1
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Saral A, Sudha P, Muthu S, Irfan A. Spectroscopic profiling, DFT computations, molecular docking and molecular dynamic simulation of biologically active 5-isoquinolinesulfonic acid. J Biomol Struct Dyn 2023; 41:722-735. [PMID: 34882072 DOI: 10.1080/07391102.2021.2011417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The title compound 5-isoquinolinesulfonic acid (5IQSA) is characterized using the FT-IR, FT-Raman, NMR and UV-Vis spectra. The optimized molecular geometry, vibrational assignments, infrared intensities and Raman scattering are precisely calculated using Density Functional Theory (DFT) with the B3LYP/6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts are computed and compared with the experimental data. The TD-DFT/M062X/6-311++G(d,p) method is used to compute UV-Vis for different solvents, and the results are compared to UV-Vis spectra obtained experimentally. The HOMO-LUMO band gap energy is calculated for various solvents and compared to the band gap of UV-Vis spectra. Molecular dynamics simulations are used to investigate the biomolecular stability. Non-Linear Optical (NLO) behaviour has been illustrated using hyperpolarizability calculations. Topological studies such as Reduced Gradient Density (RDG), Electron Localization Function (ELF) and Localized Orbital Locator (LOL) are performed. The Molecular Electrostatic Potential (MEP), Natural Bond Orbital (NBO) analysis, Fukui functions and thermodynamic properties were analysed. To explore the biological behaviour of the examined compound, molecular docking was performed to evaluate the hydrogen bond distance and binding energies with (2XA4) kinase inhibitor protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A Saral
- PG and Research Department of Chemistry, Thiru. Vi. Ka. Government Arts College, Thiruvarur, Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.,Department of Chemistry, Panimalar Institute of Technology, Chennai, Tamil Nadu, India
| | - P Sudha
- PG and Research Department of Chemistry, Thiru. Vi. Ka. Government Arts College, Thiruvarur, Tamil Nadu, India
| | - S Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu, India.,Department of Physics, Puratchi Thalaivar Dr. MGR Government Arts and Science College, Uthiramerur, Tamil Nadu, India
| | - Ahmad Irfan
- Department of Chemistry, College of Science, King Khalid University, Abha, Saudi Arabia
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2
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Construction of amphiphilic networks in blend membranes for CO2 separation. KOREAN J CHEM ENG 2023. [DOI: 10.1007/s11814-022-1236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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3
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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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Geerlings P. From Density Functional Theory to Conceptual Density Functional Theory and Biosystems. Pharmaceuticals (Basel) 2022; 15:ph15091112. [PMID: 36145333 PMCID: PMC9505550 DOI: 10.3390/ph15091112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022] Open
Abstract
The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.
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Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Faculty of Science and Bio-Engineering Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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Sistla YS, Mehraj S. Molecular Simulations to Understand the Moisture, Carbon Dioxide, and Oxygen Barrier Properties of Pectin Films. J Mol Model 2022; 28:83. [DOI: 10.1007/s00894-022-05069-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022]
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6
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Saral A, Sudha P, Muthu S, Irfan A. Computational, spectroscopic and molecular docking investigation on a bioactive anti-cancer drug: 2-Methyl-8-nitro quinoline. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins. Curr Opin Struct Biol 2021; 72:9-17. [PMID: 34388673 DOI: 10.1016/j.sbi.2021.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022]
Abstract
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Tradeoffs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multiscale QM/MM or iterative approach. Limitations to both conventional density-functional theory and classical MM force fields remain for describing noncovalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e. electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.
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Rocha-Santos A, Chaves EJ, Grillo IB, de Freitas AS, Araújo DAM, Rocha GB. Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors. ACS OMEGA 2021; 6:8764-8777. [PMID: 33842748 PMCID: PMC8027999 DOI: 10.1021/acsomega.0c02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/30/2020] [Indexed: 05/03/2023]
Abstract
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods. Two approaches were followed (calculation of binding enthalpies, ΔH bind, and reactivity quantum chemical descriptors) and compared with the respective half-maximal inhibitory concentration (IC50) experimental data, to gain insight into RTA inhibitors and verify which quantum chemical method would better describe RTA-ligand interactions. The geometries for all RTA-ligand complexes were obtained after running classical molecular dynamics simulations in aqueous media. We found that single-point energy calculations of ΔH bind with the PM6-DH+, PM6-D3H4, and PM7 semiempirical methods and ONIOM QM/MM presented a good correlation with the IC50 data. We also observed, however, that the correlation decreased significantly when we calculated ΔH bind after full-atom geometry optimization with all semiempirical methods. Based on the results from reactivity descriptors calculations for the cases studied, we noted that both types of interactions, molecular overlap and electrostatic interactions, play significant roles in the overall affinity of these ligands for the RTA binding pocket.
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Affiliation(s)
- Acassio Rocha-Santos
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Elton José
Ferreira Chaves
- Department
of Biotechnology, Federal University of
Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Igor Barden Grillo
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Amanara Souza de Freitas
- Department
of Chemical Engineering, Federal University
of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
- . Phone/Fax: +55-83-3216-7437
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9
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Grillo IB, Urquiza-Carvalho GA, Rocha GB. PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules. J Chem Inf Model 2020; 60:5885-5890. [PMID: 33186016 DOI: 10.1021/acs.jcim.0c00655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plenty of enzymes with structural data do not have their mechanism of catalysis elucidated. Reactivity descriptors, theoretical quantities generated from resolved electronic structure, provide a way to predict and rationalize chemical processes of such systems. In this Application Note, we present PRIMoRDiA (PRIMoRDiA Macromolecular Reactivity Descriptors Access), a software built to calculate the reactivity descriptors of large biosystems by employing an efficient and accurate treatment of the large output files produced by quantum chemistry packages. Here, we show the general implementation details and the software main features. Calculated descriptors were applied for a set of enzymatic systems in order to show their relevance for biological studies and the software potential for use in large scale. Also, we test PRIMoRDiA to aid in the interaction depiction between the SARS-CoV-2 main protease and a potential inhibitor.
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Affiliation(s)
- Igor Barden Grillo
- Department of Chemistry, Federal University of Paraíba, João Pessoa - PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department of Chemistry, Federal University of Paraíba, João Pessoa - PB 58051-900, Brazil
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10
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Oller J, Saez DA, Vöhringer-Martinez E. Atom-Condensed Fukui Function in Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide. J Phys Chem A 2020; 124:849-857. [PMID: 31951411 DOI: 10.1021/acs.jpca.9b07012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Local reactivity descriptors such as atom-condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here we propose to combine quantum mechanics/molecular mechanics Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann-weighted atom-condensed local reactivity descriptors based on conceptual density functional theory. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account, allowing us to analyze the effect of the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared with an aqueous solution. Our main result is that the protein environment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α,β-unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.
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Affiliation(s)
- Javier Oller
- Departamento de Fı́sico-Quı́mica, Facultad de Ciencias Quı́micas , Universidad de Concepción , Concepción 4070386 , Chile
| | - David Adrian Saez
- Departamento de Fı́sico-Quı́mica, Facultad de Ciencias Quı́micas , Universidad de Concepción , Concepción 4070386 , Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Fı́sico-Quı́mica, Facultad de Ciencias Quı́micas , Universidad de Concepción , Concepción 4070386 , Chile
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11
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Decuyper L, Magdalenić K, Verstraete M, Jukič M, Sosič I, Sauvage E, Amoroso AM, Verlaine O, Joris B, Gobec S, D'hooghe M. α-Unsaturated 3-Amino-1-carboxymethyl-β-lactams as Bacterial PBP Inhibitors: Synthesis and Biochemical Assessment. Chemistry 2019; 25:16128-16140. [PMID: 31596974 DOI: 10.1002/chem.201904139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/08/2019] [Indexed: 01/24/2023]
Abstract
Innovative monocyclic β-lactam entities create opportunities in the battle against resistant bacteria because of their PBP acylation potential, intrinsically high β-lactamase stability and compact scaffold. α-Benzylidene-substituted 3-amino-1-carboxymethyl-β-lactams were recently shown to be potent PBP inhibitors and constitute eligible anchor points for synthetic elaboration of the chemical space around the central β-lactam ring. The present study discloses a 12-step synthesis of ten α-arylmethylidenecarboxylates using a microwave-assisted Wittig olefination as the crucial reaction step. The library was designed aiming at enhanced β-lactam electrophilicity and extended electron flow after enzymatic attack. Additionally, increased β-lactamase stability and intermolecular target interaction were envisioned by tackling both the substitution pattern of the aromatic ring and the β-lactam C4-position. The significance of α-unsaturation was validated and the R39/PBP3 inhibitory potency shown to be augmented the most through decoration of the aromatic ring with electron-withdrawing groups. Furthermore, ring cleavage by representative β-lactamases was ruled out, providing new insights in the SAR landscape of monocyclic β-lactams as eligible PBP or β-lactamase inhibitors.
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Affiliation(s)
- Lena Decuyper
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Katarina Magdalenić
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marie Verstraete
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marko Jukič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Eric Sauvage
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Ana Maria Amoroso
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Olivier Verlaine
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Bernard Joris
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Matthias D'hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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Chang CM. Rationalization and prediction of the impact of different metals and root exudates on carbon dioxide emission from soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:348-359. [PMID: 31323580 DOI: 10.1016/j.scitotenv.2019.06.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Quantitative structure-property relationship modeling method developed from the quantum four-element concept of electronic attributes is validated by the accurate prediction of the redox potentials, deprotonation constants, stability constants and the maximum biosorption capacity of various metal ions and verification of the toxicological endpoint of soil nematodes and mouse. This approach is an extremely promising tool for rationalizing and predicting the toxicity and mobility of different metals and the emission of carbon dioxide from soil. The results demonstrate that the high fungal toxicity and low ion-humic acid binding of cadmium (2+) and the strong complexation of root exudates, such as oxalic acid, citric acid and malic acid, are most likely to promote carbon release.
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Affiliation(s)
- Chia Ming Chang
- Environmental Molecular and Electromagnetic Physics (EMEP) Laboratory, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan.
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13
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Proposal for an ecofriendly and economic strategy for efficient radioiodination of coumarin derivatives. Appl Radiat Isot 2019; 151:265-273. [DOI: 10.1016/j.apradiso.2019.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/13/2019] [Accepted: 06/16/2019] [Indexed: 11/23/2022]
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14
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Zaręba P, Jaśkowska J, Czekaj I, Satała G. Design, synthesis and molecular modelling of new bulky Fananserin derivatives with altered pharmacological profile as potential antidepressants. Bioorg Med Chem 2019; 27:3396-3407. [DOI: 10.1016/j.bmc.2019.06.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 01/09/2023]
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15
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Raajaraman BR, Sheela NR, Muthu S. Spectroscopic, quantum computational and molecular docking studies on 1-phenylcyclopentane carboxylic acid. Comput Biol Chem 2019; 82:44-56. [PMID: 31260880 DOI: 10.1016/j.compbiolchem.2019.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/18/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022]
Abstract
The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Using potential energy distribution, all the assignments of the basic vibrational modes were calculated. Natural bond orbital (NBO) and atoms in molecules (AIM) topological studies applied to get the intermolecular interactions of the compound. 1H and 13C chemical shift of NMR was estimated on the molecule and also compared with the experimental spectra. In order to find the band gap, the time-dependent (TD-DFT) method is used to get the higher order energy levels properties and also compared with experimental data of UV-vis spectrum. From the analysis of various spectroscopic studies, there is a good relationship between the experimental and theoretical values obtained. Quantum characters, bio-active nature and reactive areas of the molecule are revealed by Fukui function, molecular electrostatic potential (MEP) and Hirshfeld surface studies. The human enzyme steroidogenic types and their protein targets were tested with this molecule by molecular docking.
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Affiliation(s)
- B R Raajaraman
- Department of Applied Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - N R Sheela
- Department of Applied Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - S Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604 407, Tamil Nadu, India.
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16
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de Arruda EGR, Rocha BA, Barrionuevo MVF, Aðalsteinsson HM, Galdino FE, Loh W, Lima FA, Abbehausen C. The influence of ZnII coordination sphere and chemical structure over the reactivity of metallo-β-lactamase model compounds. Dalton Trans 2019; 48:2900-2916. [DOI: 10.1039/c8dt03905d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The first coordination sphere influences the reactivity of metallo-β-lactamase monozinc model complexes.
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17
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Mehmood A, Jones SI, Tao P, Janesko BG. An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps. J Chem Inf Model 2018; 58:1836-1846. [DOI: 10.1021/acs.jcim.8b00370] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 South University Drive, Fort Worth, Texas 76129, United States
| | - Stephanie I. Jones
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 South University Drive, Fort Worth, Texas 76129, United States
| | - Peng Tao
- Department of Chemistry, Southern Methodist University, P.O. Box 750314, Dallas, Texas 75275, United States
| | - Benjamin G. Janesko
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 South University Drive, Fort Worth, Texas 76129, United States
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18
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Sotriffer C. Docking of Covalent Ligands: Challenges and Approaches. Mol Inform 2018; 37:e1800062. [PMID: 29927068 DOI: 10.1002/minf.201800062] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Covalent ligands have recently regained considerable attention in drug discovery. The rational design of such ligands, however, is still faced with particular challenges, mostly related to the fact that covalent bond formation is a quantum mechanical phenomenon which cannot adequately be handled by the force fields or empirical approaches typically used for noncovalent protein-ligand interactions. Although the necessity for quantum chemical approaches is clear, they cannot yet routinely be applied on large data sets of ligands or for a broader exploration of binding modes in docking calculations. On the other hand, technical solutions for performing docking calculations with covalent ligands are available, but their scope is normally quite limited. Scoring functions typically neglect the contribution from covalent bond formation completely. In this situation, the question arises how to approach covalent ligands and which methods to choose for their docking and design.
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Affiliation(s)
- Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, D-, 97074, Würzburg, Germany
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19
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Mena-Ulecia K, MacLeod-Carey D. Interactions of 2-phenyl-benzotriazole xenobiotic compounds with human Cytochrome P450-CYP1A1 by means of docking, molecular dynamics simulations and MM-GBSA calculations. Comput Biol Chem 2018; 74:253-262. [DOI: 10.1016/j.compbiolchem.2018.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 11/30/2022]
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20
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Da Silva MKL, Plana Simões R, Cesarino I. Evaluation of Reduced Graphene Oxide Modified with Antimony and Copper Nanoparticles for Levofloxacin Oxidation. ELECTROANAL 2018. [DOI: 10.1002/elan.201800265] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Rafael Plana Simões
- Sao Paulo State University (UNESP), School of Agriculture; Botucatu, SP Brazil
| | - Ivana Cesarino
- Sao Paulo State University (UNESP), School of Agriculture; Botucatu, SP Brazil
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21
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Zhang N, Peng D, Wu H, Ren Y, Yang L, Wu X, Wu Y, Qu Z, Jiang Z, Cao X. Significantly enhanced CO2 capture properties by synergy of zinc ion and sulfonate in Pebax-pitch hybrid membranes. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2017.10.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Wible RS, Sutter TR. Soft Cysteine Signaling Network: The Functional Significance of Cysteine in Protein Function and the Soft Acids/Bases Thiol Chemistry That Facilitates Cysteine Modification. Chem Res Toxicol 2017; 30:729-762. [DOI: 10.1021/acs.chemrestox.6b00428] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ryan S. Wible
- Department
of Chemistry, ‡Department of Biological Sciences, and §W. Harry Feinstone Center for Genomic
Research, University of Memphis, 3700 Walker Avenue, Memphis, Tennessee 38152-3370, United States
| | - Thomas R. Sutter
- Department
of Chemistry, ‡Department of Biological Sciences, and §W. Harry Feinstone Center for Genomic
Research, University of Memphis, 3700 Walker Avenue, Memphis, Tennessee 38152-3370, United States
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23
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Karelina M, Kulik HJ. Systematic Quantum Mechanical Region Determination in QM/MM Simulation. J Chem Theory Comput 2017; 13:563-576. [DOI: 10.1021/acs.jctc.6b01049] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Karelina
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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24
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Cesarino I, Simões RP, Lavarda FC, Batagin-Neto A. Electrochemical oxidation of sulfamethazine on a glassy carbon electrode modified with graphene and gold nanoparticles. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.01.178] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Parambath M, Hanley QS, Martin-Martinez FJ, Giesa T, Buehler MJ, Perry CC. The nature of the silicaphilic fluorescence of PDMPO. Phys Chem Chem Phys 2016; 18:5938-48. [DOI: 10.1039/c5cp05105c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Interactions with silica moderates the fluorescence behaviour of PDMPO.
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Affiliation(s)
- Mithun Parambath
- School of Science and Technology
- Nottingham Trent University
- Nottingham
- UK
| | - Quentin S. Hanley
- School of Science and Technology
- Nottingham Trent University
- Nottingham
- UK
| | | | - Tristan Giesa
- Department of Civil and Environmental Engineering
- Massachusetts Institute of Technology
- USA
| | - Markus J. Buehler
- Department of Civil and Environmental Engineering
- Massachusetts Institute of Technology
- USA
| | - Carole C. Perry
- School of Science and Technology
- Nottingham Trent University
- Nottingham
- UK
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26
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El-labbad EM, Ismail MAH, Abou Ei Ella DA, Ahmed M, Wang F, Barakat KH, Abouzid KAM. Discovery of Novel Peptidomimetics as Irreversible CHIKV NsP2 Protease Inhibitors Using Quantum Mechanical-Based Ligand Descriptors. Chem Biol Drug Des 2015. [DOI: 10.1111/cbdd.12621] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eman M. El-labbad
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; Ain Shams University; Abbassia Cairo 11566 Egypt
| | - Mohammed A. H. Ismail
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; Ain Shams University; Abbassia Cairo 11566 Egypt
| | - Dalal A. Abou Ei Ella
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; Ain Shams University; Abbassia Cairo 11566 Egypt
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences; University of Alberta; Edmonton AB Canada
| | - Feng Wang
- Molecular Model Discovery Laboratory; Department of Chemistry and Biotechnology; Faculty of Science, Engineering and Technology; Swinburne University of Technology; Melbourne Vic. 3122 Australia
| | - Khaled H. Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences; University of Alberta; Edmonton AB Canada
- LiKaShing Institute of Virology; University of Alberta; Edmonton AB Canada
- LiKaShing Applied Virology Institute; University of Alberta; Edmonton AB Canada
| | - Khaled A. M. Abouzid
- Department of Pharmaceutical Chemistry; Faculty of Pharmacy; Ain Shams University; Abbassia Cairo 11566 Egypt
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27
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Oftadeh M, Mahani NM, Hamadanian M. Density functional theory study of the local molecular properties of acetamide derivatives as anti-HIV drugs. Res Pharm Sci 2013; 8:285-97. [PMID: 24082898 PMCID: PMC3757594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Accurate quantum chemical computations based on density functional theory (DFT) were performed on the series of 2-(4-(naphthalen-2-yl)-1,2,3-thiadiazol-5-ylthio)-N-acetamide (TTA) derivatives. The local reactivity of the acetamide derivatives as anti-HIV drugs were studied in terms of Fukui functions in the framework of DFT. The results based on the basis set superposition error (BSSE) corrections showed that the mechanism of bond formation between the acetamide derivatives and tyrosine as a biological molecule occurs mainly through nitrogen atoms. The intramolecular interaction energies between the acetamide derivatives and tyrosine were calculated and the nature of the intermolecular interaction was revealed by natural bond orbital charge (NBO) analysis. The results suggest that acetamide derivatives with bromophenyl and nitrophenyl substitutions are the most potent as anti-HIV drugs.
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Affiliation(s)
- M. Oftadeh
- Chemistry Department, Payame Noor University, 19395-4697 Tehran, I. R. Iran
| | - N. Madadi Mahani
- Chemistry Department, Payame Noor University, 19395-4697 Tehran, I. R. Iran
| | - M. Hamadanian
- Chemistry Department, Kashan University, Kashan, I. R. Iran
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28
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Cárdenas C, Ayers PW. How reliable is the hard–soft acid–base principle? An assessment from numerical simulations of electron transfer energies. Phys Chem Chem Phys 2013; 15:13959-68. [DOI: 10.1039/c3cp51134k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Pratihar S, Roy S. Reactivity and Selectivity of Organotin Reagents in Allylation and Arylation: Nucleophilicity Parameter as a Guide. Organometallics 2011. [DOI: 10.1021/om101030c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Cárdenas C, Ayers PW, Cedillo A. Reactivity indicators for degenerate states in the density-functional theoretic chemical reactivity theory. J Chem Phys 2011; 134:174103. [PMID: 21548669 DOI: 10.1063/1.3585610] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Carlos Cárdenas
- Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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