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Kazim M, Guan L, Chopra A, Sun R, Siegler MA, Lectka T. Switching a HO···π Interaction to a Nonconventional OH···π Hydrogen Bond: A Completed Crystallographic Puzzle. J Org Chem 2020; 85:9801-9807. [PMID: 32633510 DOI: 10.1021/acs.joc.0c01121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this article, we present crystallographic and spectroscopic evidence of a tunable system wherein a HO···π interaction switches incrementally to a nonconventional OH···π hydrogen bonding (HB) interaction. More specifically, we report the synthesis of substituted forms of model system 1 to study the effects of aryl ring electronic density on the qualitative characteristics of OH···π hydrogen bonds therein. The OH stretch in experimental infrared data, in agreement with density-functional theory (DFT) calculations, shows continuous red-shifts as the adjacent ring becomes more electron rich. For example, the OH stretch of an amino-substituted analogue is red-shifted by roughly 50 cm-1 compared to the same stretch in the CF3 analogue, indicating a significantly stronger HB interaction in the former. Moreover, DFT calculations (ωB97XD/6-311+G**) predict that increasing electronic density on the adjacent top ring reduces the aryl π-OH σ* energy gap with a concomitant enhancement of the OH n-π* energy gap. Consequently, a dominant π-σ* interaction in the amino substituted analogue locks the system in the in-form while a favorable n-π* interaction reverses the orientation of the oxygen-bound hydrogen in its protonated form. Additionally, the 1H NMR data of various analogues reveal that stronger OH···π interactions in systems with electron-rich aromatic rings slow exchange of the alcoholic proton, thereby revealing coupling with the geminal proton. Finally, X-ray crystallographic analyses of a spectrum of analogues clearly visualize the three distinct stages of "switch"-starting with exclusive HO···π, to partitioned HO···π/OH···π, and finally to achieving exclusive OH···π forms. Furthermore, the crystal structure of the amino analogue reveals an interesting feature in which an extended HB network, involving two conventional (NH···O) and two nonconventional (OH···π) HBs, dimerizes and anchors the molecule in the unit cell.
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Affiliation(s)
- Muhammad Kazim
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Liangyu Guan
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States.,Calibr-A Division of Scripps Research, 11119 N Torrey Pines Rd, La Jolla, San Diego, California 92037, United States
| | - Anant Chopra
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Roy Sun
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Guan L, Holl MG, Pitts CR, Struble MD, Siegler MA, Lectka T. Through-Space Activation Can Override Substituent Effects in Electrophilic Aromatic Substitution. J Am Chem Soc 2017; 139:14913-14916. [DOI: 10.1021/jacs.7b09792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liangyu Guan
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxwell Gargiulo Holl
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Cody Ross Pitts
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Mark D. Struble
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A. Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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Bayat M, Ebrahimkhani L, Salehzadeh S. Where, how and how much the strength of interaction between a hydrated lanthanide cation and a π-system would be increased? A theoretical study. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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Larrucea J. Solvent effect on cation–π interactions with Al3+. J Mol Model 2012; 18:4349-54. [DOI: 10.1007/s00894-012-1433-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
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Benzophenone-based derivatives: a novel series of potent and selective dual inhibitors of acetylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation. Eur J Med Chem 2011; 46:1682-93. [PMID: 21397996 DOI: 10.1016/j.ejmech.2011.02.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 01/14/2011] [Accepted: 02/12/2011] [Indexed: 11/22/2022]
Abstract
The leading mechanistic theory of Alzheimer's disease (AD) is the "amyloid hypothesis" which states that the accumulation of the amyloid β protein (Aβ), and its subsequent aggregation into plaques, is responsible for the initiation of a cascade of events resulting in neurodegeneration and dementia. The anti-amyloid disease-modifying approach, based on the decrease in the production of Aβ, gained thus a paramount importance. The aim of this study was the design and synthesis of a new series of acetylcholinesterase inhibitors (AChEIs) endowed with anti-Aβ aggregating capability. These dual binding inhibitors, being able to interact both with the peripheral anionic site (PAS) of AChE and the catalytic subsite, proved to be able to inhibit the AChE-induced Aβ aggregation. Thus, starting from the lead compound 1, an AChEI composed by a benzophenone scaffold and a N,N'-methylbenzylamino group, a substantial modification aimed at targeting the PAS was performed. To this aim, different amino-terminal side chains were incorporated into this main framework, in order to mimic the diethylmethylammonium alkyl moiety of the pure PAS ligand propidium. The synthesized compounds proved to effectively and selectively inhibit AChE. Moreover, compounds 16a-c and 18a,b, with a propoxy and a hexyloxy tether respectively, showed a good activity against the AChE-induced Aβ aggregation. In particular, molecular modeling studies confirmed that compounds carrying the diethylaminopropoxy and the diethylaminohexyloxy side chains (compounds 16a and 19a, respectively) could suitably contact the PAS pocket of the enzyme.
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Targeting Alzheimer’s disease: Novel indanone hybrids bearing a pharmacophoric fragment of AP2238. Bioorg Med Chem 2010; 18:1749-60. [DOI: 10.1016/j.bmc.2010.01.071] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 01/22/2010] [Accepted: 01/29/2010] [Indexed: 11/21/2022]
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Costanzo F, Della Valle RG. Car−Parrinello MD Simulations for the Na+−Phenylalanine Complex in Aqueous Solution. J Phys Chem B 2008; 112:12783-9. [DOI: 10.1021/jp801702v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Costanzo
- Dipartimento di Chimica Fisica ed Inorganica, Università di Bologna, viale Risorgimento 4, I-40137 Bologna, Italy
| | - Raffaele Guido Della Valle
- Dipartimento di Chimica Fisica ed Inorganica, Università di Bologna, viale Risorgimento 4, I-40137 Bologna, Italy
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Costanzo F, Sulpizi M, Guido Della Valle R, Sprik M. First Principles Study of Alkali−Tyrosine Complexes: Alkali Solvation and Redox Properties. J Chem Theory Comput 2008; 4:1049-56. [DOI: 10.1021/ct8000415] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Costanzo
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Marialore Sulpizi
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Raffaele Guido Della Valle
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Michiel Sprik
- Dipartimento di Chimica Fisica e Inorganica and INSTM-UdR Bologna, Universita di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy, and, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
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Miura SI, Kiya Y, Kanazawa T, Imaizumi S, Fujino M, Matsuo Y, Karnik SS, Saku K. Differential bonding interactions of inverse agonists of angiotensin II type 1 receptor in stabilizing the inactive state. Mol Endocrinol 2008; 22:139-46. [PMID: 17901125 PMCID: PMC2725753 DOI: 10.1210/me.2007-0312] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 09/20/2007] [Indexed: 01/06/2023] Open
Abstract
Although the sartan family of angiotensin II type 1 (AT(1)) receptor blockers (ARBs), which includes valsartan, olmesartan, and losartan, have a common pharmacophore structure, their effectiveness in therapy differs. Although their efficacy may be related to their binding strength, this notion has changed with a better understanding of the molecular mechanism. Therefore, we hypothesized that each ARB differs with regard to its molecular interactions with AT(1) receptor in inducing inverse agonism. Interactions between valsartan and residues Ser(105), Ser(109), and Lys(199) were important for binding. Valsartan is a strong inverse agonist of constitutive inositol phosphate production by the wild-type and N111G mutant receptors. Substituted cysteine accessibility mapping studies indicated that valsartan, but not losartan, which has only weak inverse agonism, may stabilize the N111G receptor in an inactive state upon binding. In addition, the inverse agonism by valsatan was mostly abolished with S105A/S109A/K199Q substitutions in the N111G background. Molecular modeling suggested that Ser(109) and Lys(199) bind to phenyl and tetrazole groups of valsartan, respectively. Ser(105) is a candidate for binding to the carboxyl group of valsartan. Thus, the most critical interaction for inducing inverse agonism involves transmembrane (TM) V (Lys(199)) of AT(1) receptor although its inverse agonist potency is comparable to olmesartan, which bonds with TM III (Tyr(113)) and TM VI (His(256)). These results provide new insights into improving ARBs and development of new G protein-coupled receptor antagonists.
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Affiliation(s)
- Shin-ichiro Miura
- Department of Cardiology, Fukuoka University School of Medicine, Jonan-Ku, Fukuoka 814-0180, Japan.
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Bhayana B, Wilcox CS. A Minimal Protein Folding Model To Measure Hydrophobic and CH–π Effects on Interactions between Nonpolar Surfaces in Water. Angew Chem Int Ed Engl 2007; 46:6833-6. [PMID: 17676565 DOI: 10.1002/anie.200700932] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brijesh Bhayana
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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12
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Bhayana B, Wilcox C. A Minimal Protein Folding Model To Measure Hydrophobic and CH–π Effects on Interactions between Nonpolar Surfaces in Water. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700932] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Méndez-Andino J, Colson AO, Denton D, Mitchell MC, Cross-Doersen D, Hu XE. MCH-R1 antagonists based on an arginine scaffold: SAR studies on the amino-terminus. Bioorg Med Chem Lett 2007; 17:832-5. [PMID: 17107794 DOI: 10.1016/j.bmcl.2006.10.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 10/13/2006] [Accepted: 10/23/2006] [Indexed: 10/24/2022]
Abstract
We have identified a novel series of potent MCH-R1 antagonists based on l-arginine. As predicted by computational methods, there was an activity dependence on the pi-electronic character of the aromatic systems corresponding to the amino-terminus of these molecules. These results have enhanced our understanding of the MCH-R1 receptor and the potential for a predictive homology model.
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Affiliation(s)
- José Méndez-Andino
- Procter & Gamble Pharmaceuticals, 8700 Mason-Montgomery Road, Mason, OH 45039, USA.
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Matter H, Will DW, Nazaré M, Schreuder H, Laux V, Wehner V. Structural requirements for factor Xa inhibition by 3-oxybenzamides with neutral P1 substituents: combining X-ray crystallography, 3D-QSAR, and tailored scoring functions. J Med Chem 2005; 48:3290-312. [PMID: 15857135 DOI: 10.1021/jm049187l] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and structure-activity relationship of 3-oxybenzamides as potent inhibitors of the coagulation protease factor Xa are described on the basis of X-ray structures, privileged structure motifs, and SAR information. A total of six X-ray structures of fXa/inhibitor complexes led us to identify the major protein-ligand interactions. The binding mode is characterized by a lipophilic dichlorophenyl substituent interacting with Tyr228 in the protease S1 pocket, while polar parts are accommodated in S4. This alignment in combination with docking allowed derivation of 3D-QSAR models and tailored scoring functions to rationalize biological affinity and provide guidelines for optimization. The resulting models showed good correlation coefficients and predictions of external test sets. Furthermore, they correspond to binding site topologies in terms of steric, electrostatic, and hydrophobic complementarity. Two approaches to derive tailored scoring functions combining binding site and ligand information led to predictive models with acceptable predictions of the external set. Good correlations to experimental affinities were obtained for both AFMoC (adaptation of fields for molecular comparison) and the novel TScore function. The SAR information from 3D-QSAR and tailored scoring functions agrees with all experimental data and provides guidelines and reasonable activity estimations for novel fXa inhibitors.
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Affiliation(s)
- Hans Matter
- DI and A Chemistry, Aventis Pharma Deutschland GmbH, A Company of the Sanofi-Aventis Group, Building G 878, D-65926 Frankfurt am Main, Germany.
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Gervasio FL, Schettino V, Mangani S, Krack M, Carloni P, Parrinello M. Influence of Outer-Shell Metal Ligands on the Structural and Electronic Properties of Horse Liver Alcohol Dehydrogenase Zinc Active Site. J Phys Chem B 2003. [DOI: 10.1021/jp027567h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Luigi Gervasio
- Dip. di Chimica, Università di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy, European Laboratory for Non linear Spectroscopy (LENS), via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy, International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Center for Numerical Simulation, via Beirut 4, I-34014 Trieste, Italy, Dip. di Chimica, Università di Siena, via A. Moro, I-53100 Siena, Italy, CSCS-Centro Svizzero di Calcolo Scientifico, Via Cantonale, Galleria 2,CH-6928
| | - Vincenzo Schettino
- Dip. di Chimica, Università di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy, European Laboratory for Non linear Spectroscopy (LENS), via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy, International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Center for Numerical Simulation, via Beirut 4, I-34014 Trieste, Italy, Dip. di Chimica, Università di Siena, via A. Moro, I-53100 Siena, Italy, CSCS-Centro Svizzero di Calcolo Scientifico, Via Cantonale, Galleria 2,CH-6928
| | - Stefano Mangani
- Dip. di Chimica, Università di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy, European Laboratory for Non linear Spectroscopy (LENS), via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy, International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Center for Numerical Simulation, via Beirut 4, I-34014 Trieste, Italy, Dip. di Chimica, Università di Siena, via A. Moro, I-53100 Siena, Italy, CSCS-Centro Svizzero di Calcolo Scientifico, Via Cantonale, Galleria 2,CH-6928
| | - Matthias Krack
- Dip. di Chimica, Università di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy, European Laboratory for Non linear Spectroscopy (LENS), via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy, International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Center for Numerical Simulation, via Beirut 4, I-34014 Trieste, Italy, Dip. di Chimica, Università di Siena, via A. Moro, I-53100 Siena, Italy, CSCS-Centro Svizzero di Calcolo Scientifico, Via Cantonale, Galleria 2,CH-6928
| | - Paolo Carloni
- Dip. di Chimica, Università di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy, European Laboratory for Non linear Spectroscopy (LENS), via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy, International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Center for Numerical Simulation, via Beirut 4, I-34014 Trieste, Italy, Dip. di Chimica, Università di Siena, via A. Moro, I-53100 Siena, Italy, CSCS-Centro Svizzero di Calcolo Scientifico, Via Cantonale, Galleria 2,CH-6928
| | - Michele Parrinello
- Dip. di Chimica, Università di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy, European Laboratory for Non linear Spectroscopy (LENS), via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy, International School for Advanced Studies (SISSA/ISAS) and INFM-DEMOCRITOS Center for Numerical Simulation, via Beirut 4, I-34014 Trieste, Italy, Dip. di Chimica, Università di Siena, via A. Moro, I-53100 Siena, Italy, CSCS-Centro Svizzero di Calcolo Scientifico, Via Cantonale, Galleria 2,CH-6928
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Piazzi L, Rampa A, Bisi A, Gobbi S, Belluti F, Cavalli A, Bartolini M, Andrisano V, Valenti P, Recanatini M. 3-(4-[[Benzyl(methyl)amino]methyl]phenyl)-6,7-dimethoxy-2H-2-chromenone (AP2238) inhibits both acetylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation: a dual function lead for Alzheimer's disease therapy. J Med Chem 2003; 46:2279-82. [PMID: 12773032 DOI: 10.1021/jm0340602] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, the investigation of acetylcholinesterase (AChE) inhibitors has gained further interest, because the involvement of the peripheral site of the enzyme in the beta-amyloid (Abeta) aggregation process has been disclosed. We present here, for the first time, a direct evidence of the Abeta antiaggregating action of an AChE inhibitor (AP2238) purposely designed to bind at both the catalytic and the peripheral sites of the human enzyme.
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Affiliation(s)
- Lorna Piazzi
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, Italy
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Spiegel K, Carloni P. Electrostatic Role of Phosphate 2485 in the Large Ribosomal Unit from H. marismortui. J Phys Chem B 2003. [DOI: 10.1021/jp026572i] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katrin Spiegel
- International School for Advanced Studies and INFM-DEMOCRITOS National Simulation Center, via Beirut 2-4, 34100 Trieste, Italy
| | - Paolo Carloni
- International School for Advanced Studies and INFM-DEMOCRITOS National Simulation Center, via Beirut 2-4, 34100 Trieste, Italy
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Kim JW, Seo MY, Shelat A, Kim CS, Kwon TW, Lu HH, Moustakas DT, Sun J, Han JH. Structurally conserved amino Acid w501 is required for RNA helicase activity but is not essential for DNA helicase activity of hepatitis C virus NS3 protein. J Virol 2003; 77:571-82. [PMID: 12477861 PMCID: PMC140573 DOI: 10.1128/jvi.77.1.571-582.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hepatitis C virus (HCV) is a positive-strand RNA virus that encodes a helicase required for viral replication. Although HCV does not replicate through a DNA intermediate, HCV helicase unwinds both RNA and DNA duplexes. An X-ray crystal structure of the HCV helicase complexed with (dU)(8) has been solved, and the substrate-amino acids interactions within the catalytic pocket were shown. Among these, residues W501 and V432 were reported to have base stacking interactions and to be important for the unwinding function of HCV helicase. It has been hypothesized that specific interactions between the enzyme and substrate in the catalytic pocket are responsible for the substrate specificity phenotype. We therefore mutagenized W501 and V432 to investigate their role in substrate specificity in HCV helicase. Replacement of W501, but not V432, with nonaromatic residues resulted in complete loss of RNA unwinding activity, whereas DNA unwinding activity was largely unaffected. The loss of unwinding activity was fully restored in the W501F mutant, indicating that the aromatic ring is crucial for RNA helicase function. Analysis of ATPase and nucleic acid binding activities in the W501 mutant enzymes revealed that these activities are not directly responsible for the substrate specificity phenotype. Molecular modeling of the enzyme-substrate interaction at W501 revealed a putative pi-facial hydrogen bond between the 2'-OH of ribose and the aromatic tryptophan ring. This evidence correlates with biochemical results suggesting that the pi-facial bond may play an important role in the RNA unwinding activity of the HCV NS3 protein.
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Affiliation(s)
- Jong Won Kim
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Mi Young Seo
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Anang Shelat
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Chon Saeng Kim
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Tae Woo Kwon
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Hui-hua Lu
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Demetri Theodore Moustakas
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Jeonghoon Sun
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
| | - Jang H. Han
- Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea, Chiron Corporation, Emeryville, California 94608, Department of Pharmaceutical Chemistry, Chemistry and Chemical Biology Program, University of California, San Francisco, California 94143
- Corresponding author. Present address: Chiron Corp., 4560 Horton St., Emeryville, CA 94608. Phone: (510) 923-2937. Fax: (510) 923-2586. E-mail:
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Matter H, Defossa E, Heinelt U, Blohm PM, Schneider D, Müller A, Herok S, Schreuder H, Liesum A, Brachvogel V, Lönze P, Walser A, Al-Obeidi F, Wildgoose P. Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa. J Med Chem 2002; 45:2749-69. [PMID: 12061878 DOI: 10.1021/jm0111346] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 138 nonchiral 3-amidinobenzyl-1H-indole-2-carboxamides and analogues as inhibitors of the blood coagulation enzyme factor Xa (fXa) were designed, synthesized, and investigated by X-ray structure analysis and 3D quantitative structure-activity relationship (QSAR) studies (CoMFA, CoMSIA) in order to identify important protein-ligand interactions responsible for biological affinity and selectivity. Several compounds from this series are highly potent and selective inhibitors of this important enzyme linking extrinsic and intrinsic coagulation pathways. To rationalize biological affinity and to provide guidelines for further design, all compounds were docked into the factor Xa binding site. Those docking studies were based on X-ray structures of factor Xa in complex with literature-known inhibitors. It was possible to validate those binding modes by four X-ray crystal structures of representative ligands in factor Xa, while one ligand was additionally crystallized in trypsin to rationalize requirements for selective factor Xa inhibition. The 3D-QSAR models based on a superposition rule derived from these docking studies were validated using conventional and cross-validated r(2) values using the leave-one-out method and repeated analyses using two randomly chosen cross-validation groups plus randomization of biological activities. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which were found to correspond to experimentally determined factor Xa binding site topology in terms of steric, electrostatic, and hydrophobic complementarity. Subsets selected as smaller training sets using 2D fingerprints and maximum dissimilarity methods resulted in 3D-QSAR models with remarkable correlation coefficients and a high predictive power. The final quantitative SAR information agrees with all experimental data for the binding topology and thus provides reasonable activity predictions for novel factor Xa inhibitors.
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Affiliation(s)
- Hans Matter
- Aventis Pharma Deutschland GmbH, DI&A, Molecular Modeling, Building G 878, D-65926 Frankfurt am Main, Germany.
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Cavalli A, Carloni P. Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study. J Am Chem Soc 2002; 124:3763-8. [PMID: 11929266 DOI: 10.1021/ja015821y] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio methods were used to shed light on fundamental aspects of the enzymatic mechanism of guanosine triphosphate hydrolysis in the Cdc42/Cdc42GAP complex. The calculations focused on the nucleophilic addition of the catalytic water molecule to the gamma-phosphate phosphorus atom. A large model system was required to correctly reproduce the electrostatic properties on the active site. The model turned out to reproduce most of the electrostatic field of the biological complex at the reactants. Our calculations established the H-bond pattern of the catalytic water (WAT), which turned out to interact with Q61 and T35, in the most stable conformation. This ruled out the possibility that the catalytic water transferred its proton directly to the gamma-phosphate. Furthermore, the calculations suggested that the electronic structure of WAT was very different from that in the bulk. Finally, this study showed that during the reaction, WAT transferred a proton to Gln61, consistent with the available X-ray data on a transition-state analogue/enzyme complex(19) and with the decrease of activity in the Q61E mutant.
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Affiliation(s)
- Andrea Cavalli
- Scuola Internazionale Superiore di Studi Avanzati, Istituto Nazionale di Fisica della Materia, Via Beirut 2-4, I-34014 Trieste, Italy
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21
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Dvornikovs V, Smithrud DB. Investigation of synthetic hosts that model cation-pi sites found at protein binding domains. J Org Chem 2002; 67:2160-7. [PMID: 11925223 DOI: 10.1021/jo011124c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small cyclophanes containing aromatic groups and dialkyl ammonium ions were created as model systems of the cation-pi complexes found at some protein binding domains. The hosts had different shapes in order to investigate the effect the arrangement of ammonium ions to aromatic surfaces has on their reactivity. pK(a) values of the hosts were substantially different in DMSO or (95/5) DMSO/D(2)O solutions, which showed that the ions existed in different environments of the hosts. Electrostatic charges, as determined by density functional calculations, revealed that the magnitude of a cationic charge depends on its position relative to an aromatic ring. Association constants of the hosts bound to the sodium salt of N-acetyl phenylalanine in d(6)-DMSO and in (95/5) d(6)-DMSO/D(2)O solutions were inversely proportional to the magnitude of the hosts' acidity constants. These results suggest that the magnitude of the positive charge for cationic groups of cation-pi complexes is reduced by being associated with electron-rich faces of aromatic rings. The aromatic rings, however, lessen the desolvation penalty that must be overcome for ligand binding, giving an overall more favorable association.
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Affiliation(s)
- Vadims Dvornikovs
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
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22
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Guidoni L, Carloni P. Tetraethylammonium binding to the outer mouth of the KcsA potassium channel: implications for ion permeation. J Recept Signal Transduct Res 2002; 22:315-31. [PMID: 12503624 DOI: 10.1081/rrs-120014604] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Extracellular tetraethylammonium (TEA+) inhibits the current carried out by K+ ions in potassium channels. Structural models of wild-type (WT) and Y82C KcsA K+ channel/TEA+ complexes are here built using docking procedures, electrostatics calculations and molecular dynamics simulations. The calculations are based on the structure determined by Doyle et al. (11) Our calculations suggest that in WT, the TEA+ cation turns binds at the outer mouth of the selectivity filter, stabilized by electrostatic and hydrophobic interactions with the four Tyr82 side chains. Replacement of Tyr82 with Cys causes a decrease of the affinity of the cation for the channel, consistently with the available site-directed mutagenesis data (16). An MD simulation in which K+ replaces TEA+ provides evidence that TEA+ binding site can accommodate a potassium ion, in agreement with the high-resolution structure recently reported by Zhou et al. (20)
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Affiliation(s)
- Leonardo Guidoni
- INFM-Democritos Center for Molecular Simulations and International School for Advanced Studies (SISSA), Via Beirut 4, 1-34014 Trieste, Italy
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Minehardt TJ, Marzari N, Cooke R, Pate E, Kollman PA, Car R. A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. Biophys J 2002; 82:660-75. [PMID: 11806909 PMCID: PMC1301876 DOI: 10.1016/s0006-3495(02)75429-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We used classical molecular mechanics (MM) simulations and quantum mechanical (QM) structural relaxations to examine the active site of myosin when bound to ATP. Two conformations of myosin have been determined by x-ray crystallography. In one, there is no direct interaction between switch 2 and the nucleotide (open state). In the other (closed state), the universally conserved switch 2 glycine forms a hydrogen bond with a gamma-phosphate oxygen. MM simulations indicate that the two states are thermodynamically stable and allow us to investigate the extent to which the P-loop, switch 1, and switch 2 are involved in hydrolysis. We find that the open structure has a higher affinity for ATP than the closed structure, and that ATP is distorted toward a transition state by interactions with the protein. We also examine how the structure of the binding site changes with either MgATP or CaATP as the nucleotide in myosin in the open conformer. Our analyses suggest that higher CaATPase rates occur because the leaving phosphate (P(i)) group is more weakly bound and dissociation occurs faster. Finally, we validate the use of a particular formulation of a QM methodology (Car-Parrinello) to further refine the structures of the active site.
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Affiliation(s)
- Todd J Minehardt
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.
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Tarakeshwar P, Kim KS, Djafari S, Buchhold K, Reimann B, Barth HD, Brutschy B. Ab initio studies of π-water tetramer complexes: Evolution of optimal structures, binding energies, and vibrational spectra of π-(H2O)n (n=1–4) complexes. J Chem Phys 2001. [DOI: 10.1063/1.1343903] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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