaz DB, Yudin AK. Conformational Control of Macrocycles by Remote Structural Modification. Chem Rev 2019; 119:9724-9752. [DOI: 10.1021/acs.chemrev.8b00742] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Solomon D. Appavoo
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Sungjoon Huh
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Diego B. Diaz
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Andrei K. Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
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15
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Tiwari VS, Singh G, Gurudayal, Ampapathi RS, Haq W. Pyrrolidine ring puckering and prolyl amide bond configurations of 2-methyl-allo-hydroxyproline-based dipeptides. Org Biomol Chem 2019; 17:4460-4464. [PMID: 30994683 DOI: 10.1039/c9ob00150f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An expeditious method for the synthesis of homo and heterochiral dipeptides containing l-alanine and d/l 2-methyl allo-hydroxyl prolines was developed using direct aminolysis of bicyclic lactones derived from d/l alanine. The impact of C-2 methylation and its spatial orientation on the pyrrolidine ring puckering and prolyl amide bond configuration was ascertained by solution NMR studies. The present studies reveal that C-2 methylation causes the prolyl amide bond to exist exclusively in the trans geometry in both homo- and heterochiral dipeptides. However, the spatial orientation of the C-2 methyl group and its i + 2 position in appropriately capped model dipeptides may nucleate into a turn like structure.
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Affiliation(s)
- Vinay Shankar Tiwari
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
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16
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Poongavanam V, Danelius E, Peintner S, Alcaraz L, Caron G, Cummings MD, Wlodek S, Erdelyi M, Hawkins PCD, Ermondi G, Kihlberg J. Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations? ACS OMEGA 2018; 3:11742-11757. [PMID: 30320271 PMCID: PMC6173504 DOI: 10.1021/acsomega.8b01379] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/04/2018] [Indexed: 05/03/2023]
Abstract
Conformational flexibility is a major determinant of the properties of macrocycles and other drugs in beyond rule of 5 (bRo5) space. Prediction of conformations is essential for design of drugs in this space, and we have evaluated three tools for conformational sampling of a set of 10 bRo5 drugs and clinical candidates in polar and apolar environments. The distance-geometry based OMEGA was found to yield ensembles spanning larger structure and property spaces than the ensembles obtained by MOE-LowModeMD (MOE) and MacroModel (MC). Both MC and OMEGA but not MOE generated different ensembles for polar and apolar environments. All three conformational search methods generated conformers similar to the crystal structure conformers for 9 of the 10 compounds, with OMEGA performing somewhat better than MOE and MC. MOE and OMEGA found all six conformers of roxithromycin that were identified by NMR in aqueous solutions, whereas only OMEGA sampled the three conformers observed in chloroform. We suggest that characterization of conformers using molecular descriptors, e.g., the radius of gyration and polar surface area, is preferred to energy- or root-mean-square deviation-based methods for selection of biologically relevant conformers in drug discovery in bRo5 space.
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Affiliation(s)
| | - Emma Danelius
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen
10, SE-41296 Gothenburg, Sweden
| | - Stefan Peintner
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Lilian Alcaraz
- Medicinal
Chemistry, Johnson & Johnson Innovation, One Chapel Place, London W1G 0BG, U.K.
| | - Giulia Caron
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
| | - Maxwell D. Cummings
- Janssen
Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Stanislaw Wlodek
- OpenEye
Scientific Software, 9 Bisbee Court, Santa Fe, New Mexico 87508, United States
| | - Mate Erdelyi
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- The
Swedish NMR Centre, Medicinaregatan
5, SE-405 30 Gothenburg, Sweden
| | - Paul C. D. Hawkins
- OpenEye
Scientific Software, 9 Bisbee Court, Santa Fe, New Mexico 87508, United States
| | - Giuseppe Ermondi
- Department
of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135 Torino, Italy
- E-mail: . Phone: +39 (0)11 6708337 (G.E.)
| | - Jan Kihlberg
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- E-mail: . Phone: +46 (0)18 4713801 (J.K.)
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17
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Danelius E, Pettersson M, Bred M, Min J, Waddell MB, Guy RK, Grøtli M, Erdelyi M. Flexibility is important for inhibition of the MDM2/p53 protein-protein interaction by cyclic β-hairpins. Org Biomol Chem 2018; 14:10386-10393. [PMID: 27731454 DOI: 10.1039/c6ob01510g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions that have large, flat and featureless binding sites are difficult drug targets. In the development of their modulators conventional drug discovery strategies are often unsuccessful. Gaining a detailed understanding of the binding mode of protein-protein interaction inhibitors is therefore of vast importance for their future pharmaceutical use. The MDM2/p53 protein pair is a highly promising target for cancer treatment. Disruption of the protein complex using p53 α-helix mimetics has been shown to be a successful strategy to control p53 activity. To gain further insight into the binding of inhibitors to MDM2, the flexibility of four cyclic β-hairpins that act as α-helical mimetics and potential MDM2/p53 interaction inhibitors was investigated in relation to their inhibitory activity. MDM2-binding of the mimetics was determined using fluorescence polarization and surface plasmon resonance assays, whereas their conformation and dynamics in solution was described by the combined experimental and computational NAMFIS analysis. Molecular flexibility was shown to be important for the activity of the cyclic β-hairpin based MDM2 inhibitors.
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Affiliation(s)
- Emma Danelius
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Mariell Pettersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Matilda Bred
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Mate Erdelyi
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden. and Swedish NMR Centre, Medicinaregatan 5, SE-41390 Gothenburg, Sweden
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18
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Danelius E, Andersson H, Jarvoll P, Lood K, Gräfenstein J, Erdélyi M. Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation. Biochemistry 2017; 56:3265-3272. [PMID: 28581720 PMCID: PMC5510091 DOI: 10.1021/acs.biochem.7b00429] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Halogen
bonding is a weak chemical force that has so far mostly
found applications in crystal engineering. Despite its potential for
use in drug discovery, as a new molecular tool in the direction of
molecular recognition events, it has rarely been assessed in biopolymers.
Motivated by this fact, we have developed a peptide model system that
permits the quantitative evaluation of weak forces in a biologically
relevant proteinlike environment and have applied it for the assessment
of a halogen bond formed between two amino acid side chains. The influence
of a single weak force is measured by detection of the extent to which
it modulates the conformation of a cooperatively folding system. We
have optimized the amino acid sequence of the model peptide on analogues
with a hydrogen bond-forming site as a model for the intramolecular
halogen bond to be studied, demonstrating the ability of the technique
to provide information about any type of weak secondary interaction.
A combined solution nuclear magnetic resonance spectroscopic and computational
investigation demonstrates that an interstrand halogen bond is capable
of conformational stabilization of a β-hairpin foldamer comparable
to an analogous hydrogen bond. This is the first report of incorporation
of a conformation-stabilizing halogen bond into a peptide/protein
system, and the first quantification of a chlorine-centered halogen
bond in a biologically relevant system in solution.
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Affiliation(s)
- Emma Danelius
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Hanna Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Patrik Jarvoll
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Kajsa Lood
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology, University of Gothenburg , SE-41296 Gothenburg, Sweden.,Swedish NMR Centre , Medicinaregatan 5, SE-41390 Gothenburg, Sweden
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19
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Slabber CA, Grimmer CD, Robinson RS. Solution Conformations of Curcumin in DMSO. JOURNAL OF NATURAL PRODUCTS 2016; 79:2726-2730. [PMID: 27715050 DOI: 10.1021/acs.jnatprod.6b00726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
NAMFIS (NMR Analysis of Molecular Flexibility In Solution) has been applied to curcumin dissolved in DMSO. Quantitative 1H-1H distance constraints reduce a pool of candidate conformations to a solution collection of four enol conformations-two of these match curcumin crystallized with human transthyretin, and one is closely related to a single-crystal structure of curcumin.
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Affiliation(s)
- Cathryn A Slabber
- School of Chemistry and Physics, University of KwaZulu-Natal , Pietermaritzburg, South Africa 3209
| | - Craig D Grimmer
- School of Chemistry and Physics, University of KwaZulu-Natal , Pietermaritzburg, South Africa 3209
| | - Ross S Robinson
- School of Chemistry and Physics, University of KwaZulu-Natal , Pietermaritzburg, South Africa 3209
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20
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Allen SE, Dokholyan NV, Bowers AA. Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications. ACS Chem Biol 2016; 11:10-24. [PMID: 26575401 DOI: 10.1021/acschembio.5b00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.
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Affiliation(s)
- Scott E. Allen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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21
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Grimmer CD, Slabber CA. Conformational analysis: ³JHCOC and ³JHCCC Karplus relationships for methylene ¹H nuclei. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:590-595. [PMID: 26017915 DOI: 10.1002/mrc.4264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/26/2015] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
NAMFIS (NMR Analysis of Molecular Flexibility In Solution) was applied to 1-[2-(benzyloxy)phenyl]ethanone using quantitative (1)H-(1)H NOE distances and (3)J proton-carbon coupling constant (CC) restraints for averaged methylene proton (3)J(HCOC) and (3)J(HCCC) pathways H2-(3)J-X imposed by density functional theory-generated Karplus relationships. Comparison of the NOE-only versus the NOE + CC conformational selections illustrates that the experimentally measured average (3)J coupling constants of methylene protons can be used for solution conformational analysis, potentially valuable in the study of small-molecule drugs and natural products which lack the typically studied H1-(3)J-X Karplus relationships.
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Affiliation(s)
- Craig D Grimmer
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Cathryn A Slabber
- School of Chemistry and Physics, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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22
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Grimmer C, Moore TW, Padwa A, Prussia A, Wells G, Wu S, Sun A, Snyder JP. Antiviral atropisomers: conformational energy surfaces by NMR for host-directed myxovirus blockers. J Chem Inf Model 2014; 54:2214-23. [PMID: 25058809 DOI: 10.1021/ci500204j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biologically active organic molecules characterized by a high single bond torsional barrier generate isolable isomers (atropisomers) and offer a unique stereochemical component to the design of selective therapeutic agents. The present work presents a nanomolar active inhibitor of myxoviruses, which most likely acts by blocking one or more cellular host proteins but also, serendipitously, exhibits axial chirality with an energy barrier of ΔG((++)) ≥30 kcal/mol. The latter has been probed by variable temperature NMR and microwave irradiation and by high level DFT transition state analysis and force field calculations. Full conformational profiles of the corresponding (aR,S) and (aS,S) atropisomers at ambient temperature were derived by conformer deconvolution with NAMFIS (NMR Analysis by Molecular Flexibility In Solution) methodology to generate seven and eight individual conformations, each assigned a % population. An accurate evaluation of a key torsion angle at the center of the molecules associated with a (3)JC-S-C-H coupling constant was obtained by mapping the S-C bond rotation with the MPW1PW91/6-31G-d,p DFT method followed by fitting the resulting dihedral angles and J-values to a Karplus expression. Accordingly, we have developed a complete conformational profile of diastereomeric atropisomers consistent with both high and low rotational barriers. We expect this assessment to assist the rationalization of the selectivity of the two (aR,S) and (aS,S) forms against host proteins, while offering insights into their divergent toxicity behavior.
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Affiliation(s)
- Craig Grimmer
- School of Chemistry and Physics, University of KwaZulu-Natal , Pietermaritzburg, South Africa
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23
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Norrehed S, Johansson H, Grennberg H, Gogoll A. Improved Stereochemical Analysis of Conformationally Flexible Diamines by Binding to a Bisporphyrin Molecular Clip. Chemistry 2013; 19:14631-8. [DOI: 10.1002/chem.201300533] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 06/06/2013] [Indexed: 01/09/2023]
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24
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Blundell CD, Packer MJ, Almond A. Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. Bioorg Med Chem 2013; 21:4976-87. [PMID: 23886813 PMCID: PMC3744816 DOI: 10.1016/j.bmc.2013.06.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022]
Abstract
Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.
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Affiliation(s)
- Charles D Blundell
- C4X Discovery Ltd, Unit 310 Ducie House, Ducie Street, Manchester M1 2JW, UK
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25
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Fridén-Saxin M, Seifert T, Hansen LK, Grøtli M, Erdelyi M, Luthman K. Proline-mediated formation of novel chroman-4-one tetrahydropyrimidines. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Erdélyi M, d'Auvergne E, Navarro-Vázquez A, Leonov A, Griesinger C. Dynamics of the glycosidic bond: conformational space of lactose. Chemistry 2011; 17:9368-76. [PMID: 21755545 DOI: 10.1002/chem.201100854] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Indexed: 11/11/2022]
Abstract
The dynamics of the glycosidic bond of lactose was studied by a paramagnetic tagging-based NMR technique, which allowed the collection of an unusually large series of NMR data for a single compound. By the use of distance- and orientation-dependent residual dipolar couplings and pseudocontact shifts, the simultaneous fitting of the probabilities of computed conformations and the orientation of the magnetic susceptibility tensor of a series of lanthanide complexes of lactose show that its glycosidic bond samples syn/syn, anti/syn and syn/anti ϕ/ψ regions of the conformational space in water. The analysis indicates a higher reliability of pseudocontact shift data as compared to residual dipolar couplings with the presently available weakly orienting paramagnetic tagging technique. The method presented herein allows for an improved understanding of the dynamic behaviour of oligosaccharides.
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Affiliation(s)
- Máté Erdélyi
- NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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27
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Jogalekar AS, Damodaran K, Kriel FH, Jung WH, Alcaraz AA, Zhong S, Curran DP, Snyder JP. Dictyostatin Flexibility Bridges Conformations in Solution and in the β-Tubulin Taxane Binding Site. J Am Chem Soc 2011; 133:2427-36. [DOI: 10.1021/ja1023817] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashutosh S. Jogalekar
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Krishnan Damodaran
- Department of Chemistry, University of Pittsburgh, 1101 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260-3900, United States
| | - Frederik H. Kriel
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Won-Hyuk Jung
- Department of Chemistry, University of Pittsburgh, 1101 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260-3900, United States
| | - Ana A. Alcaraz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Shi Zhong
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Dennis P. Curran
- Department of Chemistry, University of Pittsburgh, 1101 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260-3900, United States
| | - James P. Snyder
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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28
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Andersson H, Demaegdt H, Vauquelin G, Lindeberg G, Karlén A, Hallberg M, Erdélyi M, Hallberg A. Disulfide Cyclized Tripeptide Analogues of Angiotensin IV as Potent and Selective Inhibitors of Insulin-Regulated Aminopeptidase (IRAP). J Med Chem 2010; 53:8059-71. [DOI: 10.1021/jm100793t] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hanna Andersson
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Heidi Demaegdt
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Georges Vauquelin
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Gunnar Lindeberg
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Mathias Hallberg
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry, University of Gothenburg, SE-412 96 Göteborg, Sweden
| | - Anders Hallberg
- Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
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29
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Jogalekar AS. Conformations of stevastelin C3 analogs: Computational deconvolution of NMR data reveals conformational heterogeneity and novel motifs. Biopolymers 2010; 93:968-76. [DOI: 10.1002/bip.21504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Koivisto JJ, Kumpulainen ETT, Koskinen AMP. Conformational ensembles of flexible beta-turn mimetics in DMSO-d6. Org Biomol Chem 2010; 8:2103-16. [PMID: 20401387 DOI: 10.1039/b921794k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Beta-turns play an important role in peptide and protein chemistry, biophysics, and bioinformatics. The aim of this research was to study short linear peptides that have a high propensity to form beta-turn structures in solution. In particular, we examined conformational ensembles of beta-turn forming peptides with a general sequence CBz-L-Ala-L-Xaa-Gly-L-Ala-OtBu. These tetrapeptides, APGA, A(4R)MePGA, and A(4S)MePGA, incorporate proline, (4R)-methylproline, and (4S)-methylproline, respectively, at the Xaa position. To determine the influence of the 4-methyl substituted prolines on the beta-turn populations, the NAMFIS (NMR analysis of molecular flexibility in solution) deconvolution analysis for these three peptides were performed in DMSO-d(6) solution. The NBO (natural bond orbital) method was employed to gain further insight into the results obtained from the NAMFIS analysis. The emphasis in the NBO analysis was to characterize remote intramolecular interactions that could influence the backbone-backbone interactions contributing to beta-turn stability. NAMFIS results indicate that the enantiospecific incorporation of the methyl substituent at the C(gamma) (C4) position of the proline residue can be used to selectively control the pyrrolidine ring puckering propensities and, consequently, the preferred varphi,psi angles associated with the proline residue in beta-turn forming peptides. The NAMFIS analyses show that the presence of (4S)-methylproline in A(4S)MePGA considerably increased the type II beta-turn population with respect to APGA and A(4R)MePGA. The NBO calculations suggest that this observation can be rationalized based on an n-->pi* interaction between the N-terminus alanine carbonyl oxygen and the proline carbonyl group. Several other interactions between remote orbitals in these peptides provide a more detailed explanation for the observed population distributions.
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Affiliation(s)
- Jari J Koivisto
- Aalto University School of Science and Technology, Faculty of Chemistry and Materials Sciences, Department of Chemistry, P.O.Box 16100, FI-00076 Aalto, Finland
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31
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Jogalekar AS, Kriel FH, Shi Q, Cornett B, Cicero D, Snyder JP. The discodermolide hairpin structure flows from conformationally stable modular motifs. J Med Chem 2010; 53:155-65. [PMID: 19894728 DOI: 10.1021/jm9015284] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(+)-Discodermolide (DDM), a polyketide macrolide from marine sponge, is a potent microtubule assembly promoter. Reported solid-state, solution, and protein-bound DDM conformations reveal the unusual result that a common hairpin conformational motif exists in all three microenvironments. No other flexible microtubule binding agent exhibits such constancy of conformation. In the present study, we combine force-field conformational searches with NMR deconvolution in different solvents to compare DDM conformers with those observed in other environments. While several conformational families are perceived, the hairpin form dominates. The stability of this motif is dictated primarily by steric factors arising from repeated modular segments in DDM composed of the C(Me)-CHX-C(Me) fragment. Furthermore, docking protocols were utilized to probe the DDM binding mode in beta-tubulin. A previously suggested pose is substantiated (Pose-1), while an alternative (Pose-2) has been identified. SAR analysis for DDM analogues differentiates the two poses and suggests that Pose-2 is better able to accommodate the biodata.
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Affiliation(s)
- Ashutosh S Jogalekar
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
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32
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Fragaki G, Stefanaki I, Dais P, Mikros E. Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:1102-1111. [PMID: 18924119 DOI: 10.1002/mrc.2298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phase-sensitive nuclear Overhauser enhancement spectroscopy (NOESY) experiments, (3)J couplings and computational molecular modeling (MM2* and MMFF force fields) were employed to examine the conformational properties of verrucarin A in chloroform solutions. The MMFF force field calculations resulted in a family of 12 low-energy structures along with their populations, the latter being determined by the NMR analysis of molecular flexibility in solution(NAMFIS) deconvolution analysis. The concluded model was capable of reproducing successfully the experimental NOESY cross-peak volumes and the proton-coupling constants. Among the 12 conformers, the one which was similar to the structure of verrucarin A in the solid state was the predominant accounting for 75% of the total relative population, although other low-energy conformations contributed to a lesser degree in order to explain the experimental data.
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Affiliation(s)
- Georgia Fragaki
- NMR Laboratory, Department of Chemistry, University of Crete, Voutes Campus, 71003 Heraklion, Crete, Greece
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33
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Smith SG, Paton RS, Burton JW, Goodman JM. Stereostructure Assignment of Flexible Five-Membered Rings by GIAO 13C NMR Calculations: Prediction of the Stereochemistry of Elatenyne. J Org Chem 2008; 73:4053-62. [DOI: 10.1021/jo8003138] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Steven G. Smith
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S. Paton
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Jonathan W. Burton
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Jonathan M. Goodman
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Erdélyi M, Varedian M, Sköld C, Niklasson IB, Nurbo J, Persson Å, Bergquist J, Gogoll A. Chemistry and folding of photomodulable peptides – stilbene and thioaurone-type candidates for conformational switches. Org Biomol Chem 2008; 6:4356-73. [DOI: 10.1039/b812001c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Ganesh T, Yang C, Norris A, Glass T, Bane S, Ravindra R, Banerjee A, Metaferia B, Thomas SL, Giannakakou P, Alcaraz AA, Lakdawala AS, Snyder JP, Kingston DGI. Evaluation of the tubulin-bound paclitaxel conformation: synthesis, biology, and SAR studies of C-4 to C-3' bridged paclitaxel analogues. J Med Chem 2007; 50:713-25. [PMID: 17263521 PMCID: PMC2585518 DOI: 10.1021/jm061071x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The important anticancer drug paclitaxel binds to the beta-subunit of the alphabeta-tubulin dimer in the microtubule in a stoichiometric ratio, promoting microtubule polymerization and stability. The conformation of microtubule-bound drug has been the subject of intense study, and various suggestions have been proposed. In previous work we presented experimental and theoretical evidence that paclitaxel adopts a T-shaped conformation when it is bound to tubulin. In this study we report additional experimental data and calculations that delineate the allowable parameters for effective paclitaxel-tubulin interactions.
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Affiliation(s)
- Thota Ganesh
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Chao Yang
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Andrew Norris
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Tom Glass
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Susan Bane
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902
- To whom correspondence should be addressed. Phone: 540-231-6570. Fax: 540-231-3255. E-mail:
| | - Rudravajhala Ravindra
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902
| | - Abhijit Banerjee
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902
| | - Belhu Metaferia
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Shala L. Thomas
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Ana A. Alcaraz
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | | | - James P. Snyder
- Department of Chemistry, Emory University, Atlanta, GA 30322
- To whom correspondence should be addressed. Phone: 540-231-6570. Fax: 540-231-3255. E-mail:
| | - David G. I. Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
- To whom correspondence should be addressed. Phone: 540-231-6570. Fax: 540-231-3255. E-mail:
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36
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Yamashita DS, Marquis RW, Xie R, Nidamarthy SD, Oh HJ, Jeong JU, Erhard KF, Ward KW, Roethke TJ, Smith BR, Cheng HY, Geng X, Lin F, Offen PH, Wang B, Nevins N, Head MS, Haltiwanger RC, Narducci Sarjeant AA, Liable-Sands LM, Zhao B, Smith WW, Janson CA, Gao E, Tomaszek T, McQueney M, James IE, Gress CJ, Zembryki DL, Lark MW, Veber DF. Structure activity relationships of 5-, 6-, and 7-methyl-substituted azepan-3-one cathepsin K inhibitors. J Med Chem 2006; 49:1597-612. [PMID: 16509577 DOI: 10.1021/jm050915u] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The syntheses, in vitro characterizations, and rat and monkey in vivo pharmacokinetic profiles of a series of 5-, 6-, and 7-methyl-substituted azepanone-based cathepsin K inhibitors are described. Depending on the particular regiochemical substitution and stereochemical configuration, methyl-substituted azepanones were identified that had widely varied cathepsin K inhibitory potency as well as pharmacokinetic properties compared to the 4S-parent azepanone analogue, 1 (human cathepsin K, K(i,app) = 0.16 nM, rat oral bioavailability = 42%, rat in vivo clearance = 49.2 mL/min/kg). Of particular note, the 4S-7-cis-methylazepanone analogue, 10, had a K(i,app) = 0.041 nM vs human cathepsin K and 89% oral bioavailability and an in vivo clearance rate of 19.5 mL/min/kg in the rat. Hypotheses that rationalize some of the observed characteristics of these closely related analogues have been made using X-ray crystallography and conformational analysis. These examples demonstrate the potential for modulation of pharmacological properties of cathepsin inhibitors by substituting the azepanone core. The high potency for inhibition of cathepsin K coupled with the favorable rat and monkey pharmacokinetic characteristics of compound 10, also known as SB-462795 or relacatib, has made it the subject of considerable in vivo evaluation for safety and efficacy as an inhibitor of excessive bone resorption in rat, monkey, and human studies, which will be reported elsewhere.
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Affiliation(s)
- Dennis S Yamashita
- Department of Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, USA.
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37
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Jiang Y, Alcaraz AA, Chen JM, Kobayashi H, Lu YJ, Snyder JP. Diastereomers of Dibromo-7-epi-10-deacetylcephalomannine: Crowded and Cytotoxic Taxanes Exhibit Halogen Bonds. J Med Chem 2006; 49:1891-9. [PMID: 16539375 DOI: 10.1021/jm0509243] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The diastereomers of dibromo-7-epi-10-deacetylcephalomannine (6 and 7) have been isolated and characterized. Cytotoxicity and microtubule assembly assays demonstrate that cephalomannine analogue 6 possesses a potency profile very similar to that of Taxol, while isomer 7 is slightly less active. Solid state, solution, and tubulin-bound conformations of the two diastereomers were probed by using X-ray crystallography, 2-D NMR experiments in conjunction with the NAMFIS analysis, and the Glide docking protocol. In the crystal, isomer 7 exhibits an intermolecular halogen bond that may contribute to self-assembly. Neither crystal structure appears in the NAMFIS solution analysis, but both diastereomers are represented in solution by a T-shaped Taxol conformer. Glide docking demonstrates the latter to best fill the tubulin binding pocket, as has been shown for the parent Taxol drug. Each model of the bound complexes for 6 and 7 presents a single well-defined halogen bond from one of the ligand's bromines to Glu22 or Asp26 near the N-terminus of beta-tubulin, respectively. This first report of a halogen bond between taxanes and tubulin may prove useful in guiding the design and synthesis of other microtubule-stabilizing agents with a similar capacity.
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Affiliation(s)
- Yi Jiang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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38
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Liu C, Tamm M, Nötzel MW, Rauch K, de Meijere A, Schilling JK, Lakdawala A, Snyder JP, Bane SL, Shanker N, Ravindra R, Kingston DGI. C-3′-Cyclopropanated Taxol Analogs: Synthesis, Bioassay and Biostructural Analysis. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Thepchatri P, Cicero DO, Monteagudo E, Ghosh AK, Cornett B, Weeks ER, Snyder JP. Conformations of Laulimalide in DMSO-d6. J Am Chem Soc 2005; 127:12838-46. [PMID: 16159277 DOI: 10.1021/ja042890e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Laulimalide is one of the newest naturally occurring macrolides known to act as a microtubule stabilizing agent with properties similar to Taxol. It also stands as being one of the most flexible with 18 rotatable bonds. This large number of rotatable bonds allows for approximately 3(18) potential conformers. To examine the conformational energy surface of laulimalide, we have performed an NAMFIS deconvolution analysis for laulimalide in DMSO-d6. The latter has been supplemented with a post-NAMFIS energy analysis at the Becke3LYP/6-31G level that examines the opposing effects of internal hydrogen bonding and syn-pentane interactions. In this way, we have identified 15 laulimalide conformations that can be classified into 5 different families: Supine, Convex, Cobra, Stretch, and Concave motifs.
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Affiliation(s)
- Pahk Thepchatri
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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40
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Li WI, Marquez BL, Okino T, Yokokawa F, Shioiri T, Gerwick WH, Murray TF. Characterization of the preferred stereochemistry for the neuropharmacologic actions of antillatoxin. JOURNAL OF NATURAL PRODUCTS 2004; 67:559-568. [PMID: 15104484 DOI: 10.1021/np0303409] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antillatoxin is a potent ichthyotoxin and cytotoxin previously discovered from the marine cyanobacterium Lyngbya majuscula. Ensuing studies of its mechanism of action showed it to activate the mammalian voltage-gated sodium channel at a pharmacological site that is distinct from any previously described. The structure of antillatoxin, initially formulated from spectroscopic information, was subsequently corrected at one stereocenter (C-4) as a result of synthesis of four different antillatoxin stereoisomers (all possible C-4 and C-5 diastereomers). In the current study these four stereoisomers, (4R,5R)-, (4S,5R)-, (4S,5S)-, and (4R,5S)-antillatoxin, were characterized in five different biological assay systems: ichthyotoxicity to goldfish, microphysiometry using cerebellar granule cells (CGCs), lactose dehydrogenase efflux from CGCs, monitoring of intracellular Ca(2+) concentrations in CGCs, and cytotoxicity to Neuro 2a cells. Across these various biological measures there was great consistency in that the natural antillatoxin (the 4R,5R-isomer) was greater than 25-fold more potent than any of the other stereoisomers. Detailed NMR studies provided a number of torsion and distance constraints that were modeled using the MM2 force field to yield predicted solution structures of the four antillatoxin stereoisomers. The macrocycle and side chain of natural (4R,5R)-antillatoxin present an overall "L-shaped" topology with an accumulation of polar substituents on the external surface of the macrocycle and a hydrogen bond between N(H)-7' and the C(O)-1 carbonyl. The decreased potency of the three non-naturally occurring antillatoxin stereoisomers is certainly a result of their dramatically altered overall molecular topologies.
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Affiliation(s)
- W I Li
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602-7389, USA
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41
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Kelso MJ, Beyer RL, Hoang HN, Lakdawala AS, Snyder JP, Oliver WV, Robertson TA, Appleton TG, Fairlie DP. α-Turn Mimetics: Short Peptide α-Helices Composed of Cyclic Metallopentapeptide Modules. J Am Chem Soc 2004; 126:4828-42. [PMID: 15080687 DOI: 10.1021/ja037980i] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Alpha-Helices are key structural components of proteins and important recognition motifs in biology. Short peptides (<or=15 residues) corresponding to these helical sequences are rarely helical away from their stabilizing protein environments. New techniques for stabilizing short peptide helices could be valuable for studying protein folding, modeling proteins, creating artificial proteins, and may aid the design of inhibitors or mimics of protein function. This study reports the facile incorporation of 3- and 4-alpha turns in 10-15 residue peptides through formation in situ of multiple cyclic metallopeptide modules [Pd(en)(H*XXXH*)](2+). The nonhelical peptides Ac-H*ELTH*H*VTDH*-NH(2) (1), Ac-H*ELTH*AVTDYH*ELTH*-NH(2) (2), and Ac-H*AAAH*HELTH*H*VTDH*-NH(2) (3) (H is histidine-methylated at imidazole-N3) react in N,N-dimethylformamide (DMF) or water with 2, 2, and 3 molar equivalents, respectively, of [Pd(en)(NO(3))(2)] to form exclusively [Pd(2)(en)(2)(Ac-H*ELTH*H*VTDH*-NH(2))](4+) (4), [Pd(2)(en)(2)(Ac-H*ELTH*AVTDYH*ELTH*-NH(2))](4+) (5), and [Pd(3)(en)(3)(Ac-H*AAAH*HELTH*H*VTDH*-NH(2))](6+) (6), characterized by mass spectrometry, 1D and 2D (1)H- and 1D (15)N-NMR spectroscopy. Despite the presence of multiple histidines and other possible metal-binding residues in these peptides, 2D (1)H NMR spectra reveal that Pd(en)(2+) is remarkably specific in coordinating to imidazole-N1 of only (i, i + 4) pairs of histidines (i.e., only those separated by three amino acids), resulting in 4-6 made up of cyclic metallopentapeptide modules ([Pd(en)(H*XXXH*)](2+))(n), n = 2, 2, 3, respectively, each cycle being a 22-membered ring. We have previously shown that a single metallopentapeptide can nucleate alpha-helicity (Kelso et al., Angew. Chem., Int. Ed. 2003, 42, 421-424.). We now demonstrate its use as an alpha-turn-mimicking module for the facile conversion of unstructured short peptides into helices of macrocycles and provide 1D and 2D NMR spectroscopic data, structure calculations via XPLOR and NMR analysis of molecular flexibility in solution (NAMFIS), and CD spectra in support of the alpha-helical nature of these monomeric metallopeptides in solution.
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Affiliation(s)
- Michael J Kelso
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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42
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Acocella A, Venturini A, Zerbetto F. Pyridinedicarboxamide Strands Form Double Helices via an Activated Slippage Mechanism. J Am Chem Soc 2004; 126:2362-7. [PMID: 14982440 DOI: 10.1021/ja038103f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intertwining process of two strands of oligo-pyridinecarboxamides to form a double helix (Nature 2000, 407, 720) is found to consist of a series of discrete steps, where the tail of one of the strands proceeds inside the other single helix in an eddy-like process. While a plethora of minima can be located along the pathway, they exist only for a few, well-defined supramolecular arrangements of the two molecules. The initial transition state for the introduction of one molecule in the pitch of the other has the largest barrier and is therefore the rate-determining step of an activated slippage mechanism, which is characterized by a series of roller-coasting hills. Along the entire pathway, the intramolecular energy that stabilizes the single helices is slowly transformed into intermolecular energy that finally provides the necessary stabilization only near the end of the entwining process. Solvent or other chemical factors, such as the presence of ions, able to destabilize the full formation of the double helix may therefore drastically affect its formation.
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Affiliation(s)
- Angela Acocella
- ISOF, Consiglio Nazionale delle Ricerche, and Dipartimento di Chimica G. Ciamician, Università di Bologna, Italy
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43
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Snyder JP, Lakdawala AS, Kelso MJ. On the stability of a single-turn alpha-helix: the single versus multiconformation problem. J Am Chem Soc 2003; 125:632-3. [PMID: 12526653 DOI: 10.1021/ja0278279] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pentapeptide Ac-HAAAH-NH2, cyclized through its imidazoles by PdII to give [Pd(en)(peptide)]2+, has recently been evaluated by 2-D NMR and simulated annealing as a single alpha-helix conformation in solution. In the present work, we have questioned this assumption by developing Pd2+ parameters for AMBER*, performing an extensive conformational search for the [Pd(en)(peptide)]2+, and deconvoluting the averaged NMR data into eight rapidly equilibrating conformations with populations ranging from 2 to 55%. None of the latter correspond to the alpha-helix, although a 3% form possesses a related structure. As a critical component of interpreting an averaged NMR spectrum in terms of a single conformation, we advise testing this assumption with a method that permits conformational deconvolution.
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Affiliation(s)
- James P Snyder
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
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44
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Lankin DC, Grunewald GL, Romero FA, Oren IY, Snyder JP. The NH---FC dipole orientation effect for pendant exocyclic CH(2)F. Org Lett 2002; 4:3557-60. [PMID: 12375886 DOI: 10.1021/ol026358c] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] DFT and MMFF force field calculations for 2 (R = H) predict that two conformers dominate in water (>/=95%) and both sustain a geometry in which the C-F and H-N dipoles align oppositely in a near-planar arrangement. The (1)H NMR spectra (D(2)O and DMSO-d(6)) and X-ray structure for 2 (R = SO(2)NHEt) confirm the predictions in all essentials. A novel single-conformer system is proposed.
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Affiliation(s)
- David C Lankin
- Pharmacia Corporation, 4901 Searle Parkway/P-024, Skokie, Illinois 60077, USA
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45
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Metaferia BB, Hoch J, Glass TE, Bane SL, Chatterjee SK, Snyder JP, Lakdawala A, Cornett B, Kingston DG. Synthesis and biological evaluation of novel macrocyclic paclitaxel analogues. Org Lett 2001; 3:2461-4. [PMID: 11483035 DOI: 10.1021/ol016124d] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] This work describes the synthesis of two novel macrocyclic taxoid constructs by ring-closing olefin metathesis (RCM) and their biological evaluation. Computational studies examine conformational profiles of 1 and 2 for their fit to the beta-tubulin binding site determined by electron crystallography. The results support the hypothesis that paclitaxel binds to microtubules in a "T" conformation.
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Affiliation(s)
- B B Metaferia
- Departments of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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46
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Monteagudo E, Cicero DO, Cornett B, Myles DC, Snyder JP. The conformations of discodermolide in DMSO. J Am Chem Soc 2001; 123:6929-30. [PMID: 11448201 DOI: 10.1021/ja015569u] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E Monteagudo
- Universidad Nacional de Quilmes Roque Sáenz Peña 180, Bernal, (1876) Pcia. de Buenos Aires, Argentina
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47
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Iovine PM, Veglia G, Furst G, Therien MJ. High-resolution structure and conformational dynamics of rigid, cofacially aligned porphyrin-bridge-quinone systems as determined by NMR spectroscopy and ab initio simulated annealing calculations. J Am Chem Soc 2001; 123:5668-79. [PMID: 11403598 DOI: 10.1021/ja010023t] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The high-resolution solution structure and dynamics of a cofacially aligned porphyrin--phenylene--quinone compound have been determined using (1)H NMR spectroscopy and simulated annealing calculations. Members of this class of pi-stacked assemblies feature a 1,8-naphthyl pillaring motif that enforces sub van der Waals interplanar separations between juxtaposed porphyryl, aromatic bridge, and quinonyl components of the donor--spacer--acceptor compound; this structural motif gives rise to a comprehensive set of structurally significant NOE signatures that can be used as constraints in quantitative structural calculations. Examination of such data using ab initio simulated annealing analytical methods shows that 5-[8'-(4' '-[8' "-(2' " ',5' "-benzoquinonyl)-1' "-naphthyl]-1' '-phenyl)-1'-naphthyl]-10,20-diphenylporphyrin displays an unusual degree of conformational homogeneity in the condensed phase, and represents a rare example where such an analysis determines unequivocally a single unique structure in solution.
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Affiliation(s)
- P M Iovine
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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48
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Barboni L, Lambertucci C, Appendino G, Vander Velde DG, Himes RH, Bombardelli E, Wang M, Snyder JP. Synthesis and NMR-driven conformational analysis of taxol analogues conformationally constrained on the C13 side chain. J Med Chem 2001; 44:1576-87. [PMID: 11334567 DOI: 10.1021/jm001103v] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analogues of Taxol (paclitaxel) with the side chain conformationally restricted by insertion of a carbon linker between the 2'-carbon and the ortho-position of the 3'-phenyl ring were synthesized. Biological evaluation of these new taxoids showed that activity was dependent on the length of the linker and the configuration at C2' and C3'. Two analogues in the homo series, 9a and 24a, showed tubulin binding and cytotoxicity comparable to that of Taxol. NAMFIS (NMR analysis of molecular flexibility in solution) deconvolution of the averaged 2-D NMR spectra for 9a yields seven conformations. Within the latter set, the hydrophobically collapsed "nonpolar" and "polar" classes are represented by one conformation each with predicted populations of 12-15%. The five remaining conformers, however, are extended, two of which correspond to the T-conformation (47% of the total population). The latter superimpose well with the recently proposed T-Taxol binding conformer in beta-tubulin. The results provide evidence for the existence of two previously unrecognized structural features that support Taxol-like activity: (1) a reduced torsion angle between C2' and C3' and (2) an orthogonal arrangement of the mean plane through C1', C2' and the 2'-hydroxyl and the 3'-phenyl plane, the latter ring bisected by the former plane. By contrast, epimerization at 2',3' and homologation of the tether to CH2-CH2 were both detrimental for activity. The decreased activity of these analogues is apparently due to configurational and steric factors, respectively.
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Affiliation(s)
- L Barboni
- Dipartimento di Scienze Chimiche, Università di Camerino, Italy.
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49
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Nikiforovich GV, Kövér KE, Zhang WJ, Marshall GR. Cyclopentapeptides as Flexible Conformational Templates. J Am Chem Soc 2000. [DOI: 10.1021/ja991728m] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory V. Nikiforovich
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
| | - Katalin E. Kövér
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
| | - Wei-Jun Zhang
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
| | - Garland R. Marshall
- Contribution from the Center for Molecular Design and Department of Molecular Biology and Pharmacology, Washington University, St. Louis, Missouri 63130, and L. Kossuth University, H-4010 Debrecen, Hungary
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