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Ibrahim MAA, Shehata MNI, Soliman MES, Moustafa MF, El-Mageed HRA, Moussa NAM. Unusual chalcogen⋯chalcogen interactions in like⋯like and unlike YCY⋯YCY complexes (Y = O, S, and Se). Phys Chem Chem Phys 2022; 24:3386-3399. [PMID: 35072679 DOI: 10.1039/d1cp02706a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chalcogen⋯chalcogen interactions were investigated within four types of like⋯like and unlike YCY⋯YCY complexes (where Y = O, S, or Se). A plethora of quantum mechanical calculations, including molecular electrostatic potential (MEP), surface electrostatic potential extrema, point-of-charge (PoC), quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI), and symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) calculations, were executed. The energetic findings revealed a preferential tendency of the studied chalcogen-bearing molecules to engage in type I, II, III, or IV chalcogen⋯chalcogen interactions. Notably, the selenium-bearing molecules exhibited the most potent ability to favorably participate in all the explored chalcogen⋯chalcogen interactions. Among like⋯like complexes, type IV interactions showed the most favorable negative binding energies, whereas type III interactions exhibited the weakest binding energies. Unexpectedly, oxygen-containing complexes within type IV interactions showed an alien pattern of binding energies that decreased along with an increase in the chalcogen atomic size level. QTAIM analysis provided a solo BCP, via chalcogen⋯chalcogen interactions, with no clues as to any secondary ones. SAPT-EDA outlined the domination of the explored interactions by the dispersion forces and indicated the pivotal shares of the electrostatic forces, except type III σ-hole⋯σ-hole and di-σ-hole interactions. These observations demonstrate in better detail all the types of chalcogen⋯chalcogen interactions, providing persuasive reasons for their more intensive use in versatile fields related to materials science and drug design.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt.
| | - Mohammed N I Shehata
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt.
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - H R Abd El-Mageed
- Micro-Analysis, Environmental Research and Community Affairs Center (MAESC), Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt.
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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Reid RC, Yau MK, Singh R, Lim J, Fairlie DP. Stereoelectronic effects dictate molecular conformation and biological function of heterocyclic amides. J Am Chem Soc 2014; 136:11914-7. [PMID: 25102224 DOI: 10.1021/ja506518t] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heterocycles adjacent to amides can have important influences on molecular conformation due to stereoelectronic effects exerted by the heteroatom. This was shown for imidazole- and thiazole-amides by comparing low energy conformations (ab initio MP2 and DFT calculations), charge distribution, dipole moments, and known crystal structures which support a general principle. Switching a heteroatom from nitrogen to sulfur altered the amide conformation, producing different three-dimensional electrostatic surfaces. Differences were attributed to different dipole and orbital alignments and spectacularly translated into opposing agonist vs antagonist functions in modulating a G-protein coupled receptor for inflammatory protein complement C3a on human macrophages. Influences of the heteroatom were confirmed by locking the amide conformation using fused bicyclic rings. These findings show that stereoelectronic effects of heterocycles modulate molecular conformation and can impart strikingly different biological properties.
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Affiliation(s)
- Robert C Reid
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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González FV, Jain A, Rodríguez S, Sáez JA, Vicent C, Peris G. Stereoisomerization of β-Hydroxy-α-sulfenyl-γ-butyrolactones Controlled by Two Concomitant 1,4-Type Nonbonded Sulfur−Oxygen Interactions As Analyzed by X-ray Crystallography. J Org Chem 2010; 75:5888-94. [DOI: 10.1021/jo1009454] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Florenci V. González
- Departament de Química Inorgànica i Orgànica and Serveis Centrals d’Instrumentació Científica, Universitat Jaume I, 12080 Castelló, Spain
| | - Amit Jain
- Departament de Química Inorgànica i Orgànica and Serveis Centrals d’Instrumentació Científica, Universitat Jaume I, 12080 Castelló, Spain
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica and Serveis Centrals d’Instrumentació Científica, Universitat Jaume I, 12080 Castelló, Spain
| | - José A. Sáez
- Departament de Química Inorgànica i Orgànica and Serveis Centrals d’Instrumentació Científica, Universitat Jaume I, 12080 Castelló, Spain
| | - Cristian Vicent
- Departament de Química Inorgànica i Orgànica and Serveis Centrals d’Instrumentació Científica, Universitat Jaume I, 12080 Castelló, Spain
| | - Gabriel Peris
- Departament de Química Inorgànica i Orgànica and Serveis Centrals d’Instrumentació Científica, Universitat Jaume I, 12080 Castelló, Spain
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Affiliation(s)
- Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South Street, Waltham, Massachusetts 02454, USA.
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Sączewski J, Frontera A, Gdaniec M, Brzozowski Z, Sączewski F, Tabin P, Quiñonero D, Deyà PM. Synthesis, X-ray structure analysis and computational studies of novel bis(thiocarbamoyl) disulfides with non-covalent S⋯N and S⋯S interactions. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.02.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Adelfinskaya O, Wu W, Davisson VJ, Davisson VJ, Bergstrom DE. Synthesis and structural analysis of oxadiazole carboxamide deoxyribonucleoside analogs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 24:1919-45. [PMID: 16438058 DOI: 10.1080/15257770500269267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Two novel C-linked oxadiazole carboxamide nucleosides 5-(2'-deoxy-3',5'-beta-D-erythro-pentofuranosyl)-1,2,4-oxadiazole-5-carboxamide (1) and 5-(2'-deoxy-3',5'-beta-D-erythro-pentofuranosyl)-1,2,4-oxadiazole-3-carboxamide (2) were successfully synthesized and characterized by X-ray crystallography. The crystallographic analysis shows that both unnatural nucleoside analogs 1 and 2 adapt the C2'-endo ("south") conformation. The orientation of the oxadiazole carboxamide nucleobase moiety was determined as anti (conformer A) and high anti (conformer B) in the case of the nucleoside analog 1 whereas the syn conformation is adapted by the unnatural nucleoside 2. Furthermore, nucleoside analogs 1 and 2 were converted with high efficiency to corresponding nucleoside triphosphates through the combination chemo-enzymatic approach. Oxadiazole carboxamide deoxyribonucleoside analogs represent valuable tools to study DNA polymerase recognition, fidelity of nucleotide incorporation, and extension.
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Merino P, Tejero T, Unzurrunzaga FJ, Franco S, Chiacchio U, Saita MG, Iannazzo D, Piperno A, Romeo G. An efficient approach to enantiomeric isoxazolidinyl analogues of tiazofurin based on nitrone cycloadditions. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2005.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mugesh G, du Mont WW, Sies H. Chemistry of biologically important synthetic organoselenium compounds. Chem Rev 2001; 101:2125-79. [PMID: 11710243 DOI: 10.1021/cr000426w] [Citation(s) in RCA: 1230] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- G Mugesh
- Institut für Anorganische und Analytische Chemie, Technischen Universität, Postfach 3329, D-38023 Braunschweig, Germany
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Jiménez-Barbero J, Espinosa JF, Asensio JL, Cañada FJ, Poveda A. The conformation of C-glycosyl compounds. Adv Carbohydr Chem Biochem 2001; 56:235-84. [PMID: 11039113 DOI: 10.1016/s0065-2318(01)56006-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Franchetti P, Marchetti S, Cappellacci L, Yalowitz JA, Jayaram HN, Goldstein BM, Grifantini M. A new C-nucleoside analogue of tiazofurin: synthesis and biological evaluation of 2-beta-D-ribofuranosylimidazole-4-carboxamide (imidazofurin). Bioorg Med Chem Lett 2001; 11:67-9. [PMID: 11140736 DOI: 10.1016/s0960-894x(00)00594-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-Beta-D-ribofuranosylimidazole-4-carboxamide, an imidazole analogue of the antitumor agent tiazofurin, was synthesized and evaluated for the growth inhibitory activity of human myelogenous leukemia K562 cells.
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Affiliation(s)
- P Franchetti
- Departamento di Science Chimiche, Università di Camerino, Italy.
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Goldstein BM, Colby TD. Conformational constraints in NAD analogs: implications for dehydrogenase binding and specificity. ADVANCES IN ENZYME REGULATION 2000; 40:405-26. [PMID: 10828360 DOI: 10.1016/s0065-2571(99)00056-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- B M Goldstein
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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Shaban MA, Nasr AZ. The Chemistry of C-Nucleosides and Their Analogs I: C-Nucleosides of Hetero Monocyclic Bases. ADVANCES IN HETEROCYCLIC CHEMISTRY 1997. [DOI: 10.1016/s0065-2725(08)60363-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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