1
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Dolezal R. Accuracy and precision of binding free energy prediction for a tacrine related lead inhibitor of acetylcholinesterase with an arsenal of supercomputerized molecular modelling methods: a comparative study. J Biomol Struct Dyn 2022; 40:11291-11319. [PMID: 34323654 DOI: 10.1080/07391102.2021.1957716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Nowadays, advanced computational chemistry methods offer various strategies for revealing prospective hit structures in drug development essentially through accurate binding free energy predictions. After the era of molecular docking and quantitative structure-activity relationships, much interest has been lately oriented to perturbed molecular dynamic approaches like replica exchange with solute tempering and free energy perturbation (REST/FEP) and the potential of the mean force with adaptive biasing and accelerated weight histograms (PMF/AWH). Both of these receptor-based techniques can exploit exascale CPU&GPU supercomputers to achieve high throughput performance. In this fundamental study, we have compared the predictive power of a panel of supercomputerized molecular modelling methods to distinguish the major binding modes and the corresponding binding free energies of a promising tacrine related potential antialzheimerics in human acetylcholinesterase. The binding free energies were estimated using flexible molecular docking, molecular mechanics/generalized Born surface area/Poisson-Boltzmann surface area (MM/GBSA/PBSA), transmutation REST/FEP with 12 x 5 ns/λ windows, annihilation FEP with 20 x 5 ns/λ steps, PMF with weight histogram analysis method (WHAM) and 40 x 5 ns samples, and PMF/AWH with 10 x 100 ns replicas. Confrontation of the classical approaches such as canonical molecular dynamics and molecular docking with alchemical calculations and steered molecular dynamics enabled us to show how large errors in ΔG predictions can be expected if these in silico methods are employed in the elucidation of a common case of enzyme inhibition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rafael Dolezal
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.,Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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2
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Nunes RS, Vila-Viçosa D, Costa PJ. Halogen Bonding: An Underestimated Player in Membrane–Ligand Interactions. J Am Chem Soc 2021; 143:4253-4267. [DOI: 10.1021/jacs.0c12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rafael Santana Nunes
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Paulo J. Costa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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3
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Campetella M, De Mitri N, Prampolini G. Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase. J Chem Phys 2020; 153:044106. [PMID: 32752684 DOI: 10.1063/5.0014280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions of the systems of interest, it would be therefore desirable to increase the FF accuracy maintaining the simplicity of the standard Lennard-Jones (LJ) plus point charge description to avoid an excessive computational cost. A simple yet effective strategy consists in introducing a number of virtual sites able to mimic the so-called "explicit σ-hole." In this work, we present an automated FF parameterization strategy based on a global optimization of both LJ and charge parameters with respect to accurate quantum mechanical data, purposely computed for the system under investigation. As a test case, we report on two homologue series, characterized either by weak or strong XBs, namely, the di-halogenated methanes and the mono-, di-, and tri-substituted acetonitriles, taking into consideration Cl, Br, and I substituents. The resulting quantum mechanically derived FFs are validated for each compound in the gas and in the condensed phase by comparing them to general purpose and specific FFs without virtual sites and to highly accurate reference quantum mechanical data. The results strongly support the adoption of the specific FFs with virtual sites, which overcome the other investigated models in representing both gas phase energetics and the structural patterns of the liquid phase structure related to the presence of XBs.
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Affiliation(s)
- Marco Campetella
- Institut des Nanosciences de Paris, Sorbonne Université, CNRS, UMR7588, F-75252 Paris, France
| | - Nicola De Mitri
- Enthought Ltd., Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, United Kingdom
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici (ICCOM), CNR Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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4
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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5
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Dong TG, Peng H, He XF, Wang X, Gao J. Hybrid Molecular Dynamics for Elucidating Cooperativity Between Halogen Bond and Water Molecules During the Interaction of p53-Y220C and the PhiKan5196 Complex. Front Chem 2020; 8:344. [PMID: 32457871 PMCID: PMC7221198 DOI: 10.3389/fchem.2020.00344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/02/2020] [Indexed: 12/15/2022] Open
Abstract
The cooperativity between hydrogen and halogen bonds plays an important role in rational drug design. However, mimicking the dynamic cooperation between these bonds is a challenging issue, which has impeded the development of the halogen bond force field. In this study, the Y220C–PhiKan5196 complex of p53 protein was adopted as a model, and the functions of three water molecules that formed hydrogen bonds with halogen atoms were analyzed by the simulation method governed by the hybrid quantum mechanical/molecular mechanical molecular dynamics. A comparison with the water-free model revealed that the strength of the halogen bond in the complex was consistently stronger. This confirmed that the water molecules formed weak hydrogen bonds with the halogen atom and cooperated with the halogen atom to enhance the halogen bond. Further, it was discovered that the roles of the three water molecules were not the same. Therefore, the results obtained herein can facilitate a rational drug design. Further, this work emphasizes on the fact that, in addition to protein pockets and ligands, the role of voids should also be considered with regard to the water molecules surrounding them.
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Affiliation(s)
- Tian-Ge Dong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hui Peng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xue-Feng He
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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6
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Margiotta E, van der Lubbe SCC, de Azevedo Santos L, Paragi G, Moro S, Bickelhaupt FM, Fonseca Guerra C. Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. J Chem Inf Model 2020; 60:1317-1328. [PMID: 32003997 PMCID: PMC7093837 DOI: 10.1021/acs.jcim.9b00946] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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Halogen bonds are highly important
in medicinal chemistry as halogenation
of drugs, generally, improves both selectivity and efficacy toward
protein active sites. However, accurate modeling of halogen bond interactions
remains a challenge, since a thorough theoretical investigation of
the bonding mechanism, focusing on the realistic complexity of drug–receptor
systems, is lacking. Our systematic quantum-chemical study on ligand/peptide-like
systems reveals that halogen bonding is driven by the same bonding
interactions as hydrogen bonding. Besides the electrostatic and the
dispersion interactions, our bonding analyses, based on quantitative
Kohn–Sham molecular orbital theory together with energy decomposition
analysis, reveal that donor–acceptor interactions and steric
repulsion between the occupied orbitals of the halogenated ligand
and the protein need to be considered more carefully within the drug
design process.
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Affiliation(s)
- Enrico Margiotta
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas de Azevedo Santos
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Gabor Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,MTA-SZTE Biomimetic Systems Research Group, Dom ter 8, 6720 Szeged, Hungary.,Institute of Physics, University of Pecs, Ifjusag utja 6, 7624 Pecs, Hungary
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Institute of Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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7
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Theoretical Description of R-X⋯NH 3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion. Molecules 2020; 25:molecules25030530. [PMID: 31991810 PMCID: PMC7037998 DOI: 10.3390/molecules25030530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
In the present work, a number of R–X⋯NH3 (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme’s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R–Br⋯NH3 complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback–Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R–X bond is significantly polarized due to the presence of the NH3 molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br—CN]n system (n = 1–8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.
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8
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Santos LDA, Prandi IG, Ramalho TC. Could Quantum Mechanical Properties Be Reflected on Classical Molecular Dynamics? The Case of Halogenated Organic Compounds of Biological Interest. Front Chem 2019; 7:848. [PMID: 31921771 PMCID: PMC6923750 DOI: 10.3389/fchem.2019.00848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022] Open
Abstract
Essential to understanding life, the biomolecular phenomena have been an important subject in science, therefore a necessary path to be covered to make progress in human knowledge. To fully comprehend these processes, the non-covalent interactions are the key. In this review, we discuss how specific protein-ligand interactions can be efficiently described by low computational cost methods, such as Molecular Mechanics (MM). We have taken as example the case of the halogen bonds (XB). Albeit generally weaker than the hydrogen bonds (HB), the XBs play a key role to drug design, enhancing the affinity and selectivity toward the biological target. Along with the attraction between two electronegative atoms in XBs explained by the σ-hole model, important orbital interactions, as well as relief of Pauli repulsion take place. Nonetheless, such electronic effects can be only well-described by accurate quantum chemical methods that have strong limitations dealing with supramolecular systems due to their high computational cost. To go beyond the poor description of XBs by MM methods, reparametrizing the force-fields equations can be a way to keep the balance between accuracy and computational cost. Thus, we have shown the steps to be considered when parametrizing force-fields to achieve reliable results of complex non-covalent interactions at MM level for In Silico drug design methods.
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Affiliation(s)
| | - Ingrid G. Prandi
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czechia
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9
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Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
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Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
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10
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Franchini D, Dapiaggi F, Pieraccini S, Forni A, Sironi M. Halogen bonding in the framework of classical force fields: The case of chlorine. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Structure and bonding in NbX5 X = (F, Cl, Br and I) complexes: a molecular orbital perspective in the C–H bond activation. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2348-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Szell PMJ, Cavallo G, Terraneo G, Metrangolo P, Gabidullin B, Bryce DL. Comparing the Halogen Bond to the Hydrogen Bond by Solid-State NMR Spectroscopy: Anion Coordinated Dimers from 2- and 3-Iodoethynylpyridine Salts. Chemistry 2018; 24:11364-11376. [DOI: 10.1002/chem.201801279] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/01/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Patrick M. J. Szell
- Department of Chemistry and Biomolecular Sciences; University of Ottawa; 10 Marie Curie Private Ottawa Ontario K1N 6N5 Canada
| | - Gabriella Cavallo
- Laboratory of Supramolecular and Bionanomaterials; Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Via L. Mancinelli 7 20131 Milano Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bionanomaterials; Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Via L. Mancinelli 7 20131 Milano Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bionanomaterials; Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Via L. Mancinelli 7 20131 Milano Italy
| | - Bulat Gabidullin
- Department of Chemistry and Biomolecular Sciences; University of Ottawa; 10 Marie Curie Private Ottawa Ontario K1N 6N5 Canada
| | - David L. Bryce
- Department of Chemistry and Biomolecular Sciences; University of Ottawa; 10 Marie Curie Private Ottawa Ontario K1N 6N5 Canada
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13
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Structural analysis of two tetraketones and theoretical investigation of the reactions involved in their preparation. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Kesharwani MK, Manna D, Sylvetsky N, Martin JML. The X40×10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n–1)d Subvalence Correlation. J Phys Chem A 2018; 122:2184-2197. [DOI: 10.1021/acs.jpca.7b10958] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Debashree Manna
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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15
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Reis AFVF, Gonçalves ILP, Neto AFG, Santos AS, Kuca K, Nepovimova E, Neto AMJC. Intermolecular interactions between DNA and methamphetamine, amphetamine, ecstasy and their major metabolites. J Biomol Struct Dyn 2017; 36:3047-3057. [PMID: 28978251 DOI: 10.1080/07391102.2017.1386592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this work, we carried out a theoretical investigation regarding amphetamine-type stimulants, which can cause central nervous system degeneration, interacting with human DNA. These include amphetamine, methamphetamine, 3,4-Methylenedioxymethamphetamine (also known as ecstasy), as well as their main metabolites. The studies were performed through molecular docking and molecular dynamics simulations, where molecular interactions of the receptor-ligand systems, along with their physical-chemical energies, were reported. Our results show that 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine (ecstasy) present considerable reactivity with the receptor (DNA), suggesting that these molecules may cause damage due to human-DNA. These results were indicated by free Gibbs change of bind (ΔGbind) values referring to intermolecular interactions between the drugs and the minor grooves of DNA, which were predominant for all simulations. In addition, it was observed that 3,4-Dihydroxymethamphetamine (ΔGbind = -13.15 kcal/mol) presented greater spontaneity in establishing interactions with DNA in comparison to 3,4-Methylenedioxymethamphetamine (ΔGbind = -8.61 kcal/mol). Thus, according with the calculations performed our results suggest that the 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine have greater probability to provide damage to human DNA fragments.
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Affiliation(s)
- Arthur F V F Reis
- a Laboratory of Preparation and Computation of Nanomaterial , Faculty of Physics-ICEN-Federal University of Pará , Augusto Correa Street N°.1 C. P. 479, 66075-110 Belém , PA , Brazil.,b Federal University of Pará , Institute of Exact and Natural Sciences, Faculty of Chemistry . Augusto Correa Street, 01, Guamá66075-110, Belém , PA , Brazil
| | - Igor L P Gonçalves
- a Laboratory of Preparation and Computation of Nanomaterial , Faculty of Physics-ICEN-Federal University of Pará , Augusto Correa Street N°.1 C. P. 479, 66075-110 Belém , PA , Brazil.,b Federal University of Pará , Institute of Exact and Natural Sciences, Faculty of Chemistry . Augusto Correa Street, 01, Guamá66075-110, Belém , PA , Brazil
| | - Abel F G Neto
- a Laboratory of Preparation and Computation of Nanomaterial , Faculty of Physics-ICEN-Federal University of Pará , Augusto Correa Street N°.1 C. P. 479, 66075-110 Belém , PA , Brazil
| | - Alberdan S Santos
- b Federal University of Pará , Institute of Exact and Natural Sciences, Faculty of Chemistry . Augusto Correa Street, 01, Guamá66075-110, Belém , PA , Brazil
| | - Kamil Kuca
- c Biomedical Research Center , University Hospital Hradec Kralove , Sokolska 581, 500 05 Hradec Kralove , Czech Republic.,d Department of Chemistry, Faculty of Science , University of Hradec Kralove , Rokitanskeho 62, 500 03 Hradec Kralove , Czech Republic
| | - Eugenie Nepovimova
- c Biomedical Research Center , University Hospital Hradec Kralove , Sokolska 581, 500 05 Hradec Kralove , Czech Republic.,d Department of Chemistry, Faculty of Science , University of Hradec Kralove , Rokitanskeho 62, 500 03 Hradec Kralove , Czech Republic
| | - Antonio M J C Neto
- a Laboratory of Preparation and Computation of Nanomaterial , Faculty of Physics-ICEN-Federal University of Pará , Augusto Correa Street N°.1 C. P. 479, 66075-110 Belém , PA , Brazil
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