1
|
Bento MA, Gomes T, Martins FF, Gil A, Ferreira LP, Barroso S, Gomes CSB, Garcia Y, Martinho PN. The role of intermolecular interactions in [Fe(X-salEen) 2]ClO 4 spin crossover complexes. Dalton Trans 2024; 53:8791-8802. [PMID: 38713065 DOI: 10.1039/d4dt00400k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Two new spin crossover (SCO) Fe(III) compounds were prepared, their structures were analysed and their magnetic properties were investigated. An exhaustive analysis of the effects of halogen substitution and aromatic ring functionalisation on the magnetic properties of non-solvated Fe(III) perchlorate complexes has been performed. Through comparative analysis, different magnetic profiles were found for the compounds studied, namely F (1), Cl (2), H (3), Br (4a, 4b), and I (5). Using tools like Hirshfeld analysis, the study revealed patterns in octahedral distortions and deviations from the ideal octahedral geometry. The SCO phenomenon as the conducting wire in this study, emphasises the influence of intermolecular interactions on the low spin (LS) to high spin (HS) transitions in these halogen-substituted complexes. The prevalence of H⋯H contributions has been demonstrated, albeit being the weakest and an inverse strength relationship in H⋯X interactions ranging from F to I. The findings not only interpret the intricate balance between halogen substitution, functionalisation, and intermolecular interactions in modulating magnetic properties but also direct future works in designing similar molecular systems.
Collapse
Affiliation(s)
- Marcos A Bento
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Tiago Gomes
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Frederico F Martins
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Adrià Gil
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Departament de Química, Física i Ciències Ambientals i del Sòl, ETSEA - Escola Tècnica Superior d'Enginyeria Agrària, Universitat de Lleida, Av. de l'alcalde Rovira Roure, 191, E25198, Lleida, Catalunya, Spain
| | - Liliana P Ferreira
- Department of Physics, University of Coimbra, 3004-516 Coimbra, Portugal
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C8, 1749-016 Lisboa, Portugal
| | - Sónia Barroso
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- i4HB, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Clara S B Gomes
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Yann Garcia
- Institute of Condensed Matter and Nanosciences, Molecular Chemistry, Materials and Catalysis (IMCN/MOST), Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Paulo N Martinho
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| |
Collapse
|
2
|
Miranda TG, Ciribelli NN, Bihain MFR, Santos Pereira AKD, Cavallini GS, Pereira DH. Interactions between DNA and the acridine intercalator: A computational study. Comput Biol Chem 2024; 109:108029. [PMID: 38387123 DOI: 10.1016/j.compbiolchem.2024.108029] [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: 12/15/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Cancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and makes replication impossible. In this context, this study aimed to computationally investigate how acridine intercalators interact with DNA by evaluating the mechanism of interactions, binding, and interaction energies using quantum mechanics calculations. Molecular electrostatic potential (MEP) analysis revealed that acridine has well- distributed negative charges in the center of the molecule, indicative of a dominant electron-rich region. Acridine exhibits well-defined π orbitals (HOMO and LUMO) on the aromatic rings, suggesting that charge transfer occurs within the molecule and may be responsible for the pharmacological activity of the compound. Structural analysis revealed that acridine interacts with DNA mainly through hydrogen bonds between HAcridine… ODNA with bond lengths ranging from 2.370 Å to 3.472 Å. The Binding energy (ΔEBind) showed that acridine interacts with DNA effectively for all complexes and the electronic energy results (E+ZPE) for complexes revealed that the complexes are more stable when the DNA-centered acridine molecule. The Laplacian-analysis topological QTAIM parameter (∇2ρ(r)) and total energy (H(r)) categorized the interactions as being non-covalent in nature. The RGD peak distribution in the NCI analysis reveals the presence of van der Waals interactions, predominantly between the intercalator and DNA. Accordingly, we confirm that acridine/DNA interactions are relevant for understanding how the intercalator acts within nucleic acids.
Collapse
Affiliation(s)
- Thaynara Guimarães Miranda
- Programa de Pós Graduação em Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | - Nicolas Nascimento Ciribelli
- Programa de Pós Graduação em Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | | | - Anna Karla Dos Santos Pereira
- Programa de Pós Graduação em Química, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | - Grasiele Soares Cavallini
- Programa de Pós Graduação em Química, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil
| | - Douglas Henrique Pereira
- Programa de Pós Graduação em Biotecnologia, Universidade Federal do Tocantins (UFT), Gurupi, Tocantins CEP 77.402-970, Brazil; Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), Praça Marechal Eduardo Gomes, 50, Vila das Acácias, São José dos Campos SP CEP 12228-900, Brazil.
| |
Collapse
|
3
|
Ortiz de Luzuriaga I, Sánchez-González Á, Synoradzki W, Lopez X, Gil A. Unravelling the binding affinity and selectivity of molybdenum(II) phenanthroline complexes with DNA G-quadruplexes by using linear-scaling DFT studies. The important role of ancillary ligands. Phys Chem Chem Phys 2022; 24:25918-25929. [PMID: 36260061 DOI: 10.1039/d2cp02241a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We have used near linear-scaling density functional theory (LS-DFT) methods including dispersion, for the first time, to study the interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with the DNA G-quadruplexes (GQ) to gain insight into its cytotoxicity. The LMKLL/DZDP level of calculation, which includes van der Waals contributions, with the SIESTA software was used to treat by means of first-principles computations the whole biological studied model system with ∼1000 atoms. Computed formation energies point to systems containing the Ax isomer as the most stable although the nearest system in energy containing the Eq isomer is only 7.5 kcal mol-1 above. On the other hand, the energy decomposition analysis (EDA) favours interaction energies for the systems containing the Eq isomer. However, when solvent effects are taken into account the systems containing the Ax isomer are again the most stable. This Ax isomer was found interacting by means of end-stacking with the GQ and surprisingly totally inside the non-canonical secondary structure, where all the ligands of the metal complex produce several weak interactions with the DNA structure. On the other hand, the Eq isomer prefers to interact from outside by means of intercalation in which the ancillary ligands also have some role in the interaction. Such features and comparison with the results regarding the interaction of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with duplex DNA suggest that the [Mo(η3-C3H5)Br(CO)2(phen)] would have a higher affinity and eventual selectivity for non-canonical DNA GQ structures.
Collapse
Affiliation(s)
- Iker Ortiz de Luzuriaga
- CIC-nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018, Donostia - San Sebastián, Euskadi, Spain.
- Polímero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, 20080, Donostia, Euskadi, Spain
| | - Ángel Sánchez-González
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Wojciech Synoradzki
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Xabier Lopez
- Polímero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, 20080, Donostia, Euskadi, Spain
- Donostia International Physics Center (DIPC), P. K. 1072, 20080, Donostia, Euskadi, Spain
| | - Adrià Gil
- CIC-nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018, Donostia - San Sebastián, Euskadi, Spain.
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
- ARAID Foundation, Zaragoza, Spain
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) - Consejo Superior de Investigaciones Científicas (CSIC). Universidad de Zaragoza, c/Pedro Cerbuna 12, 50009, Zaragoza, Spain
| |
Collapse
|
4
|
Esteves T, Ferreira FA, Mota AT, Sánchez-González Á, Gil A, Andrade KH, Afonso CAM, Ferreira FC. Greener Strategy for Lupanine Purification from Lupin Bean Wastewaters Using a Molecularly Imprinted Polymer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:18910-18921. [PMID: 35420019 PMCID: PMC9773177 DOI: 10.1021/acsami.2c02053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lupanine is an alkaloid used in the pharma industry as a building block or precursor in the synthesis of sparteine and also explored for drug synthesis in the pharma industry as a chiral selector. This alkaloid is found in lupin bean processing wastewaters originated from the debittering process to make these beans edible. In this work, a computational chemistry approach was taken to design molecularly imprinted polymers (MIPs) selecting itaconic acid, a biobased building block, as a functional monomer that can provide higher affinities for lupanine. MIP-1 was prepared using lupanine as the template, itaconic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linker by bulk polymerization. Lupanine was concentrated from lupin bean wastewater by nanofiltration, extracted with ethyl acetate, and purified using the synthesized MIP. MIP-1 was able to selectively recognize lupanine and improve the purity of lupanine from 78 to 88%, with 82% recovery of the alkaloid. These results show the potential application of this strategy to render the industrial process more sustainable.
Collapse
Affiliation(s)
- Teresa Esteves
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- . Phone: +351 218419167
| | - Flávio A. Ferreira
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| | - Ana Teresa Mota
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| | - Ángel Sánchez-González
- Centro
de Química e Bioquímica and BioISI—Biosystems
and Integrative Sciences Institute, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Adrià Gil
- Centro
de Química e Bioquímica and BioISI—Biosystems
and Integrative Sciences Institute, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Késsia H.
S. Andrade
- Research
Institute for Medicine (iMED, ULisboa); Faculty of Pharmacy, Universidade de Lisboa, Avenida Prof. Gama Pinto, Lisboa 1649-003, Portugal
| | - Carlos A. M. Afonso
- Research
Institute for Medicine (iMED, ULisboa); Faculty of Pharmacy, Universidade de Lisboa, Avenida Prof. Gama Pinto, Lisboa 1649-003, Portugal
| | - Frederico Castelo Ferreira
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, Lisboa 1049-001, Portugal
| |
Collapse
|
5
|
Sánchez-González Á, Grenut P, Gil A. Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone. J Comput Chem 2022; 43:804-821. [PMID: 35297513 PMCID: PMC9313584 DOI: 10.1002/jcc.26836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022]
Abstract
The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH2. The trends in the energy decomposition analysis for the interaction energy, ΔEint, showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp. Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal
| | - Pierre Grenut
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal
| | - Adrià Gil
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal.,ARAID Foundation, Zaragoza, Spain.,Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC-Universidad de Zaragoza, c/ Pedro Cerbuna 12, Zaragoza, Spain
| |
Collapse
|
6
|
Vaishnavi BJ, Sujith S, Rajashekhar Vaibhava KM, Bhat PJ, Vetrivel R, Shanbhag GV. Selective synthesis of furfuryl acetate over solid acid catalysts and active site exploration using density functional theory. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00334a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfated zirconia is reported to be an efficient catalyst to make furfuryl acetate via esterification. This study is an integration of experimental and DFT that correlates the hydrogen removal energy with catalytic activity.
Collapse
Affiliation(s)
- B. J. Vaishnavi
- Materials Science and Catalysis Division, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India
| | - S. Sujith
- Materials Science and Catalysis Division, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
| | - K. M. Rajashekhar Vaibhava
- Center for Quantum and Computational Studies, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
| | - P. Jyothi Bhat
- Materials Science and Catalysis Division, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
| | - Rajappan Vetrivel
- Center for Quantum and Computational Studies, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
| | - Ganapati V. Shanbhag
- Materials Science and Catalysis Division, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
- Center for Quantum and Computational Studies, Poornaprajna Institute of Scientific Research, Bidalur, Devanahalli, Bengaluru, 562164, India
| |
Collapse
|
7
|
Zeng Z, Cai J, Li F, Weng Y, Huang Q, Yang H, Huang Q, Wei Y. Synthesis, crystal structures, DNA interactions, and antitumor activity of two new dinuclear copper(ii) complexes with thiazole ligand. RSC Adv 2021; 11:40040-40050. [PMID: 35494110 PMCID: PMC9044605 DOI: 10.1039/d1ra05798g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/01/2021] [Indexed: 12/24/2022] Open
Abstract
Two new dinuclear copper(ii) complexes, [Cu(ambt)2(cnba)4] (1) and [Cu(ambt)2(clba)4] (2) were synthesized with 2-amino-6-methoxybenzothiazole (ambt) as the main ligand. The structures of the two complexes were characterized by single-crystal XRD. The binding between CT-DNA (calf thymus DNA) and the complexes was evaluated by viscometry, electronic absorption, and fluorescence spectroscopy, and the binding constants were calculated using the Stern-Volmer equation. The complexes were intercalatively bound to CT-DNA, and [Cu(ambt)2(clba)4] having a greater binding constant than [Cu(ambt)2(cnba)4]. The two complexes had better antitumor properties against HepG2 (human hepatocellular carcinoma), A549 (human lung carcinoma), and HeLa (human cervical carcinoma) tumor cell lines than their respective ligands and cisplatin. Furthermore, [Cu(ambt)2(clba)4] had a stronger inhibitory ability on the three types of tumor cells than [Cu(ambt)2(cnba)4], which is congruent with the binding power of the complexes with DNA. Flow cytometry revealed that [Cu(ambt)2(cnba)4] and [Cu(ambt)2(clba)4] could trigger apoptosis or necrosis, arrest the HepG2 cell cycles, and cause G0/G1-phase cells to accumulate.
Collapse
Affiliation(s)
- Zhenfang Zeng
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Jiehui Cai
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Fuyan Li
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Yanying Weng
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Qiuping Huang
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Honglan Yang
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Qiuchan Huang
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| | - Youhuan Wei
- School of Chemical and Biological Engineering, Guangxi Normal University for Nationalities 23 Fozi Road Chongzuo 532200 PR China +86-771-787-0799 +86-771-787-0799
| |
Collapse
|
8
|
Sánchez-González Á, Castro TG, Melle-Franco M, Gil A. From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA. Phys Chem Chem Phys 2021; 23:26680-26695. [PMID: 34825685 DOI: 10.1039/d1cp04529f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]2+ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)2 DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Adrià Gil
- Centro de Química e Bioquímica and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 1749-016, Lisboa, Portugal. .,CIC nanoGUNE BRTA, Tolosa Hiribidea 76, E-20018 Donostia - San Sebastian, Euskadi, Spain
| |
Collapse
|
9
|
Li N, Gao Y, Qiu F, Zhu T. Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes. Molecules 2021; 26:5379. [PMID: 34500812 PMCID: PMC8434458 DOI: 10.3390/molecules26175379] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/29/2022] Open
Abstract
G-quadruplexes have drawn widespread attention for serving as a potential anti-cancer target and their application in material science. Molecular dynamics (MD) simulation is the key theoretical tool in the study of GQ's structure-function relationship. In this article, we systematically benchmarked the five force fields of parmbsc0, parmbsc1, OL15, AMOEBA, and Drude2017 on the MD simulation of G-quadruplex from four aspects: structural stability, central ion channel stability, description of Hoogsteen hydrogen bond network, and description of the main chain dihedral angle. The results show that the overall performance of the Drude force field is the best. Although there may be a certain over-polarization effect, it is still the best choice for the MD simulation of G-quadruplexes.
Collapse
Affiliation(s)
- Na Li
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China;
| | - Ya Gao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Feng Qiu
- Institute of Artificial Intelligence on Education, Shanghai Normal University, Shanghai 200234, China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China;
- NYU-ECNU Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| |
Collapse
|
10
|
Sánchez-González Á, Bandeira NAG, Ortiz de Luzuriaga I, Martins FF, Elleuchi S, Jarraya K, Lanuza J, Lopez X, Calhorda MJ, Gil A. New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes. Molecules 2021; 26:4737. [PMID: 34443326 PMCID: PMC8397986 DOI: 10.3390/molecules26164737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Nuno A. G. Bandeira
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
| | - Frederico F. Martins
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Jose Lanuza
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Maria José Calhorda
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Adrià Gil
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
| |
Collapse
|
11
|
Veclani D, Tolazzi M, Cerón-Carrasco JP, Melchior A. Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action. J Chem Inf Model 2021; 61:4391-4399. [PMID: 34156233 PMCID: PMC8479807 DOI: 10.1021/acs.jcim.1c00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Phenanthriplatin
(PtPPH) is a monovalent platinum(II)-based complex
with a large cytotoxicity against cancer cells. Although the aqua-activated
drug has been assumed to be the precursor for DNA damage, it is still
under debate whether the way in which that metallodrug attacks to
DNA is dominated by a direct binding to a guanine base or rather by
an intercalated intermediate product. Aiming to capture the mechanism
of action of PtPPH, the present contribution used theoretical tools
to systematically assess the sequence of all possible mechanisms on
drug activation and reactivity, for example, hydrolysis, intercalation,
and covalent damage to DNA. Ab initio quantum mechanical
(QM) methods, hybrid QM/QM′ schemes, and independent gradient
model approaches are implemented in an unbiased protocol. The performed
simulations show that the cascade of reactions is articulated in three
well-defined stages: (i) an early and fast intercalation of the complex
between the DNA bases, (ii) a subsequent hydrolysis reaction that
leads to the aqua-activated form, and (iii) a final formation of the
covalent bond between PtPPH and DNA at a guanine site. The permanent
damage to DNA is consequently driven by that latter bond to DNA but
with a simultaneous π–π intercalation of the phenanthridine
into nucleobases. The impact of the DNA sequence and the lateral backbone
was also discussed to provide a more complete picture of the forces
that anchor the drug into the double helix.
Collapse
Affiliation(s)
- Daniele Veclani
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - Marilena Tolazzi
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - José P Cerón-Carrasco
- Reconocimiento y Encapsulación Molecular, Universidad Católica San Antonio de Murcia (UCAM). Campus de los Jerónimos, 30107 Murcia, Spain
| | - Andrea Melchior
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| |
Collapse
|
12
|
Vermeeren P, Hamlin TA, Bickelhaupt FM. Chemical reactivity from an activation strain perspective. Chem Commun (Camb) 2021; 57:5880-5896. [PMID: 34075969 PMCID: PMC8204247 DOI: 10.1039/d1cc02042k] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Chemical reactions are ubiquitous in the universe, they are at the core of life, and they are essential for industrial processes. The drive for a deep understanding of how something occurs, in this case, the mechanism of a chemical reaction and the factors controlling its reactivity, is intrinsically valuable and an innate quality of humans. The level of insight and degree of understanding afforded by computational chemistry cannot be understated. The activation strain model is one of the most powerful tools in our arsenal to obtain unparalleled insight into reactivity. The relative energy of interacting reactants is evaluated along a reaction energy profile and related to the rigidity of the reactants' molecular structure and the strength of the stabilizing interactions between the deformed reactants: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). Owing to the connectedness between the activation strain model and Kohn-Sham molecular orbital theory, one is able to obtain a causal relationship between both the sterics and electronics of the reactants and their mutual reactivity. Only when this is accomplished one can eclipse the phenomenological explanations that are commonplace in the literature and textbooks and begin to rationally tune and optimize chemical transformations. We showcase how the activation strain model is the ideal tool to elucidate fundamental organic reactions, the activation of small molecules by metallylenes, and the cycloaddition reactivity of cyclic diene- and dipolarophiles.
Collapse
Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
13
|
Sánchez-González Á, Gil A. Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions. RSC Adv 2021; 11:1553-1563. [PMID: 35424132 PMCID: PMC8693566 DOI: 10.1039/d0ra07646e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Flat molecules like phenanthroline derivatives intercalate between base pairs of deoxyribonucleic acid and produce cytotoxic effects against tumoral cells. Elucidating the way of intercalation and its modulation on their efficiency by substitution still remains a challenging topic of research. In this work we analysed the intercalation via the major groove of methylated derivatives of phenanthroline, in different number and position, between guanine-cytosine base pairs. We studied our systems by using semi-empirical methods and density functional theory including dispersion corrections with the PM6-DH2 Hamiltonian and the B3LYP-D3 functional. We explored the geometry and electronic structure by means of the quantum theory of atoms in molecules and non-covalent interactions index analyses, whereas the interaction energy was estimated by means of two different approaches: one taking into account the results from the quantum theory of atoms in molecules analysis and the other based on the so-called energy decomposition analysis. The effect of solvation was also taken into consideration. Our studies show that CH/π and CH/n interactions by means of the -CH3 groups of methylated phen follow a clear pattern for any number of -CH3 groups and their position in the methylated phen ligand. That is, they try to produce the CH/π and CH/n interactions with the O and N heteroatoms of the base pairs and with the O atoms of the sugar and phosphate backbone. These findings suggest that the modulation of the intercalation of ligands that are able to form CH/π and CH/n weak interactions with the deoxyribonucleic acid is ruled not only by the number and position of the substitutions of the ligands but also by some key sites, which are the O and N atoms of the deoxyribonucleic acid in our analysed systems. It suggests some key and lock mechanism in which the interacting fragments fit like puzzle pieces in order to achieve the optimal interaction for the stabilization of the system. Interaction energies were calculated by using different approaches which converged to similar trends about the number and position of the -CH3 groups. The important weight of the CH/H interactions in the total interaction energy must be highlighted.
Collapse
Affiliation(s)
- Ángel Sánchez-González
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande 1749-016 Lisboa Portugal
| | - Adrià Gil
- BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa Campo Grande 1749-016 Lisboa Portugal
- CIC nanoGUNE BRTA Tolosa Hiribidea 76 E-20018 Donostia - San Sebastian Euskadi Spain
| |
Collapse
|
14
|
Sánchez-Lara E, García-García A, González-Vergara E, Cepeda J, Rodríguez-Diéguez A. Magneto-structural correlations of cyclo-tetravanadates functionalized with mixed-ligand copper(ii) complexes. NEW J CHEM 2021. [DOI: 10.1039/d0nj06004f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bimetallic materials based on tetravanadate anions and mixed ligand copper(ii) complexes were readily synthesized under non-hydrothermal conditions. The compounds show interesting structural and magnetic diversity mediated by copper symmetry.
Collapse
Affiliation(s)
- Eduardo Sánchez-Lara
- Instituto de Ciencias
- Benemérita Universidad Autónoma de Puebla
- Colonia San Manuel
- Puebla
- Mexico
| | - Amalia García-García
- Departamento de Química Inorgánica
- Facultad de Ciencias
- Universidad de Granada
- Avda. Fuentenueva
- 18071 Granada
| | | | - Javier Cepeda
- Departamento de Química Aplicada
- Facultad de Química
- Universidad del País Vasco UPV/EHU
- 20018 Donostia-San Sebastián
- Spain
| | - Antonio Rodríguez-Diéguez
- Departamento de Química Inorgánica
- Facultad de Ciencias
- Universidad de Granada
- Avda. Fuentenueva
- 18071 Granada
| |
Collapse
|