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Varfaj I, Labikova M, Sardella R, Hettegger H, Lindner W, Kohout M, Carotti A. A journey in unraveling the enantiorecognition mechanism of 3,5-dinitrobenzoyl-amino acids with two Cinchona alkaloid-based chiral stationary phases: The power of molecular dynamic simulations. Anal Chim Acta 2024; 1314:342791. [PMID: 38876520 DOI: 10.1016/j.aca.2024.342791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Innovations in computer hardware and software capabilities have paved the way for advances in molecular modelling techniques and methods, leading to an unprecedented expansion of their potential applications. In contrast to the docking technique, which usually identifies the most stable selector-selectand (SO-SA) complex for each enantiomer, the molecular dynamics (MD) technique enables the consideration of a distribution of the SO-SA complexes based on their energy profile. This approach provides a more truthful representation of the processes occurring within the column. However, benchmark procedures and focused guidelines for computational treatment of enantioselectivity at the molecular level are still missing. RESULTS Twenty-eight molecular dynamics simulations were performed to study the enantiorecognition mechanisms of seven N-3,5-dinitrobenzoylated α- and β-amino acids (DNB-AAs), occurring with the two quinine- and quinidine-based (QN-AX and QD-AX) chiral stationary phases (CSPs), under polar-ionic conditions. The MD protocol was optimized in terms of box size, simulation run time, and frame recording frequency. Subsequently, all the trajectories were analyzed by calculating both the type and amount of the interactions engaged by the selectands (SAs) with the two chiral selectors (SOs), as well as the conformational and interaction energy profiles of the formed SA-SO associates. All the MDs were in strict agreement with the experimental enantiomeric elution order and allowed to establish (i) that salt-bridge and H-bond interactions play a pivotal role in the enantiorecognition mechanisms, and (ii) that the π-cation and π-π interactions are the discriminant chemical features between the two SOs in ruling the chiral recognition mechanism. SIGNIFICANCE The results of this work clearly demonstrate the high contribution given by MD simulations in the comprehension of the enantiorecognition mechanism with Cinchona alkaloid-based CSPs. However, from this research endeavor it clearly emerged that the MD protocol optimization is crucial for the quality of the produced results.
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Affiliation(s)
- Ina Varfaj
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, 06123, Perugia, Italy
| | - Magdalena Labikova
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, 06123, Perugia, Italy
| | - Hubert Hettegger
- Institute of Chemistry of Renewable Resources, Department of Chemistry, BOKU University, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria; Christian Doppler Laboratory for Cellulose High-Tech Materials, BOKU University, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Wolfgang Lindner
- Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Michal Kohout
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic.
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, 06123, Perugia, Italy.
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Konjaria ML, Kakava R, Volonterio A, Chankvetadze B, Scriba GK. Enantioseparation of chiral (benzylsulfinyl)benzamide sulfoxides by capillary electrophoresis using cyclodextrins as chiral selectors. J Chromatogr A 2022; 1672:463027. [DOI: 10.1016/j.chroma.2022.463027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022]
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Chankvetadze B. Our research cooperation with Professor Yoshio Okamoto. Chirality 2022; 34:630-645. [PMID: 35048410 DOI: 10.1002/chir.23418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
This article summarizes our cooperation with the research group of Prof. Yoshio Okamoto at Nagoya University during the period of time between 1992 and 2005. Although the text deals entirely with enantioseparations in high-performance liquid chromatography, capillary electrophoresis, and capillary electrochromatography, this is not a detailed review in any of these areas. The text highlights selected aspects of these techniques, which have been the subject of our joint research and in part their reflection in follow-up research by our and other research groups. Together with more systematically studied topics, aspects such as ultrafast separation of enantiomers, uncommonly high separation factor of enantiomers and other related issues are also addressed.
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Affiliation(s)
- Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Tbilisi, Georgia
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Estrada-Valenzuela D, Ramos-Sánchez VH, Zaragoza-Galán G, Espinoza-Hicks JC, Bugarin A, Chávez-Flores D. Lipase Assisted ( S)-Ketoprofen Resolution from Commercially Available Racemic Mixture. Pharmaceuticals (Basel) 2021; 14:ph14100996. [PMID: 34681221 PMCID: PMC8541352 DOI: 10.3390/ph14100996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Ketoprofen is a commercially available drug sold as a racemic mixture that belongs to the family of non-steroidal anti-inflammatory drugs known as profens. It has been demonstrated (in vitro) that (S)-ketoprofen is around 160 times more potent than its enantiomer (R)-ketoprofen, while accumulation of (R)-ketoprofen can cause serious side effects, such as dyspepsia, gastrointestinal ulceration/bleeding, pain, salt and fluid retention, and hypertension. In this work, four commercially available lipases were systematically assessed. Parameters such as conversion, enantiomeric excess, and enantioselectivity were considered. Among them, and by evaluating lipase load, temperature, solvent, and alcohol, Candida rugosa lipase exhibited the best results in terms of enantioselectivity E = 185 ((S)-enantiopreference) with esterification conversions of c = 47% (out of 50%) and enantiomeric excess of 99%. The unreacted (R)-enantiomer was recovered by liquid-liquid extraction and racemized under basic media, which was recycled as starting material. Finally, the (S)-alkyl ketoprofen ester was successfully enzymatically hydrolyzed to the desired (S)-ketoprofen with c = 98.5% and 99% ee. This work demonstrated the benefit and efficiency of using Candida rugosa lipase to kinetically resolve racemic ketoprofen by an environmentally friendly protocol and with the recycling of the undesired (R)-ketoprofen.
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Affiliation(s)
- Daniela Estrada-Valenzuela
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario, Chihuahua 31125, Mexico; (D.E.-V.); (V.H.R.-S.); (G.Z.-G.); (J.C.E.-H.)
| | - Víctor H. Ramos-Sánchez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario, Chihuahua 31125, Mexico; (D.E.-V.); (V.H.R.-S.); (G.Z.-G.); (J.C.E.-H.)
| | - Gerardo Zaragoza-Galán
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario, Chihuahua 31125, Mexico; (D.E.-V.); (V.H.R.-S.); (G.Z.-G.); (J.C.E.-H.)
| | - Jose C. Espinoza-Hicks
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario, Chihuahua 31125, Mexico; (D.E.-V.); (V.H.R.-S.); (G.Z.-G.); (J.C.E.-H.)
| | - Alejandro Bugarin
- Department of Chemistry & Physics, Florida Gulf Coast University, Fort Myers, FL 33965, USA
- Correspondence: (A.B.); (D.C.-F.)
| | - David Chávez-Flores
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario, Chihuahua 31125, Mexico; (D.E.-V.); (V.H.R.-S.); (G.Z.-G.); (J.C.E.-H.)
- Correspondence: (A.B.); (D.C.-F.)
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Craven GB, Briggs EL, Zammit CM, McDermott A, Greed S, Affron DP, Leinfellner C, Cudmore HR, Tweedy RR, Luisi R, Bull JA, Armstrong A. Synthesis and Configurational Assignment of Vinyl Sulfoximines and Sulfonimidamides. J Org Chem 2021; 86:7403-7424. [PMID: 34003635 DOI: 10.1021/acs.joc.1c00373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Vinyl sulfones and sulfonamides are valued for their use as electrophilic warheads in covalent protein inhibitors. Conversely, the S(VI) aza-isosteres thereof, vinyl sulfoximines and sulfonimidamides, are far less studied and have yet to be applied to the field of protein bioconjugation. Herein, we report a range of different synthetic methodologies for constructing vinyl sulfoximine and vinyl sulfonimidamide architectures that allows access to new areas of electrophilic chemical space. We demonstrate how late-stage functionalization can be applied to these motifs to incorporate alkyne tags, generating fully functionalized probes for future chemical biology applications. Finally, we establish a workflow for determining the absolute configuration of enantioenriched vinyl sulfoximines and sulfonimidamides by comparing experimentally and computationally determined electronic circular dichroism spectra, enabling access to configurationally assigned enantiomeric pairs by separation.
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Affiliation(s)
- Gregory B Craven
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K.,The Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Edward L Briggs
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Charlotte M Zammit
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alexander McDermott
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Stephanie Greed
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Dominic P Affron
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Charlotte Leinfellner
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Hannah R Cudmore
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Ruth R Tweedy
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Renzo Luisi
- Department of Pharmacy-Drug Sciences, University of Bari, "A. Moro" Via E. Orabona 4, Bari 70125, Italy
| | - James A Bull
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alan Armstrong
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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The molecular bases of chiral recognition in 2-(benzylsulfinyl)benzamide enantioseparation. Anal Chim Acta 2021; 1141:194-205. [DOI: 10.1016/j.aca.2020.10.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022]
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7
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Ianni F, Carotti A, Intagliata S, Macchiarulo A, Chankvetadze B, Pittalà V, Sardella R. Laboratory-Scale Semipreparative Enantioresolution of Phenylethanolic-Azole Heme Oxygenase-1 Inhibitors. Chromatographia 2020. [DOI: 10.1007/s10337-020-03972-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Application of the “inverted chirality columns approach” for the monitoring of asymmetric synthesis protocols. Talanta 2019; 203:147-152. [DOI: 10.1016/j.talanta.2019.05.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
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9
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Xiong F, Yang BB, Zhang J, Li L. Enantioseparation, Stereochemical Assignment and Chiral Recognition Mechanism of Sulfoxide-Containing Drugs. Molecules 2018; 23:molecules23102680. [PMID: 30340337 PMCID: PMC6222453 DOI: 10.3390/molecules23102680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/04/2018] [Accepted: 10/15/2018] [Indexed: 01/11/2023] Open
Abstract
The distinct pharmacodynamic and pharmacokinetic properties of enantiopure sulfoxide drugs have stimulated us to systematically investigate their chiral separation, stereochemical assignment, and chiral recognition mechanism. Herein, four clinically widely-used sulfoxide drugs were chosen and optically resolved on various chiral stationary phases (CSPs). Theoretical simulations including electronic circular dichroism (ECD) calculation and molecular docking were adopted to assign the stereochemistry and reveal the underlying chiral recognition mechanism. Our results showed that the sequence of calculated mean binding energies between each pair of enantiomers and CSP matched exactly with experimentally observed enantiomeric elution order (EEO). It was also found that the length of hydrogen bond might contribute dominantly the interaction between two enantiomers and CSP. We hope our study could provide a fresh perspective to explore the stereochemistry and chiral recognition mechanism of chiral drugs.
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Affiliation(s)
- Fei Xiong
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Bei-Bei Yang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Jie Zhang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Li Li
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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Ren J, Mistry TL, Su PC, Mehboob S, Demissie R, Fung LWM, Ghosh AK, Johnson ME. Determination of absolute configuration and binding efficacy of benzimidazole-based FabI inhibitors through the support of electronic circular dichroism and MM-GBSA techniques. Bioorg Med Chem Lett 2018; 28:2074-2079. [PMID: 29730028 DOI: 10.1016/j.bmcl.2018.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/12/2023]
Abstract
We have previously reported benzimidazole-based compounds to be potent inhibitors of FabI for Francisella tularensis (FtFabI), making them promising antimicrobial hits. Optically active enantiomers exhibit markedly differing affinities toward FtFabI. The IC50 of benzimidazole (-)-1 is ∼100× lower than the (+)-enantiomer, with similar results for the 2 enantiomers. Determining the absolute configuration for these optical compounds and elucidating their binding modes is important for further design. Electronic circular dichroism (ECD) quantum calculations have become important in determining absolute configurations of optical compounds. We determined the absolute configuration of (-)/(+)-1 and (-)/(+)-2 by comparing experimental spectra and theoretical density functional theory (DFT) simulations of ECD spectra at the B3LYP/6-311+G(2d, p) level using Gaussian09. Comparison of experimental and calculated ECD spectra indicates that the S configuration corresponds to the (-)-rotation for both compounds 1 and 2, while the R configuration corresponds to the (+)-rotation. Further, molecular dynamics simulations and MM-GBSA binding energy calculations for these two pairs of enantiomers with FtFabI show much tighter binding MM-GBSA free energies for S-1 and S-2 than for their enantiomers, R-1 and R-2, consistent with the S configuration being the more active one, and with the ECD determination of the S configuration corresponding to (-) and the R configuration corresponding to (+). Thus, our computational studies allow us to assign (-) to (S)- and (+) to (R)- for compounds 1 and 2, and to further evaluate structural changes to improve efficacy.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Tina L Mistry
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Pin-Chih Su
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Shahila Mehboob
- Novalex Therapeutics, Inc., 2242 W Harrison, Chicago, IL 60612, USA
| | - Robel Demissie
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St, Chicago, IL 60607, USA
| | - Leslie Wo-Mei Fung
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St, Chicago, IL 60607, USA
| | - Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Novalex Therapeutics, Inc., 2242 W Harrison, Chicago, IL 60612, USA.
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Kadkhodaei K, Forcher L, Schmid MG. Separation of enantiomers of new psychoactive substances by high-performance liquid chromatography. J Sep Sci 2018; 41:1274-1286. [DOI: 10.1002/jssc.201701239] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Kian Kadkhodaei
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences; University of Graz; Graz Austria
| | - Lisa Forcher
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences; University of Graz; Graz Austria
| | - Martin G. Schmid
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences; University of Graz; Graz Austria
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