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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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2
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Peña D, Lápez-Piñeiro A, Fernández D, Light ME, Prieto JM, Santisteban L, Valladares RX, Cintas P, Babiano R. A new series of acylhydrazones derived from metribuzin with modulated herbicidal activity. Heliyon 2023; 9:e21313. [PMID: 37942154 PMCID: PMC10628692 DOI: 10.1016/j.heliyon.2023.e21313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
This paper reports the preparation and herbicidal evaluation of a small library of acylhydrazones based on the synthetic herbicide metribuzin. The hydrazone linkage easily obtained by reaction of metribuzin with aliphatic and aromatic aldehydes, masks efficiently the exocyclic amino group, thereby altering significantly H-bonding with the receptor and increasing the lipophilicity relative to the parent herbicide. The structures of all compounds, including key stereochemical issues on conformation and E/Z configuration around the C[bond, double bond]N bond were thoroughly elucidated by spectroscopic methods, and unambiguously corroborated by X-ray diffraction analysis. The herbicidal assays using an aliphatic and an aromatic acylhydrazone were performed on tomato and rapeseed plants grown in greenhouse. Our results demonstrate, regardless of rate application, that such acylhydrazone formulations do not alter the selectivity of metribuzin. Moreover, the herbicide activity was even higher in the alkyl derivative than that achieved by commercial metribuzin, thus suggesting that this substance can be applied with no need of combination with chemical coadjuvants, unlike most formulations of commercially available herbicides. Therefore, the study shows the promising effect of chemical derivatization of a common herbicide as metribuzin, to improve the herbicide activity without compromising selectivity, and allowing the farmers its use in crop protection safely and effectively.
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Affiliation(s)
- David Peña
- Área de Edafología y Química Agrícola, Escuela de Ingenierías Agrarias– IACYS, Universidad de Extremadura, Ctra de Cáceres, 06071, Badajoz, Spain
| | - Antonio Lápez-Piñeiro
- Área de Edafología y Química Agrícola, Facultad de Ciencias-IACYS, Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain
| | - Damian Fernández
- Área de Producción Vegetal, Escuela de Ingenierías Agrarias-IACYS, Universidad de Extremadura, Ctra. de Cáceres s/n, 06006, Badajoz, Spain
| | - Mark E. Light
- Department of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Juan Manuel Prieto
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Lucía Santisteban
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Richardo Xhavier Valladares
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Reyes Babiano
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, 06006, Badajoz, Spain
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3
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Zhao H, Brånalt J, Perry M, Tyrchan C. The Role of Allylic Strain for Conformational Control in Medicinal Chemistry. J Med Chem 2023. [PMID: 37285219 DOI: 10.1021/acs.jmedchem.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
It is axiomatic in medicinal chemistry that optimization of the potency of a small molecule at a macromolecular target requires complementarity between the ligand and target. In order to minimize the conformational penalty on binding, both enthalpically and entropically, it is therefore preferred to have the ligand preorganized in the bound conformation. In this Perspective, we highlight the role of allylic strain in controlling conformational preferences. Allylic strain was originally described for carbon-based allylic systems, but the same principles apply to other types of structure with sp2 or pseudo-sp2 arrangements. These systems include benzylic (including heteroaryl methyl) positions, amides, N-aryl groups, aryl ethers, and nucleotides. We have derived torsion profiles from small molecule X-ray structures for these systems. Through multiple examples, we show how these effects have been applied in drug discovery and how they can be used prospectively to influence conformation in the design process.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Jonas Brånalt
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Matthew Perry
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
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4
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Fraga GG, Colasurdo DD, Santiago CC, Ponzinibbio A, Sasiambarrena LD. Rotamerization equilibrium in novel N,N-disubstituted chloroacetamides: An NMR spectroscopic study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Abrams R, Jesani MH, Browning A, Clayden J. Triarylmethanes and their Medium-Ring Analogues by Unactivated Truce-Smiles Rearrangement of Benzanilides. Angew Chem Int Ed Engl 2021; 60:11272-11277. [PMID: 33830592 PMCID: PMC8252078 DOI: 10.1002/anie.202102192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/01/2021] [Indexed: 12/17/2022]
Abstract
Intramolecular nucleophilic aromatic substitution (Truce–Smiles rearrangement) of the anions of 2‐benzyl benzanilides leads to triarylmethanes in an operationally simple manner. The reaction succeeds even without electronic activation of the ring that plays the role of electrophile in the SNAr reaction, being accelerated instead by the preferred conformation imposed by the tertiary amide tether. The amide substituent of the product may be removed or transformed into alternative functional groups. A ring‐expanding variant (n to n+4) of the reaction provided a route to doubly benzo‐fused medium ring lactams of 10 or 11 members. Hammett analysis returned a ρ value consistent with the operation of a partially concerted reaction mechanism.
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Affiliation(s)
- Roman Abrams
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Mehul H Jesani
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Alex Browning
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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6
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Abrams R, Jesani MH, Browning A, Clayden J. Triarylmethanes and their Medium‐Ring Analogues by Unactivated Truce–Smiles Rearrangement of Benzanilides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Roman Abrams
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
| | - Mehul H. Jesani
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
| | - Alex Browning
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
| | - Jonathan Clayden
- School of Chemistry University of Bristol, Cantock's Close Bristol BS8 1TS UK
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7
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Testa A, Hughes SJ, Lucas X, Wright JE, Ciulli A. Structure-Based Design of a Macrocyclic PROTAC. Angew Chem Int Ed Engl 2020; 59:1727-1734. [PMID: 31746102 PMCID: PMC7004083 DOI: 10.1002/anie.201914396] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Indexed: 12/21/2022]
Abstract
Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Herein, we report the design and synthesis of a macrocyclic PROTAC by adding a cyclizing linker to the BET degrader MZ1. A co-crystal structure of macroPROTAC-1 bound in a ternary complex with VHL and the second bromodomain of Brd4 validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12-fold loss of binary binding affinity for Brd4, macroPROTAC-1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets.
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Affiliation(s)
- Andrea Testa
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Scott J. Hughes
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Xavier Lucas
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
- Current address: Roche Pharma Research and Early DevelopmentRoche Innovation Center BaselF. Hoffmann-La Roche Ltd.Grenzacherstrasse 124CH-4070BaselSwitzerland
| | - Jane E. Wright
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
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8
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Testa A, Hughes SJ, Lucas X, Wright JE, Ciulli A. Structure‐Based Design of a Macrocyclic PROTAC. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrea Testa
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland UK
| | - Scott J. Hughes
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland UK
| | - Xavier Lucas
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland UK
- Current address: Roche Pharma Research and Early Development Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 CH-4070 Basel Switzerland
| | - Jane E. Wright
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland UK
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9
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Pros GJ, Bloomfield AJ. Why Do N-Alkylated Anilides Bend Over? The Factors Dictating the Divergent Conformational Preferences of 2° and 3° N-Aryl Amides. J Phys Chem A 2019; 123:7609-7618. [DOI: 10.1021/acs.jpca.9b04555] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Gabrielle J. Pros
- Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Aaron J. Bloomfield
- Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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10
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Krüger K, Lüdke V, Pettinger J, Ashton L, Bonnet L, Motti CA, Lex J, Oelgemöller M. Photochemical synthesis of cyclic peptide models from phthalimido acetamides and phthaloyl dipeptide esters. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.02.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Tukachev N, Bataev V, Godunov I. Conformational analysis of N-methylacetamide molecule in the ground and excited electronic states. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Forsting T, Gottschalk HC, Hartwig B, Mons M, Suhm MA. Correcting the record: the dimers and trimers of trans-N-methylacetamide. Phys Chem Chem Phys 2017; 19:10727-10737. [DOI: 10.1039/c6cp07989j] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman jet spectroscopy reveals three N-methylacetamide molecules organizing into a ring structure, previously overlooked in computations.
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Affiliation(s)
- Thomas Forsting
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | | | - Beppo Hartwig
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Michel Mons
- LIDYL; CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
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13
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Inoue R, Kawamorita S, Naota T. Single-Point Remote Control of Flapping Motion in Clothespin-Shaped Bimetallic Palladium Complexes Based on the N(sp2)-N(sp3) Interconversion in Amide Functionalities. Chemistry 2016; 22:5712-26. [DOI: 10.1002/chem.201504775] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Ryo Inoue
- Department of Chemistry; Graduate School of Engineering Science; Osaka University; Machikaneyama, Toyonaka Osaka 560-8531 Japan
| | - Soichiro Kawamorita
- Department of Chemistry; Graduate School of Engineering Science; Osaka University; Machikaneyama, Toyonaka Osaka 560-8531 Japan
| | - Takeshi Naota
- Department of Chemistry; Graduate School of Engineering Science; Osaka University; Machikaneyama, Toyonaka Osaka 560-8531 Japan
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14
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González-de-Castro Á, Broughton H, Martínez-Pérez JA, Espinosa JF. Conformational features of secondary N-cyclopropyl amides. J Org Chem 2015; 80:3914-20. [PMID: 25803271 DOI: 10.1021/acs.joc.5b00236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR studies in conjunction with ab initio calculations revealed unexpected conformational behavior of N-cyclopropylacetamide (1). This secondary amide displays 16-19% E-rotamer (cis) around the carbonyl-nitrogen bond in apolar solvents, in contrast to other aliphatic secondary acetamides in which significant E-rotamer populations are rare due to steric contacts between the substituents on the amide bond. In addition, 1 adopts an ortho conformation around the N-cPr bond instead of the anti conformation generally preferred by secondary acetamides. This distinct conformational behavior was also observed for other secondary N-cyclopropyl amides.
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Affiliation(s)
| | - Howard Broughton
- Centro de Investigación Lilly, Avda. de la Industria, 30, 28108-Alcobendas, Madrid, Spain
| | - José A Martínez-Pérez
- Centro de Investigación Lilly, Avda. de la Industria, 30, 28108-Alcobendas, Madrid, Spain
| | - Juan F Espinosa
- Centro de Investigación Lilly, Avda. de la Industria, 30, 28108-Alcobendas, Madrid, Spain
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15
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A review of the effect of multiple conformers on crystallization from solution and strategies for crystallizing slow inter-converting conformers. Chem Eng Sci 2014. [DOI: 10.1016/j.ces.2013.11.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Li S, Li H, Chen C, Yue X, Cao X, Ke S. Novel aroylhydrazine-amide derivatives bearing pyridine core: synthesis, characterisations and selective colorimetric recognition properties. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.783919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Shaowei Li
- a College of Science, Huazhong Agricultural University , Wuhan , 430070 , People's Republic of China
| | - Huangyong Li
- a College of Science, Huazhong Agricultural University , Wuhan , 430070 , People's Republic of China
| | - Changshui Chen
- a College of Science, Huazhong Agricultural University , Wuhan , 430070 , People's Republic of China
| | - Xiali Yue
- a College of Science, Huazhong Agricultural University , Wuhan , 430070 , People's Republic of China
| | - Xiufang Cao
- a College of Science, Huazhong Agricultural University , Wuhan , 430070 , People's Republic of China
| | - Shaoyong Ke
- b National Biopesticide Engineering Research Center, Hubei Academy of Agricultural Science , Wuhan , 430064 , People's Republic of China
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17
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He JH, Liu HY, Li Z, Tan JH, Ou TM, Huang SL, An LK, Li D, Gu LQ, Huang ZS. New quinazoline derivatives for telomeric G-quadruplex DNA: effects of an added phenyl group on quadruplex binding ability. Eur J Med Chem 2013; 63:1-13. [PMID: 23454529 DOI: 10.1016/j.ejmech.2013.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/19/2013] [Accepted: 01/24/2013] [Indexed: 01/06/2023]
Abstract
To improve the selectivity of indoloquinoline or benzofuroquinoline derivatives, we previously reported several quinazoline derivatives [17]. These compounds could mimic a tetracyclic aromatic system through intramolecular hydrogen bond. Studies showed that these quinazoline derivatives were effective and selective telomeric G-quadruplex ligands. With this encouragement, here we synthesized a series of N-(2-(quinazolin-2-yl)phenyl)benzamide (QPB) compounds as modified quinazoline derivatives. In this modification, a phenyl group was introduced to the aromatic core. The evaluation results showed that part of QPB derivatives had stronger binding ability and better selectivity for telomeric G-quadruplex DNA than LZ-11, the most potential compound of reported quinazoline derivatives. Furthermore, telomerase inhibition of QPB derivatives and their cellular effects were studied.
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Affiliation(s)
- Jin-Hui He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China
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18
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Kumar S, Sharma R, Garcia M, Kamel J, McCarthy C, Muth A, Phanstiel O. Chemoselective Amide Formation Using O-(4-Nitrophenyl)hydroxylamines and Pyruvic Acid Derivatives. J Org Chem 2012. [DOI: 10.1021/jo302175g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sonali Kumar
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
| | - Rashi Sharma
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
| | - Megan Garcia
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
| | - Joseph Kamel
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
| | - Caroline McCarthy
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
| | - Aaron Muth
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
| | - Otto Phanstiel
- Department of Medical
Education, College of Medicine, University of Central Florida, 6850 Lake Nona Boulevard, Orlando,
Florida 32827, United States
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19
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Li Z, Tan JH, He JH, Long Y, Ou TM, Li D, Gu LQ, Huang ZS. Disubstituted quinazoline derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA. Eur J Med Chem 2011; 47:299-311. [PMID: 22104971 DOI: 10.1016/j.ejmech.2011.10.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 12/12/2022]
Abstract
A series of 2,4-disubstituted quinazoline derivatives found to be a new type of highly selective ligand to bind with telomeric G-quadruplex DNA, and their biological properties were reported for the first time.Their interactions with telomeric G-quadruplex DNA were evaluated by using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and molecular modeling. Our results showed that these derivatives could well recognize G-quadruplex and have high selectivity toward G-quadruplex over duplex DNA. The structure-activity relationships (SARs) study revealed that the disubstitution of quinazoline and the length of the amide side chain were important for its interaction with the G-quadruplex. Furthermore, telomerase inhibition of the quinazoline derivatives and their cellular effects were studied.
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Affiliation(s)
- Zeng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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20
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Ruppert M, Spänig F, Wielopolski M, Jäger CM, Bauer W, Clark T, Hirsch A, Guldi DM. Dendronizing and Metalating trans-2 C60 Tetraaryl Porphyrins-A Versatile Approach Toward Water-Soluble Donor-Acceptor Conjugates. Chemistry 2010; 16:10797-807. [DOI: 10.1002/chem.201000760] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Oger F, Lecorgne A, Sala E, Nardese V, Demay F, Chevance S, Desravines DC, Aleksandrova N, Le Guével R, Lorenzi S, Beccari AR, Barath P, Hart DJ, Bondon A, Carettoni D, Simonneaux G, Salbert G. Biological and biophysical properties of the histone deacetylase inhibitor suberoylanilide hydroxamic acid are affected by the presence of short alkyl groups on the phenyl ring. J Med Chem 2010; 53:1937-50. [PMID: 20143840 DOI: 10.1021/jm901561u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inhibition of histone deacetylases (HDACs) leads to growth arrest, differentiation, or apoptosis of tumor cell lines, suggesting HDACs as promising targets for cancer therapy. At present, only one HDAC inhibitor (HDACi) is used in therapy: suberoylanilide hydroxamic acid (SAHA). Here, we describe the synthesis and biological evaluation of a new series of compounds derived from SAHA by substituting short alkyl chains at various positions of the phenyl ring. Such modifications induced variable effects ranging from partial loss of activity to increased potency. Through molecular modeling, we describe a possible interaction between HDAC7 proline 809, a residue that is strictly conserved within class 2 enzymes only, and the amide group of HDACi, while nuclear magnetic resonance experiments indicated that dimethyl m-substitution may stabilize the inhibitor in the active site. Our data provide novel information on the structure-activity relationship of HDACi and suggest new ways for developing second generation SAHA-like molecules.
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Affiliation(s)
- Frédérik Oger
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, France, Cedex
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22
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Barneto JL, Avalos M, Babiano R, Cintas P, Jiménez JL, Palacios JC. A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins. Org Biomol Chem 2010; 8:857-63. [PMID: 20135044 DOI: 10.1039/b921121g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.
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Affiliation(s)
- José Luis Barneto
- Departamento de Química Orgánica e Inorgánica, QUOREX Research Group, Facultad de Ciencias, Universidad de Extremadura, E-06071, Badajoz, Spain.
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23
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Pérez EMS, Avalos M, Babiano R, Cintas P, Light ME, Jiménez JL, Palacios JC, Sancho A. Schiff bases from D-glucosamine and aliphatic ketones. Carbohydr Res 2010; 345:23-32. [PMID: 19914606 DOI: 10.1016/j.carres.2009.08.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/31/2009] [Accepted: 08/13/2009] [Indexed: 11/28/2022]
Abstract
Despite the comprehensive literature and enormous versatility of chiral imines derived from aminosugars and aldehydes, the corresponding counterparts generated from ketones remain an underestimated research subject. Filling in the gap, this manuscript sheds light on the synthetic and structural aspects of such substances and updates the few antecedents reported so far.
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Affiliation(s)
- Esther M S Pérez
- Departamento de Química Orgánica e Inorgánica, QUOREX Research Group, Universidad de Extremadura, E-06071 Badajoz, Spain.
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24
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Simón L, Goodman JM. DFT Study on the Factors Determining the Enantioselectivity of Friedel−Crafts Reactions of Indole with N-Acyl and N-Tosylimines Catalyzed by BINOL−Phosphoric Acid Derivatives. J Org Chem 2009; 75:589-97. [DOI: 10.1021/jo902120s] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis Simón
- Facultad de Ciencias Químicas, Universidad de Salamanca, Plaza de los Caídos 1-5, Salamanca, E37004, Spain
| | - Jonathan M. Goodman
- Unilever Centre For Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
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25
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Huang XY, Wang HJ, Shi J. Theoretical Study on Acidities of (S)-Proline Amide Derivatives in DMSO and Its Implications for Organocatalysis. J Phys Chem A 2009; 114:1068-81. [DOI: 10.1021/jp909043a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiong-Yi Huang
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Hua-Jing Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Jing Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
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26
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Discovery of a novel class of isoxazoline voltage gated sodium channel blockers. Bioorg Med Chem Lett 2009; 19:5329-33. [DOI: 10.1016/j.bmcl.2009.07.125] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 07/27/2009] [Accepted: 07/28/2009] [Indexed: 11/21/2022]
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27
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Albrecht M, Rice CA, Suhm MA. Elementary Peptide Motifs in the Gas Phase: FTIR Aggregation Study of Formamide, Acetamide, N-Methylformamide, and N-Methylacetamide. J Phys Chem A 2008; 112:7530-42. [DOI: 10.1021/jp8039912] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Merwe Albrecht
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Corey A. Rice
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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28
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Mathieu S, Poteau R, Trinquier G. Estimating the "steric clash" at cis peptide bonds. J Phys Chem B 2008; 112:7894-902. [PMID: 18543981 DOI: 10.1021/jp711082d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.
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Affiliation(s)
- Simon Mathieu
- Laboratoire de Chimie et Physique Quantique, IRSAMC, Université Paul-Sabatier, Toulouse Cedex 9, France
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29
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Deveau AM, Costa NE, Joshi EM, Macdonald TL. Synthesis of diketopiperazine-based carboline homodimers and in vitro growth inhibition of human carcinomas. Bioorg Med Chem Lett 2008; 18:3522-5. [DOI: 10.1016/j.bmcl.2008.05.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/03/2008] [Accepted: 05/06/2008] [Indexed: 11/29/2022]
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30
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Gonçalves BT, Esteves PM, Pinto AC, Kaiser CR, da Silva FL, Miguez E, da Silva JFM. Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:418-426. [PMID: 18327891 DOI: 10.1002/mrc.2192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.
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Affiliation(s)
- Biank T Gonçalves
- Departamento de Química Orgânica, Instituto de Química, Bloco A, 6 a Andar do CT, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, RJ, Brazil, 21949900
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31
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Two New Alkaloids fromBrachystemma calycinum and Their Inhibitory Effects on Lymphocyte Proliferation. Chem Biodivers 2007; 4:2948-52. [DOI: 10.1002/cbdv.200790244] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Urban JJ, Tillman BG, Cronin WA. Fluoroolefins as peptide mimetics: a computational study of structure, charge distribution, hydration, and hydrogen bonding. J Phys Chem A 2007; 110:11120-9. [PMID: 16986846 DOI: 10.1021/jp062881n] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design of peptide mimetic compounds is greatly facilitated by the identification of functionalities that can act as peptide replacements. The fluoroalkene moiety has recently been employed for that purpose. The purpose of this work is to characterize prototypical fluoroalkenes (fluoroethylene and 2-fluoro-2-butene) with respect to key properties of peptides (amides) including structure, charge distribution, hydration, and hydrogen bonding. The results are compared to those obtained for model peptides (formamide, N-methylacetamide). Calculations have been carried out at the MP2 and B3LYP levels of theory with the 6-311++G(2d,p) and 6-311++G(2d,2p) basis sets. The results suggest that the fluoroalkene is similar in steric requirements to a peptide bond but that there is less charge separation. Calculations of the hydration free energies with the PCM bulk continuum solvent model indicate that the fluoroalkene has much smaller hydration free energies than an amide but that the difference in solvation free energy for cis and trans isomers is comparable. In studies of complexes with water molecules, the fluoroalkene is found to engage in interactions that are analogous to backbone hydrogen-bonding interactions that govern many properties of natural peptides and proteins but with smaller interaction energies. In addition, key structural differences are noted when the fluoroalkene is playing the role of hydrogen-bond acceptor which may have implications in binding, aggregation, and conformational preferences in fluoroalkene peptidomimetics. The issue of cooperativity in hydrogen-bonding interactions in complexes with multiple waters has also been investigated. The fluoroalkene is found to exhibit cooperative effects that mirror those of the peptide but are smaller in magnitude. Thus, pairwise addivitity of interactions appears to more adequately describe the fluoroalkenes than the peptides they are intended to mimic.
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Affiliation(s)
- Joseph J Urban
- Chemistry Department, United States Naval Academy, 572 Holloway Road, Annapolis, Maryland 21402, USA.
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33
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Dolain C, Léger JM, Delsuc N, Gornitzka H, Huc I. Probing helix propensity of monomers within a helical oligomer. Proc Natl Acad Sci U S A 2005; 102:16146-51. [PMID: 16258066 PMCID: PMC1297517 DOI: 10.1073/pnas.0506262102] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A simple strategy is proposed to assess the propensity of a given monomer to follow or not follow a particular helical scheme and to study helix reversal phenomena within helical oligomers. It consists of placing a monomer having a low helix propensity between two conformationally stable helical segments. Helix reversion then occurs preferentially at the site of this monomer, leading to the formation of isomers having P (right-handed) or M (left-handed) helicities at each of the two helical segments. The proportion between the P-P/M-M and P-M isomers is indicative of the stereochemical relations between the inserted monomer and the helical frame. Thus, xylylene or carboxylic acid anhydride spacers have been introduced between two helical oligoamides of 8-amino-2-quinolinecarboxylic acid. Both these spacers presumably lack some of the structural features that confer quinoline units with a high helix propensity. Only one species is observed in solution in the case of an anhydride spacer. This species was shown by x-ray crystallography to be a racemic mixture of P-P and M-M helices. Unexpectedly, the anhydride is consistently incorporated within helical oligoamides. For the xylylene spacer, the P-P/M-M racemate and P-M meso compound are in equal proportions in chloroform, showing that this spacer does not have a propensity to adopt any helical conformation in this solvent. However, the equilibria between the various isomers are shifted in toluene, where one species largely prevails. This species was shown by x-ray crystallography to be the P-P/M-M racemate. Molecular dynamics simulations are consistent with these solution data.
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Affiliation(s)
- Christel Dolain
- Institut Européen de Chimie et Biologie, 2 Rue Robert Escarpit, F-33607 Pessac, France
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34
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Abstract
Amide bonds -NH-CO- preferentially exist in trans conformations, the cis conformation being thermodynamically unfavored with respect to the trans by about 2 kcal/mol. Yet, the main reason most proteins or peptides cannot be made from cis-peptide plaques only lies in that connecting them into open chains appears to be sterically impracticable. It is possible, however, to build all-cis cyclic peptides in which all cis-plaques are efficiently locked. The present work examines, through quantum calculations, the structural and energetic issues associated with these peculiar arrangements. Systematic exploration at DFT-B3LYP level of the potential-energy surfaces for all-cis cyclopolyglycines cG(n)(c) (n = 2-10,15), and to a lesser extent, for all-cis cyclopolyalanines and all-cis cyclopolyphenylalanines confirms that all these structures are true minima. Optimal ring size occurs around eight peptide units, resulting in planar cG7(c), cG8(c), and cG9(c). In smaller systems, the ring strain is relieved through nonplanar cup-like distortions, particularly in cG6(c). From 10 peptide units and beyond, the ring framework distorts into a saddle-edge shape. These molecules disclose some molecular flexibility, as combinatorial tilting of the plaques may give sets of minima close in energy. Indexes based on isodesmic reactions are used to estimate the energy for joining all-cis or all-trans plaques into cyclic peptides. One of them, the mean plaque-junction energy (MPJE) suggests that within sensible sizes from six peptide units and beyond, all-cis plaque association is almost equally favorable as all-trans one. The frame of radiating cis-amide bonds can be considered as defining a new kind of peptidic material, endowed with specific self-assembling properties.
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Affiliation(s)
- Romuald Poteau
- Laboratoire de Physique Quantique (CNRS, UMR5626), IRSAMC, Université Paul-Sabatier, 31062 Toulouse Cedex, France.
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35
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Luzhkov VB, Nilsson J, Arhem P, Aqvist J. Computational modelling of the open-state Kv1.5 ion channel block by bupivacaine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2003; 1652:35-51. [PMID: 14580995 DOI: 10.1016/j.bbapap.2003.08.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Binding of R(+)-bupivacaine to open-state homology models of the mammalian K(v)1.5 membrane ion channel is studied using automated docking and molecular dynamics (MD) methods. Homology models of K(v)1.5 are built using the 3D structures of the KcsA and MthK channels as a template. The packing of transmembrane (TM) alpha-helices in the KcsA structure corresponds to a closed channel state. Opening of the channel may be reached by a conformational transition yielding a bent structure of the internal S6 helices. Our first model of the K(v) open state involves a PVP-type of bending hinge in the internal helices, while the second model corresponds to a Gly-type of bending hinge as found in the MthK channel. Ligand binding to these models is probed using the common local anaesthetic bupivacaine, where blocker binding from the intracellular side of the channel is considered. Conformational properties and partial atomic charges of bupivacaine are determined from quantum mechanical HF/6-31G* calculations with inclusion of solvent effects. The automated docking and MD calculations for the PVP-bend model predict that bupivacaine could bind either in the central cavity or in the PVP region of the channel pore. Linear interaction energy (LIE) estimates of the binding free energies for bupivacaine predict strongest binding to the PVP region. Surprisingly, no binding is predicted for the Gly-bend model. These results are discussed in light of electrophysiological data which show that the K(v)1.5 channel is unable to close when bupivacaine is bound.
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Affiliation(s)
- Victor B Luzhkov
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden
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36
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Wu FY, Li Z, Wen ZC, Zhou N, Zhao YF, Jiang YB. A novel thiourea-based dual fluorescent anion receptor with a rigid hydrazine spacer. Org Lett 2002; 4:3203-5. [PMID: 12227749 DOI: 10.1021/ol026357k] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] A neutral receptor with a rigid hydrazine spacer, N-p-(dimethylamino)benzamido-N'-phenylthiourea, was prepared, and its dual fluorescence in acetonitrile was found to show response toward the presence of anions such as AcO(-), H(2)PO(4)(-), HSO(4)(-), Br(-), Cl(-), F(-), and ClO(4)(-) with high sensitivity and selectivity toward AcO(-).
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Affiliation(s)
- Fang-Ying Wu
- Department of Chemistry and the MOE Key Laboratory of Analytical Sciences, Xiamen University, China
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37
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Würthwein EU, Hergenröther T, Quast H. exo/endoPreferences of Double Bonds in Three-Membered Ring Compounds − The Bias Toward Endocyclic Unsaturation in 3-Alkyl- and 3-Amino-2H-azirines: A Theoretical and Experimental Study. European J Org Chem 2002. [DOI: 10.1002/1099-0690(200206)2002:11<1750::aid-ejoc1750>3.0.co;2-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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