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Rasul HO, Sabir DK, Aziz BK, Guillermo Salgado M, Mendoza-Huizar LH, Belhassan A, Candia LG, Villada WC, Thomas NV, Ghafour DD. Identification of natural diterpenes isolated from Azorella species targeting dispersin B using in silico approaches. J Mol Model 2023; 29:182. [PMID: 37209272 DOI: 10.1007/s00894-023-05592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
CONTEXT A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and difficulties in treating these infections are of concern. This work aimed to identify the inhibitor with the highest binding affinity for the receptor protein by screening various inhibitors obtained from Azorella species for a potential target to inhibit dispersin B. This work shows that azorellolide has the highest binding affinity (- 8.2 kcal/mol) among the compounds tested, followed by dyhydroazorellolide, mulinone A, and 7-acetoxy-mulin-9,12-diene which all had a binding affinity of - 8.0 kcal/mol. To the best of our knowledge, this is the first study to evaluate and contrast several diterpene compounds as antibacterial biofilm chemicals. METHODS Here, molecular modelling techniques tested 49 diterpene compounds of Azorella and six FDA-approved antibiotics medicines for antibiofilm activity. Since protein-like interactions are crucial in drug discovery, AutoDock Vina was initially employed to carry out structure-based virtual screening. The drug-likeness and ADMET properties of the chosen compounds were examined to assess the antibiofilm activity further. Lipinski's rule of five was then applied to determine the antibiofilm activity. Then, molecular electrostatic potential was used to determine the relative polarity of a molecule using the Gaussian 09 package and GaussView 5.08. Following three replica molecular dynamic simulations (using the Schrodinger program, Desmond 2019-4 package) that each lasted 100 ns on the promising candidates, binding free energy was estimated using MM-GBSA. Structural visualisation was used to test the binding affinity of each compound to the crystal structure of dispersin B protein (PDB: 1YHT), a well-known antibiofilm compound.
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Affiliation(s)
- Hezha O Rasul
- Department of Pharmaceutical Chemistry, College of Science, Charmo University, Peshawa Street, Chamchamal, Sulaymaniyah, 46023, Iraq.
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, College of Science, Charmo University, 46023 Chamchamal, Sulaymaniyah, Iraq
| | - Bakhtyar K Aziz
- Department of Nanoscience and Applied Chemistry, College of Science, Charmo University, Peshawa Street, Chamchamal, Sulaymaniyah, 46023, Iraq
| | - M Guillermo Salgado
- Facultad de Ciencias Químicas, Investigador Extramural, Universidad de Concepcion, Concepcion, Chile
| | - L H Mendoza-Huizar
- Autonomous University of Hidalgo State, Academic Area of Chemistry, Mineral de la Reforma, Hidalgo, Mexico
| | - Assia Belhassan
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Meknes, Morocco
| | - Lorena Gerli Candia
- Departamento de Química Ambiental, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Wilson Cardona Villada
- Facultad de Ciencias Exactas, Departamento de Quimica, Universidad Andres Bello, Concepcion, Chile
| | - Noel Vinay Thomas
- Department of BioMedical Science, College of Science, Komar University of Science and Technology, Sulaymaniyah, 46001, Iraq
| | - Dlzar D Ghafour
- Department of Medical Laboratory Science, College of Science, Komar University of Science and Technology, Sulaymaniyah, 46001, Iraq
- Department of Chemistry, College of Science, University of Sulaimani, Sulaymaniyah, 46001, Iraq
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Escobedo-González RG, Moyers-Montoya ED, Martínez-Pérez CA, García-Casillas PE, Miranda-Ruvalcaba R, Nicolás-Vázquez MIN. In Silico Study of Novel Cyclodextrin Inclusion Complexes of Polycaprolactone and Its Correlation with Skin Regeneration. Int J Mol Sci 2023; 24:ijms24108932. [PMID: 37240276 DOI: 10.3390/ijms24108932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Three novel biomaterials obtained via inclusion complexes of β-cyclodextrin, 6-deoxi-6-amino-β-cyclodextrin and epithelial growth factor grafted to 6-deoxi-6-amino-β-cyclodextrin with polycaprolactone. Furthermore, some physicochemical, toxicological and absorption properties were predicted using bioinformatics tools. The electronic, geometrical and spectroscopical calculated properties agree with the properties obtained via experimental methods, explaining the behaviors observed in each case. The interaction energy was obtained, and its values were -60.6, -20.9 and -17.1 kcal/mol for β-cyclodextrin/polycaprolactone followed by the 6-amino-β-cyclodextrin-polycaprolactone complex and finally the complex of epithelial growth factor anchored to 6-deoxy-6-amino-β-cyclodextrin/polycaprolactone. Additionally, the dipolar moments were calculated, achieving values of 3.2688, 5.9249 and 5.0998 Debye, respectively, and in addition the experimental wettability behavior of the studied materials has also been explained. It is important to note that the toxicological predictions suggested no mutagenic, tumorigenic or reproductive effects; moreover, an anti-inflammatory effect has been shown. Finally, the improvement in the cicatricial effect of the novel materials has been conveniently explained by comparing the poly-caprolactone data obtained in the experimental assessments.
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Affiliation(s)
- René Gerardo Escobedo-González
- Department of Industrial Maintenance, Technological University of the City of Juárez, Av. Universidad Tecnológica No. 3051, Col. Lote Bravo II, Ciudad Juárez 32695, Mexico
| | - Edgar Daniel Moyers-Montoya
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
| | - Carlos Alberto Martínez-Pérez
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
| | - Perla Elvia García-Casillas
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
- Applied Chemistry Research Center, Blvd. Enrique Reyna Hermosillo No. 140, Saltillo 25294, Mexico
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Alimi Z, Shiroudi A, Hatamjafari F, Oliaey AR, Pourshamsian K. Quantum Chemical Investigation of the New 1,2,4-Triazoles and Their Derivatives: Solvent and Substituent Effects. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422110036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Yousefnejad S, Shojaei SR, Morini F, Shiroudi A. A theoretical study of potential energy surface and some chemo-physical descriptors of Aspirin, Coupling the rotation of the ester and carboxyl groups. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Synthesis, structural characterization, DFT, kinetics and mechanism of oxidation of bromothymol blue: application to textile industrial wastewater treatment. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01299-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Méndez-Albores A, Escobedo-González R, Aceves-Hernández JM, García-Casillas P, Nicolás-Vázquez MI, Miranda-Ruvalcaba R. A Theoretical Study of the Adsorption Process of B-aflatoxins Using Pyracanthakoidzumii (Hayata) Rehder Biomasses. Toxins (Basel) 2020; 12:E283. [PMID: 32354011 PMCID: PMC7290487 DOI: 10.3390/toxins12050283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/11/2020] [Accepted: 04/24/2020] [Indexed: 12/03/2022] Open
Abstract
Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) functional and basis set, the interaction of the aflatoxin B1 (AFB1) molecule and the functional groups present in the Pyracantha koidzumii biosorbent was investigated. Dissociation free energy and acidity equilibrium constant values were obtained theoretically both in solution (water) and gas phases. Additionally, the molecular electrostatic potential for the protonated molecules was calculated to verify the reactivity. Thus, methanol (hydroxyl group), methylammonium ion (amino group), acetate ion (carboxyl group), and acetone (carbonyl group), were used as representatives of the substrates present in the biomass; these references were considered using the corresponding protonated or unprotonated forms at a pH value of 5. The experimental infrared spectrophotometric data suggested the participation of these functional groups in the AFB1 biosorption process, indicating that the mechanism was dominated by electrostatic interactions between the charged functional groups and the positively charged AFB1 molecule. The theoretical determination indicated that the carboxylate ion provided the highest interaction energy with the AFB1 molecule. Consequently, an enriched biosorbent with compounds containing carboxyl groups could improve the yield of the AFB1 adsorption when using in vitro and in vivo trials.
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Affiliation(s)
- Abraham Méndez-Albores
- UNAM–FESC, Campus 4, Multidisciplinary Research Unit L14 (Food, Mycotoxins and Mycotoxicosis), Cuautitlan Izcalli 54714, Mexico;
| | - René Escobedo-González
- Department of industrial maintenance and nanotechnology, Technological University of Juarez City, Ciudad Juarez, Chihuahua 32695, Mexico;
| | - Juan Manuel Aceves-Hernández
- UNAM–FESC, Campus 1, Chemical Sciences Department, Cuautitlan Izcalli C. P. 54740, Mexico; (J.M.A.-H.); (R.M.-R.)
| | - Perla García-Casillas
- Institute of Engineering and Technology, Autonomous University of the City of Juarez, UACJ, City Juarez, Chihuahua 32584, Mexico;
| | - María Inés Nicolás-Vázquez
- UNAM–FESC, Campus 1, Chemical Sciences Department, Cuautitlan Izcalli C. P. 54740, Mexico; (J.M.A.-H.); (R.M.-R.)
| | - René Miranda-Ruvalcaba
- UNAM–FESC, Campus 1, Chemical Sciences Department, Cuautitlan Izcalli C. P. 54740, Mexico; (J.M.A.-H.); (R.M.-R.)
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Ceylan M, Erkan S, Yaglioglu AS, Akdogan Uremis N, Koç E. Antiproliferative Evaluation of Some 2‐[2‐(2‐Phenylethenyl)‐cyclopent‐3‐en‐1‐yl]‐1,3‐benzothiazoles: DFT and Molecular Docking Study. Chem Biodivers 2020; 17:e1900675. [DOI: 10.1002/cbdv.201900675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/05/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Mustafa Ceylan
- Department of ChemistryTokat Gaziosmanpaşa University 60250 Tokat Turkey
| | - Sultan Erkan
- Department of Chemistry and Chemical Process TechnologySivas Cumhuriyet University 58140 Sivas Turkey
| | - Ayse Sahin Yaglioglu
- Department of ChemistryFaculty of ScienceÇankırı Karatekin University 18100 Çankırı Turkey
| | | | - Esra Koç
- Department of ChemistryTokat Gaziosmanpaşa University 60250 Tokat Turkey
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Escobedo-González R, Vargas-Requena CL, Moyers-Montoya E, Aceves-Hernández JM, Nicolás-Vázquez MI, Miranda-Ruvalcaba R. In silico Study of the Pharmacologic Properties and Cytotoxicity Pathways in Cancer Cells of Various Indolylquinone Analogues of Perezone. Molecules 2017; 22:E1060. [PMID: 28672837 PMCID: PMC6152338 DOI: 10.3390/molecules22071060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 12/23/2022] Open
Abstract
Several indolylquinone analogues of perezone, a natural sesquiterpene quinone, were characterized in this work by theoretical methods. In addition, some physicochemical, toxicological and metabolic properties were predicted using bioinformatics software. The predicted physicochemical properties are in agreement with the solubility and cLogP values, the penetration across the cell membrane, and absorption values, as well as with a possible apoptosis-activated mechanism of cytotoxic action. The toxicological predictions suggest no mutagenic, tumorigenic or reproductive effects of the four target molecules. Complementarily, the results of a performed docking study show high scoring values and hydrogen bonding values in agreement with the cytotoxicity IC50 value ranking, i.e: indolylmenadione > indolylperezone > indolylplumbagine > indolylisoperezone. Consequently, it is possible to suggest an appropriate apoptotic pathway for each compound. Finally, potential metabolic pathways of the molecules were proposed.
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Affiliation(s)
- René Escobedo-González
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
| | - Claudia Lucia Vargas-Requena
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Henry Dunant #4600, Ciudad Juárez 32310, México.
| | - Edgar Moyers-Montoya
- Instituto de Ingeniería y tecnología, Universidad Autónoma de Ciudad Juárez, Ave. Del Charro 450 Norte, Ciudad Juárez 32310, México.
| | - Juan Manuel Aceves-Hernández
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
| | - René Miranda-Ruvalcaba
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
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Zhang J, Guo L. Theoretical investigations of structures and properties of Au and S substituted poly (2,3-di-(4′-hydroxyphenyl)-1,4-phenylene ethynyl) at different electric field intensities. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Theoretical investigations on Au and S substituted poly (2,3-di-(4′-hydroxyphenyl)-1,4-phenylene ethynyl) as a molecular wire have been carried out by incorporating the external electric field (EF). The results demonstrate that both geometric and electronic structures of conjugated molecular wire are sensitive to EF. The Z component of the dipole moment and total dipole moment increases continuously since EF polarizes the molecule. Static EF modifies the frontline molecular orbitals and HLG. The I-V curve indicates the symmetrical trend respect to the original point.
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Affiliation(s)
- Jian Zhang
- School of Chemistry and Material Science, Shanxi Normal University, Linfen 041004, P. R. China
| | - Li Guo
- School of Chemistry and Material Science, Shanxi Normal University, Linfen 041004, P. R. China
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Selvaraju K, Jothi M, Kumaradhas P. Exploring the charge density distribution and the electrical characteristics of Oligo phenylene ethylene molecular nanowire using quantum chemical and charge density analysis. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Charge Density Distribution, Electrostatic Properties, and Impact Sensitivity of the High Energetic Molecule TNB: A Theoretical Charge Density Study. PROPELLANTS EXPLOSIVES PYROTECHNICS 2011. [DOI: 10.1002/prep.201000073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Stephen AD, Pawar RB, Kumaradhas P. Exploring the bond topological properties and the charge depletion-impact sensitivity relationship of high energetic TNT molecule via theoretical charge density analysis. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A theoretical study of three and four proton donors on linear HX···BeH2···HX and bifurcate BeH2···2HX trimolecular dihydrogen-bonded complexes with X = CN and NC. Struct Chem 2009. [DOI: 10.1007/s11224-009-9567-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Mata I, Molins E, Espinosa E. Zero-flux surfaces of the electrostatic potential: the border of influence zones of nucleophilic and electrophilic sites in crystalline environment. J Phys Chem A 2007; 111:9859-70. [PMID: 17727276 DOI: 10.1021/jp074032l] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The topology of the electrostatic potential varphi(r) has been studied for single molecules using geometries and electron distributions rho(r) determined from high-resolution single-crystal X-ray diffraction data. The electrostatic potential gradient nablavarphi(r), which is the negative of the electric field E = -nablavarphi, has been represented, revealing the position of zero-flux surfaces and critical points. Local maxima and minima of the electrostatic potential are interpreted in terms of electrophilic and nucleophilic sites, which present influence zones delimited by zero-flux surfaces containing saddle points. The influence zones of the nucleophilic and electrophilic sites define two alternative partitions of the space in disjoint volumes, the completeness of these partitions depending on either the neutral or ionic character of the molecule. The results obtained by using this methodology are useful for the interpretation of the saddle points of the electrostatic potential, which are related to the limits of the influence zones and reveal the path for preferred attack on reactive sites with finite influence zones.
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Affiliation(s)
- Ignasi Mata
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
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Study of relationship of atomic orbital hybridization with bonding using hybridization displacement charge: optimal hybridization principle. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.08.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hybridization displacement charges in molecules involving second and third row atoms: correlation with polarizability. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.03.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Molecular electrostatic potential maps of the anti-cancer drugs daunomycin and adriamycin: an ab initio theoretical study. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00472-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Molecular electrostatic properties using point charges: ab initio hybridization displacement charges combined with bond-centered charges. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(02)00642-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Electronic spectra, excited-state geometries and molecular electrostatic potentials of aromatic amino acids. J Photochem Photobiol A Chem 2000. [DOI: 10.1016/s1010-6030(00)00369-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mohan CG, Suresh CH, Mishra PC. Effect of optimised hybridization displacement charge on the description of molecular electrostatic potentials of some substituted acetaldehydes. J CHEM SCI 1996. [DOI: 10.1007/bf02869552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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