1
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Isert C, Atz K, Riniker S, Schneider G. Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning. RSC Adv 2024; 14:4492-4502. [PMID: 38312732 PMCID: PMC10835705 DOI: 10.1039/d3ra08650j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Rational structure-based drug design relies on accurate predictions of protein-ligand binding affinity from structural molecular information. Although deep learning-based methods for predicting binding affinity have shown promise in computational drug design, certain approaches have faced criticism for their potential to inadequately capture the fundamental physical interactions between ligands and their macromolecular targets or for being susceptible to dataset biases. Herein, we propose to include bond-critical points based on the electron density of a protein-ligand complex as a fundamental physical representation of protein-ligand interactions. Employing a geometric deep learning model, we explore the usefulness of these bond-critical points to predict absolute binding affinities of protein-ligand complexes, benchmark model performance against existing methods, and provide a critical analysis of this new approach. The models achieved root-mean-squared errors of 1.4-1.8 log units on the PDBbind dataset, and 1.0-1.7 log units on the PDE10A dataset, not indicating significant advantages over benchmark methods, and thus rendering the utility of electron density for deep learning models context-dependent. The relationship between intermolecular electron density and corresponding binding affinity was analyzed, and Pearson correlation coefficients r > 0.7 were obtained for several macromolecular targets.
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Affiliation(s)
- Clemens Isert
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Sereina Riniker
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
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2
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Lefrancois-Gagnon KM, Mawhinney RC. Toward Universal Substituent Constants: Relating QTAIM Functional Group Descriptors to Substituent Effect Proxies. J Chem Inf Model 2023; 63:6068-6080. [PMID: 37729015 DOI: 10.1021/acs.jcim.3c00987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Substituents modulate reactions, but their effects are commonly described by using proxies to their functional group properties. Substituent descriptors from the quantum theory of atoms in molecules, which are true functional group properties, are related here to these proxies, which have historically had chemically relevant meaning. Due to the large number of descriptors, multivariate analysis is used to intuit their significance. Multiple linear regression, principal component, and partial least squares regression analyses highlight that these substituent descriptors contain similar information to the proxies while being intrinsic, predictable substituent properties. Sources of error limiting quantitative reproduction of the proxy data include transferability, experimental accuracy, and solvation issues.
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Affiliation(s)
| | - Robert C Mawhinney
- Department of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada
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3
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Bogado ML, Villafañe RN, Gómez Chavez JL, Angelina EL, Sosa GL, Peruchena NM. Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment. J Chem Inf Model 2022; 62:6494-6507. [PMID: 36044012 DOI: 10.1021/acs.jcim.2c00475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein pockets that form a halogen bond (X-bond) with a halogenated ligand molecule simultaneously form other (mainly hydrophobic) interactions with the halogen atom that can be considered as its "X-bond environment" (XBenv). Most studies in the field have focused on the X-bond, with the properties of the XBenv usually overlooked. In this work, we derived a protocol that evaluates the XBenv strength as a measure of the propensity of a protein pocket to host an X-bond. The charge density-based topological descriptors in combination with machine learning tools were employed to predict formation and strength of the interactions that conform the XBenv as a function of their geometrical parameters. On the basis of these results, we propose that the XBenv can be used as a footprint to judge the chance of a protein pocket to form an X-bond.
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Affiliation(s)
- María Lucrecia Bogado
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Roxana Noelia Villafañe
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - José Leonardo Gómez Chavez
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Emilio Luis Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Gladis Laura Sosa
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Nélida María Peruchena
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
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4
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Solgun DG, Tanriverdi AA, Yildiko U, Ağirtaş MS. Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups, DFT and molecular docking studies. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-022-01164-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Sgariglia MA, Garibotto FM, Soberón JR, Angelina EL, Andujar SA, Vattuone MA. Study of polyphenols from Caesalpinia paraguariensis as α-glucosidase inhibitors: kinetics and structure–activity relationship. NEW J CHEM 2022. [DOI: 10.1039/d1nj04619e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ellagic derivatives isolated from Caesalpinia paraguariensis bark: (1) ellagic acid, (2) 3-O-methylellagic, (3) 3,3′-O-dimethylellagic acid, and (4) 3,3′-O-dimethylellagic-4-O-β-d-xylopyranoside and their binding modes on α-glucosidase.
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Affiliation(s)
- Melina A. Sgariglia
- National University of Tucumán, Faculty of Biochemistry Chemistry and Pharmacy, Pharmacological Studies Institute, Phytochemical Cathedra, Tucumán (4000), Argentina
- National Scientific and Technical Research Council (CONICET-Argentina), Argentina
| | - Francisco M. Garibotto
- Nacional University of San Luis, Faculty of Chemistry Biochemistry and Pharmacy, Argentina
- IMIBIO-CONICET-San Luis (5700), Argentina
| | - José R. Soberón
- National University of Tucumán, Faculty of Biochemistry Chemistry and Pharmacy, Pharmacological Studies Institute, Phytochemical Cathedra, Tucumán (4000), Argentina
- National Scientific and Technical Research Council (CONICET-Argentina), Argentina
| | - Emilio L. Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FACENA, Corrientes (3400), Argentina
| | - Sebastián A. Andujar
- Nacional University of San Luis, Faculty of Chemistry Biochemistry and Pharmacy, Argentina
- IMIBIO-CONICET-San Luis (5700), Argentina
| | - Marta A. Vattuone
- National Scientific and Technical Research Council (CONICET-Argentina), Argentina
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6
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K. J, P. V, S. P, S. D, Siddiqui MK. Molecular Structural Descriptors of Donut Benzenoid Systems. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1885456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Julietraja K.
- Department of Mathematics, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, India
| | - Venugopal P.
- Department of Mathematics, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, India
| | - Prabhu S.
- Department of Mathematics, Sri Venkateswara College of Engineering, Sriperumbudur, India
| | - Deepa S.
- Department of Mathematics, Easwari Engineering College, Chennai, India
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7
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Rojas S, Parravicini O, Vettorazzi M, Tosso R, Garro A, Gutiérrez L, Andújar S, Enriz R. Combined MD/QTAIM techniques to evaluate ligand-receptor interactions. Scope and limitations. Eur J Med Chem 2020; 208:112792. [PMID: 32949964 DOI: 10.1016/j.ejmech.2020.112792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022]
Abstract
In medicinal chemistry, it is extremely important to evaluate, as accurately as possible, the molecular interactions involved in the formation of different ligand-receptor (L-R) complexes. Evaluating the different molecular interactions by quantum mechanics calculations is not a simple task, since formation of an L-R complex is a dynamic process. In this case, the use of combined techniques of molecular dynamics (MD) and quantum calculations is one the best possible approaches. In this work we report a comparative study using combined MD and QTAIM (Quantum Theory of Atoms In Molecules) calculations for five biological systems with different levels of structural complexity. We have studied Acetylcholinesterase (AChE), D2 Dopamine Receptor (D2DR), beta Secretase (BACE1), Dihydrofolate Reductase (DHFR) and Sphingosine Kinase 1 (SphK1). In these molecular targets, we have analyzed different ligands with diverse structural characteristics. The inhibitory activities of most of them have been previously measured in our laboratory. Our results indicate that QTAIM calculations can be extremely useful for in silico studies. It is possible to obtain very accurate information about the strength of the molecular interactions that stabilize the formation of the different L-R complexes. Better correlations can be obtained between theoretical and experimental data by using QTAIM calculations, allowing us to discriminate among ligands with similar affinities. QTAIM analysis gives fairly accurate information for weak interactions which are not well described by MD simulations. QTAIM study also allowed us to evaluate and determine which parts of the ligand need to be modified in order to increase its interactions with the molecular target. In this study we have discussed the importance of combined MD/QTAIM calculations for this type of simulations, showing their scopes and limitations.
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Affiliation(s)
- Sebastián Rojas
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Oscar Parravicini
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Marcela Vettorazzi
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Rodrigo Tosso
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Adriana Garro
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Lucas Gutiérrez
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Sebastián Andújar
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina
| | - Ricardo Enriz
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina.
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8
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Duchowicz PR. QSPR studies on water solubility, octanol-water partition coefficient and vapour pressure of pesticides. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:135-148. [PMID: 31842624 DOI: 10.1080/1062936x.2019.1699602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
The assessment of the environmental fate and (eco)toxicological effects of pesticide compounds is of crucial importance. The present review is focused on Quantitative Structure-Property Relationships (QSPR) applications on three environmentally relevant physicochemical properties of pesticides, which can be used for assessing their environmental partition and transport, as well as exposure potential namely water solubility, octanol-water partition coefficient and vapour pressure. This article revises various interesting QSPR applications with special emphasis on studies developed during the 2009-2019 period.
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Affiliation(s)
- P R Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET, UNLP, La Plata, Argentina
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9
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Duchowicz PR, Aranda JF, Bacelo DE, Fioressi SE. QSPR study of the Henry’s law constant for heterogeneous compounds. Chem Eng Res Des 2020. [DOI: 10.1016/j.cherd.2019.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Insights into the weak Csp3–H···H–Csp3 mediated supramolecular architecture in ethyl 2-(5-bromopentanamido)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxylate, a probable selective COX-2 lead molecule: An integrated crystallographic and theoretical approach. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Luchi A, Villafañe RN, Gómez Chávez JL, Bogado ML, Angelina EL, Peruchena NM. Combining Charge Density Analysis with Machine Learning Tools To Investigate the Cruzain Inhibition Mechanism. ACS OMEGA 2019; 4:19582-19594. [PMID: 31788588 PMCID: PMC6881835 DOI: 10.1021/acsomega.9b01934] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/18/2019] [Indexed: 05/28/2023]
Abstract
Trypanosoma cruzi, a flagellate protozoan parasite, is responsible for Chagas disease. The parasite major cysteine protease, cruzain (Cz), plays a vital role at every stage of its life cycle and the active-site region of the enzyme, similar to those of other members of the papain superfamily, is well characterized. Taking advantage of structural information available in public databases about Cz bound to known covalent inhibitors, along with their corresponding activity annotations, in this work, we performed a deep analysis of the molecular interactions at the Cz binding cleft, in order to investigate the enzyme inhibition mechanism. Our toolbox for performing this study consisted of the charge density topological analysis of the complexes to extract the molecular interactions and machine learning classification models to relate the interactions with biological activity. More precisely, such a combination was useful for the classification of molecular interactions as "active-like" or "inactive-like" according to whether they are prevalent in the most active or less active complexes, respectively. Further analysis of interactions with the help of unsupervised learning tools also allowed the understanding of how these interactions come into play together to trigger the enzyme into a particular conformational state. Most active inhibitors induce some conformational changes within the enzyme that lead to an overall better fit of the inhibitor into the binding cleft. Curiously, some of these conformational changes can be considered as a hallmark of the substrate recognition event, which means that most active inhibitors are likely recognized by the enzyme as if they were its own substrate so that the catalytic machinery is arranged as if it is about to break the substrate scissile bond. Overall, these results contribute to a better understanding of the enzyme inhibition mechanism. Moreover, the information about main interactions extracted through this work is already being used in our lab to guide docking solutions in ongoing prospective virtual screening campaigns to search for novel noncovalent cruzain inhibitors.
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12
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Indole-substituted 2,4-diamino-5,8-dihydropyrido[2,3-d]pyrimidines from one-pot process and evaluation of their ability to bind dopamine receptors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.10.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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13
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Gutiérrez LJ, Parravicini O, Sánchez E, Rodríguez R, Cobo J, Enriz RD. New substituted aminopyrimidine derivatives as BACE1 inhibitors: in silico design, synthesis and biological assays. J Biomol Struct Dyn 2018; 37:229-246. [DOI: 10.1080/07391102.2018.1424036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Emilse Sánchez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
| | - Ricaurte Rodríguez
- Departamento de Química, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30, No. 45-03, Bogotá, Colombia
| | - Justo Cobo
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 915, 5700 San Luis, Argentina
- IMIBIO-CONICET, UNSL, Chacabuco 915, 5700 San Luis, Argentina
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14
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Petelski AN, Pamies SC, Benítez EI, Rovaletti MML, Sosa GL. Molecular Insights into Protein-Polyphenols Aggregation: A Dynamic and Topological Description. ChemistrySelect 2017. [DOI: 10.1002/slct.201700726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- André N. Petelski
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET.; Avenida Libertad 5460 3400) Corrientes Argentina
| | - Silvana C. Pamies
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
| | - Elisa I. Benítez
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET.; Avenida Libertad 5460 3400) Corrientes Argentina
| | - María M. Lataza Rovaletti
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
| | - Gladis L. Sosa
- Chemical Engineering Department. Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Facultad Regional Resistencia; Universidad Tecnológica Nacional; French 414 H3500CHJ) Resistencia, Chaco Argentina
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET.; Avenida Libertad 5460 3400) Corrientes Argentina
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15
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Venkataramanan NS, Suvitha A. Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches. J Phys Chem B 2017; 121:4733-4744. [DOI: 10.1021/acs.jpcb.7b01808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Natarajan Sathiyamoorthy Venkataramanan
- Centre
for Computational Chemistry and Materials Science, SASTRA University, Thanjavur 614 001, India
- Department
of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA University, Thanjavur 614 001, India
| | - Ambigapathy Suvitha
- Department
of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA University, Thanjavur 614 001, India
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