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Multiple conformations and supramolecular synthons in almost fifty crystal structures of the anti-HIV/HBV drug lamivudine. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Palafox MA. Structure and conformational analysis of the anti-HIV reverse transcriptase inhibitor AZT using MP2 and DFT methods. Differences with the natural nucleoside thymidine. Simulation of the 1st phosphorylation step with ATP. Phys Chem Chem Phys 2015; 16:24763-83. [PMID: 25317835 DOI: 10.1039/c4cp03695f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A comprehensive quantum-chemical investigation of the conformational landscape of the HIV-1 reverse transcriptase inhibitor AZT (3'-azido-3'-deoxythymidine) nucleoside analogue was carried out. The whole conformational parameters (χ, γ, β, δ, ϕ, P, νmax) were analysed as well as the NBO charges. The search located at least 55 stable structures, 9 of which were by MP2 within a 1 kcal mol(-1) electronic energy range of the global minimum. Most conformers were anti or high-anti around the glycoside bond and with North sugar ring puckering angles. The distribution of all the conformers according to the ranges of stability of the characteristic torsional angles was established. The results obtained were in accordance with those found in related anti-HIV nucleoside analogues. The best conformer in the anti form corresponded to the calculated values by MP2 of χ = -126.9°, β = 176.4° and γ = 49.1°. An analysis of the lowest vibrations in conformer C1 was carried out. The first hydration shell was simulated and the structural differences with the natural nucleoside deoxythymidine (dT) were determined. The first phosphorylation step was simulated by interacting ATP with the best hydrated clusters of AZT and dT. The Na cations act as a bridge between the phosphate moieties of ATP making it easy for -P3O3 to receive the H5' proton from AZT or dT. A proton-transfer mechanism is proposed through the water molecules. When the number of the water molecules surrounding AZT is lower than 8, the first phosphorylation step of AZT can be carried out. However, the appropriate orientation of the O5'-H in dT avoids this limitation and it can be performed with large numbers of water molecules.
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Affiliation(s)
- M Alcolea Palafox
- Chemical Physics Department, Chemistry Faculty, Complutense University, Ciudad Universitaria, Madrid-28040, Spain.
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El-Sayed AA, Tamara Molina A, Álvarez-Ros M, Alcolea Palafox M. Conformational analysis of the anti-HIV Nikavir prodrug: comparisons with AZT and Thymidine, and establishment of structure–activity relationships/tendencies in other 6′-derivatives. J Biomol Struct Dyn 2014; 33:723-48. [DOI: 10.1080/07391102.2014.909743] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - A. Tamara Molina
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
| | - M.C. Álvarez-Ros
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
| | - M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
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Alcolea Palafox M. Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour. J Biomol Struct Dyn 2013; 32:831-51. [DOI: 10.1080/07391102.2013.789402] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Anticancer drug IUdR and other 5-halogen derivatives of 2′-deoxyuridine: conformers, hydrates, and structure–activity relationships. Struct Chem 2013. [DOI: 10.1007/s11224-013-0225-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jain N, Prabhakar S, Singh R. Fourier transform infrared spectra and normal mode analysis of drug molecules: Zidovudine. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.10.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Structure of the antiviral stavudine using quantum chemical methods: Complete conformational space analysis, 3D potential energy surfaces and solid state simulations. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.06.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Chemical reactivity analysis of deoxyribonucleosides and deoxyribonucleoside analogues (NRTIs): a first-principles density functional approach. J Mol Model 2012; 18:3969-80. [DOI: 10.1007/s00894-012-1391-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 02/21/2012] [Indexed: 11/26/2022]
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Ponomareva AG, Yurenko YP, Zhurakivsky RO, van Mourik T, Hovorun DM. Complete conformational space of the potential HIV-1 reverse transcriptase inhibitors d4U and d4C. A quantum chemical study. Phys Chem Chem Phys 2012; 14:6787-95. [DOI: 10.1039/c2cp40290d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Alcolea Palafox M, Talaya J. Hydration Analysis of Antiviral Agent AZT by Means of DFT and MP2 Calculations. J Phys Chem B 2010; 114:15199-211. [DOI: 10.1021/jp1048452] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- M. Alcolea Palafox
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain
| | - Jéssica Talaya
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain
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Yoshimura Y, Asami K, Imamichi T, Okuda T, Shiraki K, Takahata H. Design and Synthesis of Isonucleosides Constructed on a 2-Oxa-6-thiabicyclo[3.2.0]heptane Scaffold. J Org Chem 2010; 75:4161-71. [DOI: 10.1021/jo100556u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yuichi Yoshimura
- Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
| | - Kazuhiro Asami
- Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology, Applied and Development Research Program, National Institute of Allergy and Infectious Diseases at Frederick, Science Applications International Corporation-Frederick, Inc. Frederick, Maryland 21702
| | - Tomoko Okuda
- Department of Virology, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kimiyasu Shiraki
- Department of Virology, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroki Takahata
- Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan
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12
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Alcolea Palafox M, Iza N. Tautomerism of the natural thymidine nucleoside and the antiviral analogue D4T. Structure and influence of an aqueous environment using MP2 and DFT methods. Phys Chem Chem Phys 2010; 12:881-93. [DOI: 10.1039/b915566j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Palafox MA, Iza N, Fuente MDL, Navarro R. Simulation of the First Hydration Shell of Nucleosides D4T and Thymidine: Structures Obtained Using MP2 and DFT Methods. J Phys Chem B 2009; 113:2458-76. [DOI: 10.1021/jp806684v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- M. Alcolea Palafox
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
| | - N. Iza
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
| | - M. de la Fuente
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
| | - R. Navarro
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
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Pereira BG, Vianna-Soares CD, Righi A, Pinheiro MVB, Flores MZS, Bezerra EM, Freire VN, Lemos V, Caetano EWS, Cavada BS. Identification of lamivudine conformers by Raman scattering measurements and quantum chemical calculations. J Pharm Biomed Anal 2007; 43:1885-9. [PMID: 17303364 DOI: 10.1016/j.jpba.2007.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 01/06/2007] [Accepted: 01/08/2007] [Indexed: 10/23/2022]
Abstract
Characterization of nucleoside and non-nucleoside human immunodeficiency virus (HIV) reverse transcriptase inhibitors conformers, NRTIs and NNRTIs, respectively, is fundamental for an improved treatment of infected individuals. Three conformers in lamivudine I powder are quickly identified in this work by assignment of some Raman peaks to their vibrational frequencies, as obtained by first principles quantum chemical calculations. The method is proposed as a practical procedure for non-destructive identification, analysis, and process monitoring of NRTIs and NNRTIs conformers.
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Affiliation(s)
- B G Pereira
- Escola de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, 30123-970 Belo Horizonte, Minas Gerais, Brazil
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Zhang C, Xue Y. Density functional theory studies on conformational stability and vibrational spectra of 2′-deoxyinosine. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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