1
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Chan L, Hutchison GR, Morris GM. Understanding Ring Puckering in Small Molecules and Cyclic Peptides. J Chem Inf Model 2021; 61:743-755. [PMID: 33544592 PMCID: PMC8023587 DOI: 10.1021/acs.jcim.0c01144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/11/2022]
Abstract
The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, 5- and 6-membered carbohydrate rings, and specific macrocycle families. We lack a general understanding of the puckering preferences of medium-sized rings and macrocycles. To address this, we provide an extensive conformational analysis of a diverse set of rings. We used Cremer-Pople puckering coordinates to study the trends of the ring conformation across a set of 140 000 diverse small molecules, including small rings, macrocycles, and cyclic peptides. By standardizing using key atoms, we show that the ring conformations can be classified into relatively few conformational clusters, based on their canonical forms. The number of such canonical clusters increases slowly with ring size. Ring puckering motions, especially pseudo-rotations, are generally restricted and differ between clusters. More importantly, we propose models to map puckering preferences to torsion space, which allows us to understand the inter-related changes in torsion angles during pseudo-rotation and other puckering motions. Beyond ring puckers, our models also explain the change in substituent orientation upon puckering. We also present a novel knowledge-based sampling method using the puckering preferences and coupled substituent motion to generate ring conformations efficiently. In summary, this work provides an improved understanding of general ring puckering preferences, which will in turn accelerate the identification of low-energy ring conformations for applications from polymeric materials to drug binding.
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Affiliation(s)
- Lucian Chan
- Department
of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, U.K.
| | - Geoffrey R. Hutchison
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemical and Petroleum Engineering, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Garrett M. Morris
- Department
of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, U.K.
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2
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Elbatrawi YM, Pedretty KP, Giddings N, Woodcock HL, Del Valle JR. δ-Azaproline and Its Oxidized Variants. J Org Chem 2020; 85:4207-4219. [DOI: 10.1021/acs.joc.9b03384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yassin M. Elbatrawi
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle P. Pedretty
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Giddings
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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3
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Puszko AK, Sosnowski P, Tymecka D, Raynaud F, Hermine O, Lepelletier Y, Misicka A. Neuropilin-1 peptide-like ligands with proline mimetics, tested using the improved chemiluminescence affinity detection method. MEDCHEMCOMM 2019; 10:332-340. [PMID: 30881620 DOI: 10.1039/c8md00537k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022]
Abstract
Many reports have suggested that NRP-1 acts as a co-receptor for VEGF-A165 and boosts tumour growth and metastasis. This NRP-1, due to its important role in tumour progression, triggered interest in the design of new molecules able to significantly inhibit NRP-1/VEGF-A165 interaction to suppress pathological angiogenesis. Our previous SAR studies of compounds, showing affinity for NRP-1, led us to develop branched peptides with general formula Lys(hArg)-AA2-AA3-Arg. Here, three series of analogues were synthesized, in which the middle fragment (AA2 and/or AA3) of initial sequences was substituted with unnatural Pro analogues with different rigidities and ring sizes. The synthesized compounds were screened for VEGF-A165 inhibitory activity on an improved assay (ELISA), which was selected based on our comparative inhibition study of the parent compounds, indicating that the method with chemiluminescence detection gives more accurate data. The results of affinity for NRP-1 and enzymatic stability of newly obtained compounds enabled the selection of new structures, showing a 2 and 4-fold lower IC50 value compared to parent peptides.
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Affiliation(s)
- Anna K Puszko
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland . ;
| | - Piotr Sosnowski
- Department of Neuropeptides , Mossakowski Medical Research Centre , Polish Academy of Sciences , Pawinskiego 5 , 02-106 Warsaw , Poland
| | - Dagmara Tymecka
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland . ;
| | - Françoise Raynaud
- Imagine Institute , Paris Descartes University-Sorbonne Paris Cité , 24 boulevard Montparnasse , 75015 Paris , France.,Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications , INSERM UMR 1163 , 24 boulevard Montparnasse , 75015 Paris , France.,CNRS ERL 8254 , 24 boulevard Montparnasse , 75015 Paris , France
| | - Olivier Hermine
- Imagine Institute , Paris Descartes University-Sorbonne Paris Cité , 24 boulevard Montparnasse , 75015 Paris , France.,Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications , INSERM UMR 1163 , 24 boulevard Montparnasse , 75015 Paris , France.,CNRS ERL 8254 , 24 boulevard Montparnasse , 75015 Paris , France
| | - Yves Lepelletier
- Imagine Institute , Paris Descartes University-Sorbonne Paris Cité , 24 boulevard Montparnasse , 75015 Paris , France.,Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications , INSERM UMR 1163 , 24 boulevard Montparnasse , 75015 Paris , France.,CNRS ERL 8254 , 24 boulevard Montparnasse , 75015 Paris , France
| | - Aleksandra Misicka
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland . ; .,Department of Neuropeptides , Mossakowski Medical Research Centre , Polish Academy of Sciences , Pawinskiego 5 , 02-106 Warsaw , Poland
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4
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Park HS, Kang YK. Which DFT levels of theory are appropriate in predicting the prolyl cis–trans isomerization in solution? NEW J CHEM 2019. [DOI: 10.1039/c9nj02946j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DFTs were assessed for the conformational preferences of the peptides containing Pro and its derivatives in chloroform and water.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry
- Chungbuk National University
- Cheongju
- Republic of Korea
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5
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LeNouen D, Defoin A, Behr JB. Determination of the Relative Configuration and Conformational Analysis of Five-memberedN-Acyl-Iminosugars by Relevant3JCoupling Constants. ChemistrySelect 2016. [DOI: 10.1002/slct.201600287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Didier LeNouen
- Université de Haute-Alsace; Institut J. B. Donnet; 3 bis rue Alfred Werner F-68093 Mulhouse Cedex France
| | - Albert Defoin
- Université de Haute-Alsace; Institut J. B. Donnet; 3 bis rue Alfred Werner F-68093 Mulhouse Cedex France
| | - Jean-Bernard Behr
- Université de Reims-Champagne-Ardenne; ICMR-UMR 7312, BP 1039 F-51687 Reims Cedex 2 France
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6
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Kubyshkin V, Budisa N. cis-trans-Amide isomerism of the 3,4-dehydroproline residue, the 'unpuckered' proline. Beilstein J Org Chem 2016; 12:589-93. [PMID: 27340450 PMCID: PMC4901939 DOI: 10.3762/bjoc.12.57] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/08/2016] [Indexed: 11/23/2022] Open
Abstract
Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis–trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str., 10, 10623, Berlin, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str., 10, 10623, Berlin, Germany
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7
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Doerfel LK, Wohlgemuth I, Kubyshkin V, Starosta AL, Wilson DN, Budisa N, Rodnina MV. Entropic Contribution of Elongation Factor P to Proline Positioning at the Catalytic Center of the Ribosome. J Am Chem Soc 2015; 137:12997-3006. [DOI: 10.1021/jacs.5b07427] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lili K. Doerfel
- Department
of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Ingo Wohlgemuth
- Department
of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Vladimir Kubyshkin
- Institut
für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Agata L. Starosta
- Gene
Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany
| | - Daniel N. Wilson
- Gene
Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany
- Center
for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Nediljko Budisa
- Institut
für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Marina V. Rodnina
- Department
of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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8
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Soto-Delgado J, Torras J, del Valle LJ, Estrany F, Alemán C. Examining the compatibility of collagen and a polythiophene derivative for the preparation of bioactive platforms. RSC Adv 2015. [DOI: 10.1039/c4ra13812k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Poly(3,4-ethylenedioxythiophene) and collagen interact specifically forming biocomposites that mimic the growing of biological tissues.
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Affiliation(s)
- Jorge Soto-Delgado
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andrés Bello
- Viña del Mar
- Chile
| | - Juan Torras
- Departament d'Enginyeria Química
- Escola d'Enginyeria d'Igualada
- Universitat Politècnica de Catalunya
- Igualada 08700
- Spain
| | - Luis J. del Valle
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- Barcelona E-08028
- Spain
| | - Francesc Estrany
- Departament d'Enginyeria Química
- Escola Universitària d'Enginyeria Tècnica Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08036 Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- Barcelona E-08028
- Spain
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9
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Torras J, Warren JG, Revilla-López G, Jiménez AI, Cativiela C, Alemán C. Solvent-induced conformational flexibility of a bicyclic proline analogue: Octahydroindole-2-carboxylic acid. Biopolymers 2014; 102:176-90. [PMID: 24458264 DOI: 10.1002/bip.22465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/07/2014] [Accepted: 01/16/2014] [Indexed: 11/08/2022]
Abstract
The conformational preferences of the N-acetyl-N'-methylamide derivatives of the four octahydroindole-2-carboxylic acid (Oic) stereoisomers have been investigated in the gas-phase and in aqueous solution using quantum mechanical calculations. In addition to the conformational effects provoked by the stereochemical diversity of Oic, which presents three chiral centers, results provide evidence of interesting and rather unusual features. The conformational preferences of the Oic stereoisomers in solution are only well described by applying a complete and systematic search process, results achieved by simple re-optimization of the gas-phase minima being very imprecise. This is because the conformational rigidity detected in the gas-phase, which is imposed by the chemical restrictions of the fused bicyclic skeleton, disappears in aqueous solution, the four stereoisomers behaving as flexible molecules in this environment. Thus, in general, the γ-turn is the only minimum energy conformation in the gas-phase while in aqueous solution the helical, polyproline-II and γ-turn motifs are energetically favored. Molecular dynamics simulations indicate that the conformational flexibility predicted by quantum mechanical calculations for the four Oic stereoisomers in solution is satisfactorily reproduced by classical force-fields.
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Affiliation(s)
- Juan Torras
- Departament d'Enginyeria Química, EEI, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada, 08700, Spain
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10
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Held C, Hübner H, Kling R, Nagel YA, Wennemers H, Gmeiner P. Impact of the Proline Residue on Ligand Binding of Neurotensin Receptor 2 (NTS2)-Selective Peptide-Peptoid Hybrids. ChemMedChem 2013; 8:772-8. [DOI: 10.1002/cmdc.201300054] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Indexed: 01/07/2023]
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11
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Revilla-López G, Warren JG, Torras J, Jiménez AI, Cativiela C, Alemán C. Effects of ring contraction on the conformational preferences of α-substituted proline analogs. Biopolymers 2011; 98:98-110. [DOI: 10.1002/bip.21716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 08/22/2011] [Accepted: 08/29/2011] [Indexed: 11/09/2022]
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12
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Parasuk W, Parasuk V. Proline- and thioproline-derived enamines: The theoretical study of torsional and ring-puckering conformations. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.12.011] [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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13
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Warren JG, Revilla-López G, Alemán C, Jiménez AI, Cativiela C, Torras J. Conformational preferences of proline analogues with a fused benzene ring. J Phys Chem B 2011; 114:11761-70. [PMID: 20722365 DOI: 10.1021/jp105456r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of indoline-2-carboxylic acid (Inc) and its α-methylated derivative (αMeInc) have been investigated using quantum mechanical calculations. Specifically, the behavior of their N-acetyl-N'-methylamide derivatives, Ac-L-Inc-NHMe and Ac-L-αMeInc-NHMe, has been explored at the B3LYP/6-31+G(d,p) level. Such amino acids are analogues of proline and (α-methyl)proline, respectively, bearing a benzene ring fused to the C(γ)-C(δ) bond of the five-membered pyrrolidine ring. The additional aromatic group has been shown to significantly restrict the conformational space available to these residues by reducing the flexibility of both the five-membered cycle and the peptide backbone. The fused benzene ring also plays a critical role in determining the cis-trans arrangement of the amide bond involving the pyrrolidine nitrogen, which is also modulated by the presence of the α-methyl group in the αMeInc derivative. Furthermore, the influence of the environment on the conformational propensities of these compounds has been evaluated by using both a self-consistent reaction field model and a recently developed interface in a hybrid QM/MM scheme, in which the solvent molecules are treated explicitly with classical mechanics while the solute is described by quantum mechanics at the density functional theory level.
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Affiliation(s)
- Javier G Warren
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
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14
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Kang YK, Park HS. Conformational preferences and cis-trans isomerization of L-3,4-dehydroproline residue. Biopolymers 2009; 92:387-98. [PMID: 19373924 DOI: 10.1002/bip.21203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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15
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Torino D, Mollica A, Pinnen F, Lucente G, Feliciani F, Davis P, Lai J, Ma SW, Porreca F, Hruby VJ. Synthesis and evaluation of new endomorphin analogues modified at the Pro(2) residue. Bioorg Med Chem Lett 2009; 19:4115-8. [PMID: 19560919 PMCID: PMC2737817 DOI: 10.1016/j.bmcl.2009.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 05/27/2009] [Accepted: 06/01/2009] [Indexed: 10/20/2022]
Abstract
Six new endomorphin analogues, incorporating constrained amino acids in place of native proline have been synthesized. Residues of (S)-azetidine-2-carboxylic acid (Aze), 3,4-dehydro-(S)-proline (Delta(3)Pro), azetidine-3-carboxylic acid (3Aze) and dehydro-alanine (DeltaAla) have been used to prepare [Delta(3)Pro(2)]EM-2 (1), [Aze(2)]EM-1 (2), [Aze(2)]EM-2 (3), [3Aze(2)]EM-1 (4), [3Aze(2)]EM-2 (5) and [DeltaAla(2)]EM-2 (6). Binding assays and functional bioactivities for mu- and delta-receptors are reported. The highest affinity, bioactivity and selectivity are shown by peptides 2 and 3 containing the Aze residue.
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Affiliation(s)
- Domenica Torino
- Dipartimento di Chimica e Tecnologie del Farmaco e Istituto di Chimica Biomolecolare, CNR Sezione di Roma, “Sapienza”, Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - Adriano Mollica
- Dipartimento di Scienze del Farmaco, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Francesco Pinnen
- Dipartimento di Scienze del Farmaco, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Gino Lucente
- Dipartimento di Chimica e Tecnologie del Farmaco e Istituto di Chimica Biomolecolare, CNR Sezione di Roma, “Sapienza”, Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - Federica Feliciani
- Dipartimento di Scienze del Farmaco, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Peg Davis
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA 85721
| | - Josephine Lai
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA 85721
| | - Shou-Wu Ma
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA 85721
| | - Frank Porreca
- Department of Pharmacology, University of Arizona, Tucson, AZ, USA 85721
| | - Victor J. Hruby
- Department of Chemistry, University of Arizona, Tucson, AZ, USA 85721
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16
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Michaux C, Wouters J, Perpète EA, Jacquemin D. Ab initio investigation of the hydration of deprotonated amino acids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:632-638. [PMID: 19185508 DOI: 10.1016/j.jasms.2008.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 11/27/2008] [Accepted: 11/27/2008] [Indexed: 05/27/2023]
Abstract
The complexation of five deprotonated anionic amino acids (glycine, L-alanine, L-valine, L-Aspartic acid, and L-glutamine) with one water molecule, has been investigated using a MP2/63-11++G(d,p) approach fully accounting for the basis set superposition errors. For each amino acid, several energetic minima have been identified, and we provide spectroscopic information allowing to discriminate them. Our results strongly suggest that two complexes should coexist under the experimental conditions for [Ala - H](-), [Val - H](-), and [Asp - H](-). Comparisons with the experimental enthalpies, entropies, and Gibbs free energies recently obtained by Wincel [J. Am. Soc. Mass Spectrom. 2008, 19, 1091-1097] show that our simulation reproduces the most significant structure/energy experimental trends, though the entropic changes induced by hydration are slightly overestimated.
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Affiliation(s)
- Catherine Michaux
- Laboratoire de Chimie Biologique Structurale, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
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17
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Flores-Ortega A, Casanovas J, Assfeld X, Alemán C. Protonation of the Side Group in β- and γ-Aminated Proline Analogues: Effects on the Conformational Preferences. J Org Chem 2009; 74:3101-8. [DOI: 10.1021/jo900169s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Jordi Casanovas
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Xavier Assfeld
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal no. 647, 08028 Barcelona, Spain, Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II no. 69, 25001 Lleida, Spain, Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France, and Center for Research in Nano
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Flores-Ortega A, Casanovas J, Nussinov R, Alemán C. Conformational preferences of beta- and gamma-aminated proline analogues. J Phys Chem B 2008; 112:14045-55. [PMID: 18842022 PMCID: PMC2836598 DOI: 10.1021/jp807638p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cbeta- or Cgamma-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N'-methylamide derivatives of four isomers of aminoproline, which differ not only in the beta- or gamma-position of the substituent but also in its cis or trans relative disposition, has been performed. To further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of (dimethylamino)proline. In addition, the effects of solvation on aminoproline and (dimethylamino)proline dipeptides have been evaluated using a self-consistent reaction field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone...side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cgamma-position with a cis relative disposition is the most stable in the gas phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated (dimethylamino)proline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
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Michaux C, Wouters J, Perpète EA, Jacquemin D. Modeling the Microhydration of Protonated Alanine. J Phys Chem B 2008; 112:9896-902. [DOI: 10.1021/jp803476k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Michaux C, Wouters J, Perpète EA, Jacquemin D. Stepwise Hydration of Protonated Proline. J Phys Chem B 2008; 112:7702-5. [DOI: 10.1021/jp8023155] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Flores-Ortega A, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Casanovas J. Conformational preferences of alpha-substituted proline analogues. J Org Chem 2008; 73:3418-27. [PMID: 18351745 PMCID: PMC2679371 DOI: 10.1021/jo702710x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the alpha hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N'-methylamide derivatives of L-proline, L-alpha-methylproline, and L-alpha-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated by using a Self-Consistent Reaction Field model. As expected, tetrasubstitution at the alpha carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at C (alpha) may play a significant role in modulating the conformational preferences of proline.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
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22
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Kang YK, Park HS. Conformational Preferences of Pseudoproline Residues. J Phys Chem B 2007; 111:12551-62. [DOI: 10.1021/jp074128f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
| | - Hae Sook Park
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
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