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Chitre TS, Hirode PV, Lokwani DK, Bhatambrekar AL, Hajare SG, Thorat SB, Priya D, Pradhan KB, Asgaonkar KD, Jain SP. In-silico studies of 2-aminothiazole derivatives as anticancer agents by QSAR, molecular docking, MD simulation and MM-GBSA approaches. J Biomol Struct Dyn 2023:1-19. [PMID: 37811574 DOI: 10.1080/07391102.2023.2262594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/17/2023] [Indexed: 10/10/2023]
Abstract
Targeting Hec1/Nek2 is considered as crucial target for cancer treatment due to its significant role in cell proliferation. In pursuit of this, a series of twenty-five 2-aminothiazoles derivatives, along with their Hec1/Nek2 inhibitory activities were subjected to QSAR studies utilizing QSARINS software. The significant three descriptor QSAR model was generated, showing noteworthy statistical parameters: a correlation coefficient of cross validation leave one out (Q2LOO) = 0.7965, coefficient of determination (R2) = 0.8436, (R2ext) = 0.6308, cross validation leave many out (Q2LMO) = 0.7656, Concordance Correlation Coefficient (CCCCV = 0.8875), CCCtr = 0.9151, and CCCext = 0.0.7241. The descriptors integral to generated QSAR model include Moreau-Broto autocorrelation, which represents the spatial autocorrelation of a property along the molecular graph's topological structure (ATSC1i), Moran autocorrelation at lag 8, which is weighted by charges (MATS8c) and RPSA representing the total molecular surface area. It was noted that these descriptors significantly influence Hec1/Nek2 inhibitory activity of 2-aminothiazoles derivatives. New lead molecules were designed and predicted for their Hec1/Nek2 inhibitory activity based on the developed three descriptor model. Further, the ADMET and Molecular docking studies were carried out for these designed molecules. The three molecules were selected based on their docking score and further subjected for MD simulation studies. Post-MD MM-GBSA analysis were also performed to predicted the free binding energies of molecules. The study helped us to understand the key interactions between 2-aminothiazoles derivatives and Hec1/Nek2 protein that may be necessary to develop new lead molecules against cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Trupti S Chitre
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Purvaj V Hirode
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Deepak K Lokwani
- Rajarshi Shahu College of Pharmacy, Buldhana, Maharashtra, India
| | - Aniket L Bhatambrekar
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Sayli G Hajare
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Shubhangi B Thorat
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - D Priya
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur, Tamilnadu, India
| | - Kunal B Pradhan
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Kalyani D Asgaonkar
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy, Pune, Maharashtra, India
| | - Shirish P Jain
- Rajarshi Shahu College of Pharmacy, Buldhana, Maharashtra, India
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Sardella R, Ianni F, Cossignani L, Aldini G, Carotti A. Binding modes identification through molecular dynamic simulations: A case study with carnosine enantiomers and the Teicoplanin A2-2-based chiral stationary phase. J Sep Sci 2020; 43:1728-1736. [PMID: 32112671 DOI: 10.1002/jssc.202000092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/12/2022]
Abstract
In the present study, an in silico methodology able to define the binding modes adopted by carnosine enantiomers in the setting of the chiral recognition process is described. The inter- and intramolecular forces involved in the enantioseparation process with the Teicoplanin A2-2 chiral selector and carnosine as model compound are successfully identified. This approach fully rationalizes, at a molecular level, the (S) < (R) enantiomeric elution order obtained under reversed-phase conditions. Consistent explanations were achieved by managing molecular dynamics results with advanced techniques of data analysis. As a result, the time-dependent identification of all the interactions simultaneously occurring in the chiral selector-enantiomeric analyte binding process was obtained. Accordingly, it was found that only (R)-carnosine is able to engage a stabilizing charge-charge interaction through its ionized imidazole ring with the carboxylate counter-part on the chiral selector. Instead, (S)-carnosine establishes intramolecular contacts between its ionized functional groups, that limit its conformational freedom and impair the association with the chiral selector unit.
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Affiliation(s)
- Roccaldo Sardella
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, Perugia, 06123, Italy
| | - Federica Ianni
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, Perugia, 06123, Italy
| | - Lina Cossignani
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, Perugia, 06123, Italy
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, Milano, 20133, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, Perugia, 06123, Italy
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Ianni F, Pucciarini L, Carotti A, Natalini S, Raskildina GZ, Sardella R, Natalini B. Last ten years (2008-2018) of chiral ligand-exchange chromatography in HPLC: An updated review. J Sep Sci 2018; 42:21-37. [DOI: 10.1002/jssc.201800724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Federica Ianni
- Department of Pharmaceutical Sciences; Section of Chemistry and Technology of Drugs; University of Perugia; Perugia Italy
| | - Lucia Pucciarini
- Department of Pharmaceutical Sciences; Section of Chemistry and Technology of Drugs; University of Perugia; Perugia Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences; Section of Chemistry and Technology of Drugs; University of Perugia; Perugia Italy
| | - Serena Natalini
- Department of Pharmaceutical Care; S. Giovanni Battista Hospital of Foligno; Foligno Italy
| | | | - Roccaldo Sardella
- Department of Pharmaceutical Sciences; Section of Chemistry and Technology of Drugs; University of Perugia; Perugia Italy
| | - Benedetto Natalini
- Department of Pharmaceutical Sciences; Section of Chemistry and Technology of Drugs; University of Perugia; Perugia Italy
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Liang X, Zhao L, Deng M, Liu L, Ma Y, Guo X. Separation of Ofloxacin and Its Six Related Substances Enantiomers by Chiral Ligand-Exchange Chromatography. Chirality 2015; 27:843-9. [DOI: 10.1002/chir.22527] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/06/2015] [Accepted: 08/17/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Xinlei Liang
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang Liaoning Province P.R. China
| | - Longshan Zhao
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang Liaoning Province P.R. China
| | - Miaoduo Deng
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang Liaoning Province P.R. China
| | - Lijie Liu
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang Liaoning Province P.R. China
| | - Yongfu Ma
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang Liaoning Province P.R. China
| | - Xingjie Guo
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang Liaoning Province P.R. China
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Sardella R, Ianni F, Lisanti A, Scorzoni S, Marinozzi M, Natalini B. S-Trityl-(R)-Cysteine, a Multipurpose Chiral Selector for Ligand-Exchange Liquid Chromatography Applications. Crit Rev Anal Chem 2015; 45:323-33. [DOI: 10.1080/10408347.2014.937851] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yousefinejad S, Honarasa F, Saeed N. Quantitative structure-retardation factor relationship of protein amino acids in different solvent mixtures for normal-phase thin-layer chromatography. J Sep Sci 2015; 38:1771-6. [DOI: 10.1002/jssc.201401427] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Saeed Yousefinejad
- Department of Chemistry; Shiraz University; Shiraz Iran
- Department of Chemistry; Farhangian University; Tehran Iran
| | - Fatemeh Honarasa
- Department of Chemistry, Shiraz Branch; Islamic Azad University; Shiraz Iran
| | - Negar Saeed
- Department of Chemistry, Shiraz Branch; Islamic Azad University; Shiraz Iran
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Sievers-Engler A, Lindner W, Lämmerhofer M. Ligand–receptor binding increments in enantioselective liquid chromatography. J Chromatogr A 2014; 1363:79-88. [DOI: 10.1016/j.chroma.2014.04.077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/15/2014] [Accepted: 04/20/2014] [Indexed: 10/25/2022]
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Kumar R, Bhushan R. Indirect chiral ligand exchange chromatography for enantioseparation: a modification of conventional techniques. RSC Adv 2014. [DOI: 10.1039/c4ra07061e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Recent trends in the analysis of amino acids in fruits and derived foodstuffs. Anal Bioanal Chem 2013; 405:7941-56. [DOI: 10.1007/s00216-013-7025-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 02/02/2023]
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Häbich A, Qiao GG, Ducker W. Enantioselective adsorption of surfactants monitored by ATR-FTIR. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:13944-13953. [PMID: 20690589 DOI: 10.1021/la101641r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The selectivity of adsorption of chiral surfactants to a chiral monolayer at the solid-liquid interface was studied using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). One enantiomer of the chiral surfactant was deuterated, which causes a change in the IR absorption frequency, and allows independent measurement of the adsorption of each molecule. Both the surfactant, N-lauroyl phenylalanine (NLP), and the chiral monolayer, N-L-phenylalaninoyl, 11-undecyl-silicon, were amino acid derivatives. An enantiomeric excess of 56 +/- 22% of the L over D was observed for adsorption to the interface between a carbon tetrachloride solution containing a quasi-racemate of N-lauroyl phenylalanine and the N-L-phenylalaninoyl, 11-undecyl monolayer film on silicon. In contrast, equimolar adsorption occurred from an equimolar mixture of hydrogenated and deuterated forms of the L surfactant. The measured enantiomeric excess strongly depended on the density of chiral surface groups: the higher the density of chiral groups on the surface, the better the enantiodiscrimination, even though the total adsorption was roughly constant. This nonlinear behavior indicates that more than one chiral surface group is required for significant selectivity.
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Affiliation(s)
- Annette Häbich
- Department of Chemical and Biomolecular Engineering, University of Melbourne, Victoria 3010, Australia
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Affiliation(s)
- Timothy J. Ward
- Millsaps College, 1701 N. State Street, Box 150306, Jackson, Mississippi 39210
| | - Karen D. Ward
- Millsaps College, 1701 N. State Street, Box 150306, Jackson, Mississippi 39210
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Lämmerhofer M. Chiral recognition by enantioselective liquid chromatography: mechanisms and modern chiral stationary phases. J Chromatogr A 2009; 1217:814-56. [PMID: 19906381 DOI: 10.1016/j.chroma.2009.10.022] [Citation(s) in RCA: 516] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 09/30/2009] [Accepted: 10/07/2009] [Indexed: 11/19/2022]
Abstract
An overview of the state-of-the-art in LC enantiomer separation is presented. This tutorial review is mainly focused on mechanisms of chiral recognition and enantiomer distinction of popular chiral selectors and corresponding chiral stationary phases including discussions of thermodynamics, additivity principle of binding increments, site-selective thermodynamics, extrathermodynamic approaches, methods employed for the investigation of dominating intermolecular interactions and complex structures such as spectroscopic methods (IR, NMR), X-ray diffraction and computational methods. Modern chiral stationary phases are discussed with particular focus on those that are commercially available and broadly used. It is attempted to provide the reader with vivid images of molecular recognition mechanisms of selected chiral selector-selectand pairs on basis of solid-state X-ray crystal structures and simulated computer models, respectively. Such snapshot images illustrated in this communication unfortunately cannot account for the molecular dynamics of the real world, but are supposed to be helpful for the understanding. The exploding number of papers about applications of various chiral stationary phases in numerous fields of enantiomer separations is not covered systematically.
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Affiliation(s)
- Michael Lämmerhofer
- Christian Doppler Laboratory for Molecular Recognition Materials, Department of Analytical Chemistry and Food Chemistry, University of Vienna, Waehringer Strasse 38, A-1090 Vienna, Austria.
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13
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Del Rio A. Exploring enantioselective molecular recognition mechanisms with chemoinformatic techniques. J Sep Sci 2009; 32:1566-84. [DOI: 10.1002/jssc.200800693] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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