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Komarov IV, Bugrov VA, Cherednychenko A, Grygorenko OO. Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules. CHEM REC 2024; 24:e202300276. [PMID: 37847887 DOI: 10.1002/tcr.202300276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/29/2023] [Indexed: 10/19/2023]
Abstract
In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein-ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein-ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein-ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some "rules of thumb" have started to emerge on how to minimize entropy-enthalpy compensation and design efficient rigidified or flexible ligands.
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Affiliation(s)
- Igor V Komarov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Volodymyr A Bugrov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Anton Cherednychenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
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Grygorenko OO, Moskvina VS, Kleban I, Hryshchyk OV. Synthesis of saturated and partially saturated heterocyclic boronic derivatives. Tetrahedron 2022. [DOI: 10.1016/j.tet.2021.132605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Kleban I, Krokhmaliuk Y, Reut S, Shuvakin S, Pendyukh VV, Khyzhan OI, Yarmoliuk DS, Tymtsunik AV, Rassukana YV, Grygorenko OO. Multigram Synthesis of Heterabicyclo[n.1.0]alkan‐1‐yl Trifluoroborates. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ihor Kleban
- Enamine Ltd. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry National Academy of Sciences of Ukraine Murmanska Street 5 02094 Kyiv Ukraine
| | - Yevhen Krokhmaliuk
- Enamine Ltd. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Sofiia Reut
- Enamine Ltd. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Serhii Shuvakin
- Enamine Ltd. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 01601 Kyiv Ukraine
| | | | | | | | - Andriy V. Tymtsunik
- Enamine Ltd. Chervonotkatska 78 02094 Kyiv Ukraine
- National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute” Prospect Peremogy 37 03056 Kyiv Ukraine
| | - Yuliya V. Rassukana
- Institute of Organic Chemistry National Academy of Sciences of Ukraine Murmanska Street 5 02094 Kyiv Ukraine
- National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute” Prospect Peremogy 37 03056 Kyiv Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 01601 Kyiv Ukraine
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Tilvi S, Khan S, Majik MS. γ-Hydroxybutenolide Containing Marine Natural Products and Their Synthesis: A Review. CURR ORG CHEM 2020. [DOI: 10.2174/1385272823666191021122810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:γ-Hydroxybutenolides (γ-HB) is an important structural core found in many bioactive marine natural products (MNPS). The γ-HB core containing NPS served as an inspiration to medicinal chemists to undertake designing of the new synthetic strategies to construct γ-HB core. Subsequently, it further results in the development of novel physiological and therapeutic agents. The most notable example includes manoalides, cacospongionolides, petrosaspongioide M and dysidiolide from marine sponges possessing anti-inflammatory properties. γ-HB containing MNPS were known to possess various pharmacological properties such as antimicrobial (acantholide B), cytotoxic (acantholide A-E, spongianolide A), inhibitors of secretory phospholipase A2 (cladocorans A and B), BACE inhibitors (ianthellidone G), etc. Moreover, the γ-HB moiety was explored as antifouling agents as well. Owing to their numerous biological activities and attractive molecular structures, there are lots of advances in the synthetic methodology of these compounds. This review gives the account on isolation and biological studies of MNPS with γ-HB skeleton as a core unit. Furthermore, the synthesis of selective γ-HB containing bioactive MNPS like manoalide, secomanoalide, cacospongionolides, luffarielloide and dysidiolide were highlighted in the article.
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Affiliation(s)
- Supriya Tilvi
- Bio-Organic Chemistry Laboratory, Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - Safia Khan
- Bio-Organic Chemistry Laboratory, Chemical Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - Mahesh S. Majik
- Department of Chemistry, Dnyanprassarak Mandal’s College and Research Center, Assagao, Goa, India
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Leonelli F, Piergentili I, Lucarelli G, Migneco LM, Marini Bettolo R. Unexpected Racemization in the Course of the Acetalization of (+)-(S)-5-Methyl-Wieland–Miescher Ketone with 1,2-Ethanediol and TsOH under Classical Experimental Conditions. Int J Mol Sci 2019; 20:ijms20246147. [PMID: 31817544 PMCID: PMC6941009 DOI: 10.3390/ijms20246147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 11/23/2022] Open
Abstract
(+)-(S) and (−)-(R)-5-methyl-Wieland-Miescher ketone (+)-1 and (−)-1, are important synthons in the diastereo and enantioselective syntheses of biological and/or pharmacological interesting compounds. A key step in these syntheses is the chemoselective C(1)O acetalization to (+)-5 and (−)-5, respectively. Various procedures for this transformation have been described in the literature. Among them, the classical procedure based on the use of 1,2-ethanediol and TsOH in refluxing benzene in the presence of a Dean-Stark apparatus. Within our work on bioactive natural products, it occurred to us to observe the partial racemization of (+)-5 in the course of the acetalization of (+)-1 by means of the latter methodology. Aiming to investigate this drawback, which, to our best knowledge, has no precedents in the literature, we acetalized with 1,2-ethanediol and TsOH in refluxing benzene and in the presence of a Dean–Stark apparatus under various experimental conditions, enantiomerically pure (+)-1. It was found that the extent of racemization depends on the TsOH/(+)-1 and 1,2-ethanediol/(+)-1 ratios. Mechanism hypotheses for this partial and unexpected racemization are provided.
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Affiliation(s)
- Francesca Leonelli
- Dipartimento di Biologia Ambientale, Università degli Studi La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- Correspondence: ; Tel.: +39-64991-3197
| | - Irene Piergentili
- Dipartimento di Chimica, Università degli Studi La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy; (I.P.); (G.L.); (L.M.M.); (R.M.B.)
| | - Giulio Lucarelli
- Dipartimento di Chimica, Università degli Studi La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy; (I.P.); (G.L.); (L.M.M.); (R.M.B.)
| | - Luisa Maria Migneco
- Dipartimento di Chimica, Università degli Studi La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy; (I.P.); (G.L.); (L.M.M.); (R.M.B.)
| | - Rinaldo Marini Bettolo
- Dipartimento di Chimica, Università degli Studi La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy; (I.P.); (G.L.); (L.M.M.); (R.M.B.)
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Yoshioka S, Takehara T, Matsuzaki T, Suzuki T, Tsujino H, Uno T, Tsutsumi Y, Murai K, Fujioka H, Arisawa M. Direct synthesis of dialkylarylvinylsilane derivatives: metathesis of dialkylaryl-iso-propenylsilane and its application to tetracyclic silacycle dye synthesis. Chem Commun (Camb) 2019; 55:14070-14073. [DOI: 10.1039/c9cc06777a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metathesis of dialkylarylvinylsilane, which has not been accomplished to date, is achieved using dialkylaryl-iso-propenylsilane as a substrate.
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Affiliation(s)
- Shohei Yoshioka
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Japan
| | | | - Tsuyoshi Matsuzaki
- The Institute of Scientific and Industrial Research
- Osaka University
- Japan
| | - Takeyuki Suzuki
- The Institute of Scientific and Industrial Research
- Osaka University
- Japan
| | | | - Tadayuki Uno
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Japan
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Japan
| | - Kenichi Murai
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Japan
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Gnanamani E, Someshwar N, Ramanathan CR. Conformationally Rigid Chiral Pyridine N-Oxides as Organocatalyst: Asymmetric Allylation of Aldehydes. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200115] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jang H, Zhugralin AR, Lee Y, Hoveyda AH. Highly Selective Methods for Synthesis of Internal (α-) Vinylboronates through Efficient NHC–Cu-Catalyzed Hydroboration of Terminal Alkynes. Utility in Chemical Synthesis and Mechanistic Basis for Selectivity. J Am Chem Soc 2011; 133:7859-71. [DOI: 10.1021/ja2007643] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hwanjong Jang
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Adil R. Zhugralin
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Yunmi Lee
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Amir H. Hoveyda
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
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Herndon JW. The chemistry of the carbon-transition metal double and triple bond: Annual survey covering the Year 2007. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2008.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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