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Korlyukov AA, Stash AI, Romanenko AR, Trzybiński D, Woźniak K, Vologzhanina AV. Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations. Biomedicines 2023; 11:biomedicines11030743. [PMID: 36979722 PMCID: PMC10045540 DOI: 10.3390/biomedicines11030743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand–receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug’s experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of ‘Atoms in Molecules’, and their contributions to the total crystal energy or ligand–receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand–receptor complexes (320.1–394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.
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Affiliation(s)
- Alexander A. Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov St., Moscow 19334, Russia
| | - Adam. I. Stash
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov St., Moscow 19334, Russia
| | - Alexander R. Romanenko
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov St., Moscow 19334, Russia
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Anna V. Vologzhanina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov St., Moscow 19334, Russia
- Correspondence:
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Fathima Rizwana B, Prasana JC, Muthu S, Abraham CS. Vibrational spectroscopy, reactive site analysis and molecular docking studies on 2-[(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)methoxy]-3-hydroxypropyl (2S)-2-amino-3-methylbutanoate. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Shahabadi N, Khorshidi A, Zhaleh H, Kashanian S. Synthesis, characterization, cytotoxicity and DNA binding studies of Fe 3 O 4 @SiO 2 nanoparticles coated by an antiviral drug lamivudine. J Drug Deliv Sci Technol 2018. [DOI: 10.1016/j.jddst.2018.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Pan T, Li S, Zou T, Yu Z, Zhang B, Wang C, Zhang J, He M, Zhao H. Terahertz spectra of l-phenylalanine and its monohydrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 178:19-23. [PMID: 28157589 DOI: 10.1016/j.saa.2017.01.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/04/2017] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
The low-frequency vibrational property of l-phenylalanine (l-Phe) and l-phenylalanine monohydrate (l-Phe·H2O) has been investigated by terahertz time-domain spectroscopy (THz-TDS) at room and low temperature ranging from 0.5 to 4.5THz. Distinctive THz absorption spectra of the two compounds were observed. Density functional theory (DFT) calculations based on the crystal structures have been performed to simulate the vibrational modes of l-Phe and l-Phe·H2O and the results agree well with the experimental observations. The study indicates that the characterized features of l-Phe mainly originate from the collective vibration of molecules. And the characterized features of l-Phe·H2O mainly come from hydrogen bond interactions between l-Phe and water molecules. l-Phe and l-Phe·H2O were also verified by differential scanning calorimetry and thermogravimetry (DSC-TG) and powder X-ray diffraction (PXRD) examinations.
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Affiliation(s)
- Tingting Pan
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China; Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shaoping Li
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Tao Zou
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China; Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Zheng Yu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Bo Zhang
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China; Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chenyang Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jianbing Zhang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Mingxia He
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Hongwei Zhao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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Du Y, Zhang H, Xue J, Tang W, Fang H, Zhang Q, Li Y, Hong Z. Vibrational spectroscopic study of polymorphism and polymorphic transformation of the anti-viral drug lamivudine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:1158-1163. [PMID: 25305607 DOI: 10.1016/j.saa.2014.08.128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/27/2014] [Accepted: 08/31/2014] [Indexed: 06/04/2023]
Abstract
Vibrational spectra of hydrated and anhydrous lamivudines, and also the dynamic process of polymorphic transformation have been characterized by Fourier transform infrared (FT-IR) and Raman spectroscopic techniques. The vibrational modes of both polymorphic lamivudines are assigned. FT-IR and Raman spectral results show that the interaction between crystalline water and lamivudine molecular has an important effect on the molecular vibration motions of polymorphic lamivudines. The two characteristic Raman peaks at 783 and 798 cm(-1) represent hydrated and anhydrous lamivudine respectively. The relationship between changes of two characteristic peak normalized areas and heating time could be fitted with single exponential functions, and the dynamic information of polymorphic transformation of lamivudine drug is obtained. The decay rate of characteristic peak for hydrated lamivudine and the growth rate of that for anhydrous lamivudine are consistent during dehydration transformation process. The reported results provide us important benchmark for qualitatively monitoring different polymorphic drugs and also establishing the corresponding model for the polymorphic transformation of drugs in related pharmaceutical research fields.
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Affiliation(s)
- Yong Du
- Centre for THz Research, China Jiliang University, Hangzhou 310018, China.
| | - Huili Zhang
- Centre for THz Research, China Jiliang University, Hangzhou 310018, China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wenjian Tang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Hongxia Fang
- Centre for THz Research, China Jiliang University, Hangzhou 310018, China
| | - Qi Zhang
- Centre for THz Research, China Jiliang University, Hangzhou 310018, China
| | - Yafang Li
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhi Hong
- Centre for THz Research, China Jiliang University, Hangzhou 310018, China
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Swarnalatha N, Gunasekaran S, Nagarajan M, Srinivasan S, Sankari G, Ramkumaar GR. Vibrational, UV spectra, NBO, first order hyperpolarizability and HOMO-LUMO analysis of carvedilol. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:567-578. [PMID: 25448957 DOI: 10.1016/j.saa.2014.09.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/09/2014] [Accepted: 09/18/2014] [Indexed: 06/04/2023]
Abstract
In this work, we have investigated experimentally and theoretically on the molecular structure, vibrational spectra, UV spectral analysis and NBO studies of cardio-protective drug carvedilol. The FT-Raman and FT-IR spectra for carvedilol in the solid phase have been recorded in the region 4000-100 cm(-1) and 4000-400 cm(-1) respectively. Theoretical calculations were performed by using density functional theory (DFT) method at B3LYP/6-31G(d,p) and B3LYP/6-31++G(d,p) basis set levels. The harmonic vibrational frequencies, the optimized geometric parameters have been interpreted and compared with the reported experimental values. The complete vibrational assignments were performed on the basis of potential energy distribution (PED) of the vibrational modes. The thermodynamic properties and molecular electrostatic potential surfaces of the molecule were constructed. The electronic absorption spectrum was recorded in the region 400-200 nm and electronic properties such as HOMO and LUMO energies were calculated. The stability of the molecule arising from hyper conjugative interactions and charge delocalization have been analyzed from natural bond orbital (NBO) analysis. The first order hyperpolarizability of the title molecule was also calculated. The photo stability of carvedilol under different storage conditions were analyzed using UV-Vis spectral technique.
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Affiliation(s)
- N Swarnalatha
- Department of Physics, SCSVMV University, Enathur, Kanchipuram 631561, TN, India.
| | - S Gunasekaran
- Research and Development, St. Peter's Institute of Higher Education and Research, St. Peter's University, Avadi, Chennai 600054, TN, India
| | - M Nagarajan
- Department of Physics, Arulmigu Palani Andavar College of Arts and Culture, Palani 624601, TN, India
| | - S Srinivasan
- PG and Research Department of Physics, Presidency College, Chennai 600005, TN, India
| | - G Sankari
- Department of Physics, Meenakshi College for Women, Chennai 600024, TN, India
| | - G R Ramkumaar
- Department of Physics, C. Kandaswami Naidu College for Men in Anna Nagar East, Chennai 600102, TN, India
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Pisklak DM, Zielińska-Pisklak M, Szeleszczuk Ł, Wawer I. 13C cross-polarization magic-angle spinning nuclear magnetic resonance analysis of the solid drug forms with low concentration of an active ingredient-propranolol case. J Pharm Biomed Anal 2014; 93:68-72. [DOI: 10.1016/j.jpba.2013.06.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/23/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
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Chakraborty S, Ganguly S, Desiraju GR. Synthon transferability probed with IR spectroscopy: cytosine salts as models for salts of lamivudine. CrystEngComm 2014. [DOI: 10.1039/c3ce42156b] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Co-crystal screening of the anti-HIV drug lamivudine was carried out with dicarboxylic acids as co-formers. Salts of cytosine, a molecule that incorporates critical structural features of lamivudine, with the same co-formers, were taken as model systems for IR spectroscopic studies of the synthons in the salts of lamivudine.
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Affiliation(s)
- Shaunak Chakraborty
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Somnath Ganguly
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560 012, India
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