1
|
Moreno-Ceballos A, Caballero NA, Castro ME, Perez-Aguilar JM, Mammino L, Melendez FJ. In Silico Approach: Anti-Tuberculosis Activity of Caespitate in the H37Rv Strain. Curr Issues Mol Biol 2024; 46:6489-6507. [PMID: 39057029 PMCID: PMC11275643 DOI: 10.3390/cimb46070387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024] Open
Abstract
Tuberculosis is a highly lethal bacterial disease worldwide caused by Mycobacterium tuberculosis (Mtb). Caespitate is a phytochemical isolated from Helichrysum caespititium, a plant used in African traditional medicine that shows anti-tubercular activity, but its mode of action remains unknown. It is suggested that there are four potential targets in Mtb, specifically in the H37Rv strain: InhA, MabA, and UGM, enzymes involved in the formation of Mtb's cell wall, and PanK, which plays a role in cell growth. Two caespitate conformational structures from DFT conformational analysis in the gas phase (GC) and in solution with DMSO (CS) were selected. Molecular docking calculations, MM/GBSA analysis, and ADME parameter evaluations were performed. The docking results suggest that CS is the preferred caespitate conformation when interacting with PanK and UGM. In both cases, the two intramolecular hydrogen bonds characteristic of caespitate's molecular structure were maintained to achieve the most stable complexes. The MM/GBSA study confirmed that PanK/caespitate and UGM/caespitate were the most stable complexes. Caespitate showed favorable pharmacokinetic characteristics, suggesting rapid absorption, permeability, and high bioavailability. Additionally, it is proposed that caespitate may exhibit antibacterial and antimonial activity. This research lays the foundation for the design of anti-tuberculosis drugs from natural sources, especially by identifying potential drug targets in Mtb.
Collapse
Affiliation(s)
- Andrea Moreno-Ceballos
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| | - Norma A. Caballero
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Edif. BIO1, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico
| | - María Eugenia Castro
- Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Complejo de Ciencias, ICUAP, Edif. IC10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico;
| | - Jose Manuel Perez-Aguilar
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| | - Liliana Mammino
- School of Mathematical and Natural Science, University of Venda, Thohoyandou 0950, South Africa;
| | - Francisco J. Melendez
- Laboratorio de Química Teórica, Centro de Investigación, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Edif. FCQ10, 22 Sur y San Claudio, Ciudad Universitaria, Col. San Manuel, Puebla C.P. 72570, Mexico; (A.M.-C.); (J.M.P.-A.)
| |
Collapse
|
2
|
Hydrogen bonding between 1-ethyl-3-methyl-imidazolium dicyanamide ionic liquid and selected co-solvents with varying polarity: A DFT study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
3
|
Influence of temperature and concentration on the molecular interactions of pyrrolidinium-based ionic liquid with water and alcohols: An experimental and DFT studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Mammino L. Conformational preferences and intramolecular hydrogen bonding patterns of tetraflavaspidic acid BBBB – a tetrameric acylphloroglucinol. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Tetraflavaspidic acid BBBB is a tetrameric acylphloroglucinol of natural origin isolated from Dryopteris aitoniana. Its molecule consists of four acylphloroglucinol units linked by methylene bridges and having the same R = propyl in their R−C=O groups. In one of the terminal monomers, one of the OHs ortho to R−C=O is replaced by a keto O. The paper reports the results of a conformational study performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels; two options are utilised for the latter, without and with the inclusion of the Grimme’s dispersion correction. Given the importance of intramolecular hydrogen bonds (IHBs) for the stabilisation of acylphloroglucinol conformers, only conformers containing the maximum IHBs’ number were calculated. The IHBs comprise an IHB between the sp2 O of R−C=O and a neighbouring OH in each monomeric unit and two inter-monomer IHBs between each pair of units. The single C−C bonds of the methylene bridges enable a variety of mutual orientations of the monomeric units, giving rise to a variety of conformations and IHB patterns. The results indicate greater stability for conformers in which individual monomers take lower energy conformations, and significant influence of the dispersion correction on the estimation of the energetics and of other molecular properties. The inclusion of the dispersion correction also strongly limits the number of low energy conformers. The influence of dispersion effects is consistent with the presence of four aromatic rings.
Collapse
Affiliation(s)
- Liliana Mammino
- School of Mathematical and Natural Sciences , University of Venda , Thohoyandou , South Africa
| |
Collapse
|
5
|
Abstract
Trimeric acylphloroglucinols (T-ACPLs) are a subclass of the large class of acylphloroglucinols—derivatives of 1,3,5-trihydroxybenzene containing an R–C=O group. T-ACPL molecules contain three acylphloroglucinol moieties linked by methylene bridges. Many of them are present in natural sources and exhibit biological activities, often better than the corresponding activities of monomeric acylphloroglucinols. All the stable conformers of T-ACPLs contain seven intramolecular hydrogen bonds, which constitute the dominant stabilising factors. A total of 38 different T-ACPLs, including both naturally occurring and model molecules, have been calculated at the HF and DFT/B3LYP levels. The DFT/B3LYP calculations were carried out both without and with Grimme’s dispersion correction, to highlight the dispersion (and, therefore, also electron correlation) effects for these molecules. The roles of dispersion are evaluated considering the effects of Grimme’s correction on the estimation of the conformers’ energies, the description of the characteristics of the individual hydrogen bonds, the conformers’ geometries and other molecular properties. Overall, the results offer a comprehensive overview of the conformational preferences of T-ACPL molecules, their intramolecular hydrogen bond patterns, and the correlation effects on their properties.
Collapse
|
6
|
Arteaga-Ballesteros BE, Guevara-Morales A, Martín-Martínez ES, Figueroa-López U, Vieyra H. Composite of polylactic acid and microcellulose from kombucha membranes. E-POLYMERS 2020. [DOI: 10.1515/epoly-2021-0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Polylactic acid (PLA) is one of the main components of biodegradable and biocompatible composites. Bacterial cellulose from kombucha membranes is an excellent candidate to be used as a natural filler of eco-composites because it is renewable, has low cost, low density, and acceptable specific strength properties, and is biodegradable. The study aimed to prepare composites of PLA and bacterial cellulose to produce a biodegradable and compostable material. The bacterial microcellulose was obtained from kombucha membranes and blended with PLA by extrusion. The composites contained a PLA with 1%, 3%, and 5% of cellulose. We characterized the PLA, bacterial microcellulose, and composites to ascertain their size and aspect, degree of crystallinity, distribution of the cellulose into PLA, and their mechanical properties. We observed an increase in crystallinity proportional to the cellulose content for the blends and found that the 3% cellulose blend withstands the stress of up to 40 MPa and temperatures up to 120°C before distortion.
Collapse
Affiliation(s)
- Bárbara Estefanía Arteaga-Ballesteros
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Carretera Lago de Guadalupe, Km. 3.5, Colonia Margarita Maza de Juárez, Atizapán de Zaragoza , Estado de México , 52926 , México
| | - Andrea Guevara-Morales
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Carretera Lago de Guadalupe, Km. 3.5, Colonia Margarita Maza de Juárez, Atizapán de Zaragoza , Estado de México , 52926 , México
| | - Eduardo San Martín-Martínez
- Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Legaria 694 , Colonia Irrigación C.P. 11500 , Ciudad de México
| | - Ulises Figueroa-López
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Carretera Lago de Guadalupe, Km. 3.5, Colonia Margarita Maza de Juárez, Atizapán de Zaragoza , Estado de México , 52926 , México
| | - Horacio Vieyra
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Eduardo Monroy Cárdenas 2000, San Antonio Buenavista, Toluca de Lerdo , Estado de México , 50110 , México
| |
Collapse
|
7
|
Mammino L. Tube-shaped molecular structures built from acylphloroglucinols: an ab initio and DFT study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1784477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Liliana Mammino
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
| |
Collapse
|
8
|
Mammino L. Stacking interactions in cavity-containing molecular structures built from acylphloroglucinols: a computational study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1800852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Liliana Mammino
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
| |
Collapse
|
9
|
Mammino L. Five- and six-member bowl-shaped structures from acylphloroglucinols: an ab initio and DFT study. J Mol Model 2019; 26:13. [PMID: 31838594 DOI: 10.1007/s00894-019-4208-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/12/2019] [Indexed: 11/29/2022]
Abstract
Molecular structures containing bowl-shaped cavities are interesting for purposes such as hosting molecules or metal ions. Acylphloroglucinols are derivatives of phloroglucinol (1,3,5-trihydroxybenzene) containing a CRO group. A previous study had considered bowl-shaped structures consisting of 3 or 4 identical acylphloroglucinol units linked by methylene bridges, selecting representative R chains and including also a structure with phloroglucinol units. The presence of three 'binding' levels between neighbouring units (consecutive hydrogen bonds in the lower rim, the methylene bridges at intermediate level, and another set of hydrogen bonds in the upper rim) makes these bowls 'deeper' than bowls from other hydroxybenzenes. The current study considers larger bowls, consisting of 5 and 6 identical units, to investigate how the molecular properties change with the increase in the size of the bowl. The monomeric units are the same as in the previous study, and the levels of theory are the same as in the previous study, to enable meaningful comparisons. Like in the previous study, two conformers are considered for each bowl, differing by the orientation of the OH groups in the lower rim. Calculations were performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry, complemented by single-point MP2/HF/6-31G(d,p) calculations. The results show that the Cnv symmetry (with n being the number of constituting monomers) is maintained for 5-member bowls, while 6-member bowls do not show C6v symmetry but only C2v symmetry. The molecular properties of the calculated bowls are analysed in detail and also compared with the properties of the previously calculated 4- and 5-member bowls. Graphical abstract Bowls built from acylphloroglucinol units have three levels of intermonomer linkages: hydrogen bonds in the bottom rim, methylene bridges at intermediate level, and other hydrogen bonds in the upper rim. They are the deepest bowls that can be built from hydroxybenzene units.
Collapse
Affiliation(s)
- Liliana Mammino
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa.
| |
Collapse
|
10
|
Mammino L. Effects of complexation with a metal ion on the intramolecular hydrogen bonds in acylphloroglucinols. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Otukile KP, Kabanda MM. A DFT mechanistic, thermodynamic and kinetic study on the reaction of 1, 3, 5-trihydroxybenzene and 2, 4, 6-trihydroxyacetophenone with •OOH in different media. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical investigation on the reactions of 1, 3, 5-trihydroxybenzene (PG) and 2, 4, 6-trihydroxyacetophenone (ACPG) with •OOH has been performed with the aim of elucidating the peroxyl radical scavenging properties of PG and its acylated derivative. The study has considered the hydrogen atom transfer (HAT), the single electron transfer-proton transfer and the sequential proton loss-electron transfer mechanisms and determined the geometric, energetic and electronic properties of the reaction species as well as the kinetic parameters for the HAT mechanism. DFT/M06-2X, DFT/MPW1K and DFT/BHHLYP calculation methods have been utilized in combination with the 6-311++G(3df, 2p) basis set. The DFT methods were benchmarked using the CBS-QB3 method. Thermodynamic parameters such as bond dissociation enthalpy (BDE) and ionization energy suggest that the thermodynamically preferred mechanism is the HAT mechanism. The geometric, electronic and energetic parameters suggest that the preferred site for the abstraction of the free phenolic H atom in ACPG is the ortho position. Spin density and branching ratio values indicate that the most stable and preferable product formed is for the reaction of ACPG [Formula: see text] •OOH at the ortho position. The estimated rate constants obtained indicate that the reaction of ACPG [Formula: see text] •OOH is kinetically preferred to the reaction of PG [Formula: see text] •OOH, which is in agreement with experimental findings.
Collapse
Affiliation(s)
- Kgalaletso P. Otukile
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X 2046, Mmabatho 2735, South Africa
| | - Mwadham M. Kabanda
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM), Research Focus Area, Faculty of Natural and Agriculture Sciences, North-West University, Private Bag X 2046, Mmabatho 2735, South Africa
| |
Collapse
|
12
|
Otukile KP, Kabanda MM. A DFT mechanistic and kinetic study on the reaction of phloroglucinol with •OH in different media: Hydrogen atom transfer versus oxidation. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A theoretical study on the reaction of phloroglucinol with •OH has been performed with the aim of elucidating the geometric, energetic and kinetic properties of the reaction as well as identifying the preferred reaction pathway. Three reaction mechanisms have been considered, namely, direct hydrogen atom abstraction, addition–elimination mechanism in the absence and in the presence of a base catalyst and oxidation mechanism in the absence and in the presence of O2. The study has been performed using the DFT/M06[Formula: see text]2X, DFT/BHHLYP and DFT/MPW1K methods in conjunction with either the 6-31++G(d,p) or the 6-311++G(3df,2p) basis set. The energetic parameters are influenced by the type of function utilized and the media in which the calculation is done. The direct hydrogen abstraction mechanism provides the smallest branching ratio with respect to the •OH addition mechanisms. The PG + •OH reaction under atmospheric conditions saturated with O2 would predominantly form tetrahydroxybenzene; the predominant product within the biological system would largely depend on physiological conditions; under pH [Formula: see text] 7 and with oxygen dissolved within the biological system, the preferred product would be tetrahydroxybenzene; however, if the reaction takes place in some part of the biological system where the pH [Formula: see text] 7, the preferred product would be the phenoxyl radical.
Collapse
Affiliation(s)
- Kgalaletso P. Otukile
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X 2046, Mmabatho 2735, South Africa
| | - Mwadham M. Kabanda
- Department of Chemistry, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X2046, Mmabatho 2735, South Africa
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agriculture Sciences, North–West University, Private Bag X 2046, Mmabatho 2735, South Africa
| |
Collapse
|
13
|
Mammino L. Computational study of acylphloroglucinols: an investigation with many branches. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-0909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Abstract
Acylphloroglucinols (ACPLs) are a broad class of compounds structurally derived from phloroglucinol and characterised by the presence of a CRO group. They are interesting for their biological activities and their potentialities as lead compounds in drug development. The current review considers a series of works which, altogether, sum up to a systematic computational study of ACPLs in vacuo and in three solvents – chloroform, acetonitrile and water. An initial set of studies, focusing on ACPLs as a class and utilising an adequately representative selection of molecules, identified patterns in the conformational preferences and molecular properties of ACPLs, which appear valid for the whole class or for specific subclasses such as monomeric ACPLs, dimeric ACPLs, ACPLs with substituents containing C=C double bonds, etc. The validity of the identified patterns was further verified through the study of additional and significantly different ACPL molecules, as well as other molecular structures containing ACPL units. Furthermore, the computational study of ACPLs proved interesting for the insights into the factors stabilising their conformers, first of all intramolecular hydrogen bonding, which plays dominant roles in determining conformational preferences and energetics. The current review outlines the objectives, approaches and main results of these studies. The obtained information may be relevant for further studies aimed at a better understanding of the molecular bases of the biological activities of ACPLs.
Collapse
Affiliation(s)
- Liliana Mammino
- Department of Chemistry , University of Venda , Thohoyandou , South Africa
| |
Collapse
|
14
|
Mammino L. Complexes of Hyperguinones A and B with a Cu2+ Ion. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2018.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
15
|
Mammino L. Intramolecular hydrogen bonding patterns, conformational preferences and molecular properties of dimeric acylphloroglucinols: An ab initio and DFT study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
16
|
Complexes of 1-[3-geranyl-2,4,6-trihydroxyphenyl]-2-methylpropan-1-one with a Cu2+ ion: a DFT study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-018-2381-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
17
|
Computational study of mbandakamine A: a dimeric naphthylisoquinoline alkaloid with antimalarial activity. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2323-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
18
|
Mammino L. Complexes of arzanol with a Cu 2+ ion: a DFT study. J Mol Model 2017; 23:276. [PMID: 28900733 DOI: 10.1007/s00894-017-3443-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/15/2017] [Indexed: 11/29/2022]
Abstract
Arzanol (C22H26O7) is a naturally occurring acylphloroglucinol largely responsible for the anti-inflammatory, anti-oxidant, antibiotic and antiviral activities of Helichrysum italicum. Like all acylphloroglucinols, the molecule contains a carboxylic substituent (-COR group); for arzanol, this is a -COCH3 group. The molecule is further characterized by the presence of an α-pyrone ring bonded in meta to -COR through a methylene bridge, and of a prenyl chain bonded to the other meta position. The molecule can form up to three intramolecular hydrogen bonds (IHB) simultaneously, and their presence and patterns are the major stabilizing factors. This work considers complexes of representative conformers of arzanol with a Cu2+ ion, taking into account the different possibilities for the binding of the Cu2+ ion to the electron-density rich sites of the molecule and including simultaneous coordination to two geometrically suitable sites. Calculations were performed at the DFT/B3LYP level, using the 6-31+G(d,p) basis set for the C, O and H atoms and the LANL2DZ pseudopotential for the Cu2+ ion. Interaction energies show preference for simultaneous binding of Cu2+ to two sites. Simultaneous binding to the O of a phenol OH neighboring the prenyl chain and to the π bond of the prenyl chain appears to be the most favorable option, followed by simultaneous binding to the sp2 O of the α-pyrone ring and the O of the phenol OH ortho to -COR on the side of the α-pyrone ring. The charge of the Cu2+ ion is reduced to +1 or slightly less in the complexes, which is consistent with the molecules' antioxidant (reducing) ability. Graphical abstract The copper ion prefers to attach to two sites of the arzanol molecule simultaneously. The arzanol molecule reduces the charge of the copper ion from +2 to +1 by transferring an electron to it; it becomes a radical molecular cation. The distribution of the unpaired electron in the molecule (as highlighted by the spin density maps) depends on the site/s to which the Cu2+ ion binds and on the molecule's conformer.
Collapse
Affiliation(s)
- Liliana Mammino
- Department of Chemistry, University of Venda, Thohoyandou, South Africa.
| |
Collapse
|
19
|
Mammino L. Intramolecular Hydrogen Bonding and Conformational Preferences of Arzanol-An Antioxidant Acylphloroglucinol. Molecules 2017; 22:molecules22081294. [PMID: 28771203 PMCID: PMC6152391 DOI: 10.3390/molecules22081294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022] Open
Abstract
Arzanol is a naturally-occurring prenylated acylphloroglucinol isolated from Helichrysum italicum and exhibiting anti-oxidant, antibiotic and antiviral activities. The molecule contains an α-pyrone moiety attached to the phloroglucinol moiety through a methylene bridge. The presence of several hydrogen bond donor or acceptor sites makes intramolecular hydrogen bonding patterns the dominant stabilising factor. Conformers with all the possible different hydrogen bonding patterns were calculated at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry in vacuo and in three solvents—chloroform, acetonitrile and water (these levels being chosen to enable comparisons with previous studies on acylphloroglucinols). Calculations in solution were performed with the Polarisable Continuum Model. The results show that the lowest energy conformers have the highest number of stronger intramolecular hydrogen bonds. The influence of intramolecular hydrogen bonding patterns on the other molecular properties is also analysed.
Collapse
Affiliation(s)
- Liliana Mammino
- Department of Chemistry, University of Venda, Thohoyandou 0950, South Africa.
| |
Collapse
|
20
|
Affiliation(s)
- Liliana Mammino
- Department of Chemistry, University of Venda, Thohoyandou, South Africa
| |
Collapse
|
21
|
Bilonda MK, Mammino L. Intramolecular Hydrogen Bonds in Conformers of Quinine and Quinidine: An HF, MP2 and DFT Study. Molecules 2017; 22:E245. [PMID: 28178218 PMCID: PMC6155604 DOI: 10.3390/molecules22020245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/16/2016] [Accepted: 12/28/2016] [Indexed: 11/24/2022] Open
Abstract
Quinine is an alkaloid with powerful antimalarial activity, isolated from the bark of Peru's cinchona trees. Quinidine is an erythro diastereoisomer of quinine also exhibiting antimalarial activity. Conformational studies performed so far had never identified conformers with intramolecular hydrogen bonds (IHB). The current study shows the possibility of conformers with an IHB between the quinuclidine and quinoline moieties of these molecules. The study was performed at different levels of theory: Hartree Fock (HF) with the 6-31G(d,p) basis set, Density Functional Theory (DFT) with the B3LYP functional and the 6-31+G(d,p) basis set and Møller-Plesset Perturbation Theory (MP2) with the 6-31+G(d,p) basis set, to confirm the results. The results suggest that the stabilising effect of this IHB is weaker or comparable with respect to the stabilising effect of the preferred mutual orientation of the two moieties. Although the IHB-containing conformers may not be the lowest energy ones, their relative energy is sufficiently low for them to be included among the possible ones responsible for the compounds' antimalarial activity.
Collapse
Affiliation(s)
- Mireille K Bilonda
- Department of Chemistry, University of Venda, Thohoyandou 0950, South Africa.
| | - Liliana Mammino
- Department of Chemistry, University of Venda, Thohoyandou 0950, South Africa.
| |
Collapse
|
22
|
Optimizing Extraction of Cellulose and Synthesizing Pharmaceutical Grade Carboxymethyl Sago Cellulose from Malaysian Sago Pulp. APPLIED SCIENCES-BASEL 2016. [DOI: 10.3390/app6060170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
23
|
Investigating the properties of muchimangin B through comparisons with related and model structures. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
24
|
Computational study of naphthylisoquinoline alkaloids with antimalarial activity from Dioncophyllaceae and Ancistrodaceae in vacuo. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1843-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
25
|
Alfaro RAD, Gomez-Sandoval Z, Mammino L. Evaluation of the antiradical activity of hyperjovinol-A utilizing donor-acceptor maps. J Mol Model 2015; 20:2337. [PMID: 25069138 DOI: 10.1007/s00894-014-2337-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hyperjovinol-A ((2-methyl-1-(2,4,6-trihydroxy-3-(3-hydroxy-3,7-dimethyloct-6-enyl)phen yl)propan-1-one) is an acylated phloroglucinol isolated from Hypericum Jovis and exhibiting good antioxidant activity. The study investigates the compound’s antiradical ability on the basis of the electron-donor and electron-acceptor abilities of its conformers, deriving donor and acceptor indexes and mapping them in terms of donor-acceptor maps (DAM). The DAMs of vitamins C and E and of carotene astaxantine are used as comparison references. Calculations were performed at the DFT/BPW91/6-311+G(d,p) level, with optimizations on fully relaxed geometries to obtain the conformers of the neutral molecule in vacuo, and single point calculations to obtain the energies of the cationic and anionic species in vacuo and of the neutral, cationic, and anionic species in water, ethanol, and pentylethanoate. The calculations in solution utilized the polarizable continuum model (PCM). The results indicate that hyperjovinol-A may have better antiradical activity than vitamin C. This is in agreement with experimental results, showing that the antioxidant activity of hyperjovinol-A is comparable with that of the best drugs currently in clinical use. The activity is maintained in solution. The Fukui function f(·) was also calculated for all the conformers of hyperjovinol-A, to identify the regions of highest reactivity.
Collapse
|
26
|
Antioxidant and antimalarial properties of butein and homobutein based on their ability to chelate iron (II and III) cations: a DFT study in vacuo and in solution. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2520-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
27
|
A theoretical study of the antioxidant properties of phenolic acid amides investigated through the radical-scavenging and metal chelation mechanisms. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2484-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
28
|
A new approach in extracting active acylphloroglucinol derivatives from Dryopteris wallichiana and Elaphoglossum erinaceum. J Supercrit Fluids 2015. [DOI: 10.1016/j.supflu.2015.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
29
|
Orlenko EV, Latychevskaia T, Evstafev AV, Orlenko FE. Invariant time-dependent exchange perturbation theory and its application to the particles collision problem. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1646-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
30
|
Antioxidant Properties of Kanakugiol Revealed Through the Hydrogen Atom Transfer, Electron Transfer and M2+ (M2+ = Cu(II) or Co(II) Ion) Coordination Ability Mechanisms. A DFT Study In Vacuo and in Solution. FOOD BIOPHYS 2015. [DOI: 10.1007/s11483-015-9397-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
31
|
Mammino L, Bilonda MK. Computational study of antimalarial pyrazole alkaloids from Newbouldia laevis. J Mol Model 2014; 20:2464. [DOI: 10.1007/s00894-014-2464-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 09/07/2014] [Indexed: 11/27/2022]
|
32
|
Kabanda MM, Tran VT, Seema KM, Serobatse KR, Tsiepe TJ, Tran QT, Ebenso EE. Conformational, electronic and antioxidant properties of lucidone, linderone and methyllinderone: DFT, QTAIM and NBO studies. Mol Phys 2014. [DOI: 10.1080/00268976.2014.969343] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
33
|
Kabanda MM, Tran VT, Tran QT, Ebenso EE. A computational study of pyrazinamide: Tautomerism, acid–base properties, micro-solvation effects and acid hydrolysis mechanism. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
34
|
Kabanda MM, Mammino L, Murulana LC, Mwangi HM, Mabusela WT. Antioxidant Radical Scavenging Properties of Phenolic Pent-4-En-1-Yne Derivatives Isolated FromHypoxis Rooperi. A DFT Studyin vacuoand in Solution. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2014. [DOI: 10.1080/10942912.2013.825842] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
35
|
Kabanda MM, Ebenso EE. MP2, DFT and DFT-D study of the dimers of diazanaphthalenes: a comparative study of their structures, stabilisation and binding energies. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.852191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
36
|
KABANDA MWADHAMM, EBENSO ENOE. DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.
Collapse
Affiliation(s)
- MWADHAM M. KABANDA
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| | - ENO E. EBENSO
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| |
Collapse
|
37
|
Mammino L, Kabanda MM. The role of additional O–H…O intramolecular hydrogen bonds for acylphloroglucinols' conformational preferencesin vacuoand in solution. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.700483] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
38
|
Mammino L. Investigation of the antioxidant properties of hyperjovinol A through its Cu(II) coordination ability. J Mol Model 2012; 19:2127-42. [DOI: 10.1007/s00894-012-1684-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 11/06/2012] [Indexed: 11/28/2022]
|
39
|
Mammino L, Kabanda MM. A Computational Study of the Effects of Different Solvents on the Characteristics of the Intramolecular Hydrogen Bond in Acylphloroglucinols. J Phys Chem A 2009; 113:15064-77. [DOI: 10.1021/jp905180c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Liliana Mammino
- Department of Chemistry, University of Venda, P/bag X5050, Thohoyandou 0950, South Africa
| | - Mwadham M. Kabanda
- Department of Chemistry, University of Venda, P/bag X5050, Thohoyandou 0950, South Africa
| |
Collapse
|