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Vettorazzi M, Díaz I, Angelina E, Salido S, Gutierrez L, Alvarez SE, Cobo J, Enriz RD. Second generation of pyrimidin-quinolone hybrids obtained from virtual screening acting as sphingosine kinase 1 inhibitors and potential anticancer agents. Bioorg Chem 2024; 144:107112. [PMID: 38237390 DOI: 10.1016/j.bioorg.2024.107112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
We report here the virtual screening design, synthesis and activity of eight new inhibitors of SphK1. For this study we used a pre-trained Graph Convolutional Network (GCN) combined with docking calculations. This exploratory analysis proposed nine compounds from which eight displayed significant inhibitory effect against sphingosine kinase 1 (SphK1) demonstrating a high level of efficacy for this approach. Four of these compounds also displayed anticancer activity against different tumor cell lines, and three of them (5), (6) and (7) have shown a wide inhibitory action against many of the cancer cell line tested, with GI50 below 5 µM, being (5) the most promising with TGI below 10 µM for the half of cell lines. Our results suggest that the three most promising compounds reported here are the pyrimidine-quinolone hybrids (1) and (6) linked by p-aminophenylsulfanyl and o-aminophenol fragments respectively, and (8) without such aryl linker. We also performed an exhaustive study about the molecular interactions that stabilize the different ligands at the binding site of SphK1. This molecular modeling analysis was carried out by using combined techniques: docking calculations, MD simulations and QTAIM analysis. In this study we also included PF543, as reference compound, in order to better understand the molecular behavior of these ligands at the binding site of SphK1.These results provide useful information for the design of new inhibitors of SphK1 possessing these structural scaffolds.
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Affiliation(s)
- Marcela Vettorazzi
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina
| | - Iván Díaz
- Universidad de Jaén, Departamento de Química Inorgánica y Orgánica, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Emilio Angelina
- Universidad Nacional del Nordeste, Facultad de Ciencias Exactas y Naturales y Agrimensura, Departamento de Química, Área de Química Física, Laboratorio de Estructura Molecular y Propiedades, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Sofía Salido
- Universidad de Jaén, Departamento de Química Inorgánica y Orgánica, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Lucas Gutierrez
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina
| | - Sergio E Alvarez
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina
| | - Justo Cobo
- Universidad de Jaén, Departamento de Química Inorgánica y Orgánica, Campus Las Lagunillas s/n, 23071 Jaén, Spain.
| | - Ricardo D Enriz
- Universidad Nacional de San Luis, Facultad de Química, Bioquímica y Farmacia, Ejercito de los Andes 950, (5700) San Luis, Argentina; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejercito de los Andes 950, (5700) San Luis, Argentina.
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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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Khursheed S, Tabassum S, Arjmand F. Comprehensive biological {DNA/RNA binding profile, cleavage &cytotoxicity activity} of structurally well-characterized chromone-appended Cu(II)(L1-3)(phen) potential anticancer drug candidates. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Rincón D, Doerr M, Daza MC. Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study. ACS OMEGA 2021; 6:20992-21004. [PMID: 34423207 PMCID: PMC8375099 DOI: 10.1021/acsomega.1c02559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.
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Fortuna A, Costa PJ. Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges. J Chem Inf Model 2021; 61:3361-3375. [PMID: 34185532 DOI: 10.1021/acs.jcim.1c00177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In force-field methods, the usage of off-center point charges, also called extra points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics/molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X-EP distances. Poisson-Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (ΔGsolv) of small molecules, often to compute binding free energies (ΔGbind) at the MM-PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charge models and the lack of specific PB radii for halogens compatible with such implementations, in this work, we assessed the performance of PBSA calculations for the estimation of ΔGsolv values in water (ΔGhyd), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the general AMBER force field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM general force field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.
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Affiliation(s)
- Andreia Fortuna
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal.,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Paulo J Costa
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
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Nunes RS, Vila-Viçosa D, Costa PJ. Halogen Bonding: An Underestimated Player in Membrane–Ligand Interactions. J Am Chem Soc 2021; 143:4253-4267. [DOI: 10.1021/jacs.0c12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rafael Santana Nunes
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Paulo J. Costa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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Tosso RD, Parravicini O, Zarycz MNC, Angelina E, Vettorazzi M, Peruchena N, Andujar S, Enriz RD. Conformational and electronic study of dopamine interacting with theD2dopamine receptor. J Comput Chem 2020; 41:1898-1911. [DOI: 10.1002/jcc.26361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/10/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Rodrigo D. Tosso
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - M. Natalia C. Zarycz
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y PropiedadesFacultad de Ciencias Exactas y Naturales y Agrimensura Corrientes Argentina
- Instituto de Química Básica y Aplicada (IQUIBA‐NEA)CONICET Corrientes Argentina
| | - Marcela Vettorazzi
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Nélida Peruchena
- Laboratorio de Estructura Molecular y PropiedadesFacultad de Ciencias Exactas y Naturales y Agrimensura Corrientes Argentina
- Instituto de Química Básica y Aplicada (IQUIBA‐NEA)CONICET Corrientes Argentina
| | - Sebastián Andujar
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
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Kurczab R, Kucwaj-Brysz K, Śliwa P. The Significance of Halogen Bonding in Ligand-Receptor Interactions: The Lesson Learned from Molecular Dynamic Simulations of the D 4 Receptor. Molecules 2019; 25:E91. [PMID: 31881785 PMCID: PMC6983170 DOI: 10.3390/molecules25010091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022] Open
Abstract
Recently, a computational approach combining a structure-activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen bonding, also known as XB hot spots. However, the analysis of ligand-receptor complexes with halogen bonds obtained by molecular docking provides a limited ability to study the role and significance of halogen bonding in biological systems. Thus, a set of molecular dynamics simulations for the dopamine D4 receptor, recently crystallized with the antipsychotic drug nemonapride (5WIU), and the five XSAR sets were performed to verify the identified hot spots for halogen bonding, in other words, primary (V5x40), and secondary (S5x43, S5x461 and H6x55). The simulations confirmed the key role of halogen bonding with V5x40 and H6x55 and supported S5x43 and S5x461. The results showed that steric restrictions and the topology of the molecular core have a crucial impact on the stabilization of the ligand-receptor complex by halogen bonding.
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Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland;
| | - Katarzyna Kucwaj-Brysz
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland;
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
| | - Paweł Śliwa
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland;
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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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Vettorazzi M, Insuasty D, Lima S, Gutiérrez L, Nogueras M, Marchal A, Abonia R, Andújar S, Spiegel S, Cobo J, Enriz RD. Design of new quinolin-2-one-pyrimidine hybrids as sphingosine kinases inhibitors. Bioorg Chem 2019; 94:103414. [PMID: 31757412 DOI: 10.1016/j.bioorg.2019.103414] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/27/2022]
Abstract
Sphingosine-1-phosphate is now emerging as an important player in cancer, inflammation, autoimmune, neurological and cardiovascular disorders. Abundance evidence in animal and humans cancer models has shown that SphK1 is linked to cancer. Thus, there is a great interest in the development new SphK1 inhibitors as a potential new treatment for cancer. In a search for new SphK1 inhibitors we selected the well-known SKI-II inhibitor as the starting structure and we synthesized a new inhibitor structurally related to SKI-II with a significant but moderate inhibitory effect. In a second approach, based on our molecular modeling results, we designed new structures based on the structure of PF-543, the most potent known SphK1 inhibitor. Using this approach, we report the design, synthesis and biological evaluation of a new series of compounds with inhibitory activity against both SphK1 and SphK2. These new inhibitors were obtained incorporating new connecting chains between their polar heads and hydrophobic tails. On the other hand, the combined techniques of molecular dynamics simulations and QTAIM calculations provided complete and detailed information about the molecular interactions that stabilize the different complexes of these new inhibitors with the active sites of the SphK1. This information will be useful in the design of new SphK inhibitors.
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Affiliation(s)
- Marcela Vettorazzi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina
| | - Daniel Insuasty
- Departamento de Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia; Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Santiago Lima
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA
| | - Lucas Gutiérrez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina
| | - Manuel Nogueras
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Antonio Marchal
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A. 25360 Cali, Colombia
| | - Sebastián Andújar
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA
| | - Justo Cobo
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain.
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). Ejercito de los Andes 950, 5700 San Luis, Argentina.
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Nunes R, Vila-Viçosa D, Costa PJ. Tackling Halogenated Species with PBSA: Effect of Emulating the σ-Hole. J Chem Theory Comput 2019; 15:4241-4251. [PMID: 31142112 DOI: 10.1021/acs.jctc.9b00106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To model halogen-bond phenomena using classical force fields, an extra point (EP) of charge is frequently introduced at a given distance from the halogen (X) to emulate the σ-hole. The resulting molecular dynamics (MD) trajectories can be used in subsequent molecular mechanics (MM) combined with Poisson-Boltzmann and surface area calculations (PBSA) to estimate protein-ligand binding free energies (Δ Gbind). While EP addition improves the MM/MD description of halogen-containing systems, its effect on the calculation of solvation free energies (Δ Gsolv) using the PBSA approach is yet to be assessed. As the PBSA calculations depend, among other parameters, on the empirical assignment of radii (PB radii), a problematic issue arises, since standard halogen radii are smaller than the typical X···EP distances, thus placing the EP within the solvent dielectric. Herein, we took a common literature EP parametrization scheme, which uses X···EP = Rmin and RESP charges in the context of GAFF, and performed a comprehensive study on the performance of PBSA (using three different setups) in the calculation of Δ Gsolv values for 142 halogenated compounds (bearing Cl, Br, or I) for which the experimental values are known. By conducting an optimization (minimizing the error against experimental values), we provide a new optimized set of halogen PB radii, for each PBSA setup, that should be used in the context of the aforementioned scenario. A simultaneous optimization of PB radii and X···EP distances shows that a wide range of distance/radius pairs can be used without significant loss of accuracy, therefore laying the basis for expanding this halogen radii optimization strategy to other force fields and EP implementations. As ligand Δ Gsolv estimation is an important term in the determination of protein-ligand Δ Gbind, this work is particularly relevant in the framework of structure-based virtual screening and related computer-aided drug design routines.
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Xu M, Guo S, Yang F, Wang Y, Wu C, Jiang X, Zhao Q, Chen W, Tian G, Zhu F, Xie Y, Hu T, Wang Z, He Y, Shen J. Continuation of structure–activity relationship study of novel benzamide derivatives as potential antipsychotics. Arch Pharm (Weinheim) 2019; 352:e1800306. [DOI: 10.1002/ardp.201800306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/23/2018] [Accepted: 01/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mingshuo Xu
- University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Shuang Guo
- University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory for Receptor Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
| | - Feipu Yang
- University of Chinese Academy of SciencesBeijingChina
| | - Yu Wang
- University of Chinese Academy of SciencesBeijingChina
| | - Chunhui Wu
- Topharman Shanghai Co., Ltd.ShanghaiChina
| | | | - Qingjie Zhao
- University of Chinese Academy of SciencesBeijingChina
| | | | | | | | - Yuanchao Xie
- University of Chinese Academy of SciencesBeijingChina
| | - Tianwen Hu
- Topharman Shanghai Co., Ltd.ShanghaiChina
| | - Zhen Wang
- University of Chinese Academy of SciencesBeijingChina
| | - Yang He
- University of Chinese Academy of SciencesBeijingChina
| | - Jingshan Shen
- University of Chinese Academy of SciencesBeijingChina
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13
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Nunes R, Vila-Viçosa D, Machuqueiro M, Costa PJ. Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field. J Chem Theory Comput 2018; 14:5383-5392. [PMID: 30215528 DOI: 10.1021/acs.jctc.8b00278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodine corresponding to Rmin provides a good qualitative description of XBs in MD simulations, supporting the compatibility of our approach with the GROMOS 54A7 force field.
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Affiliation(s)
- Rafael Nunes
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal.,Centro de Química Estrutural, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Paulo J Costa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
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14
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Luchi A, Angelina E, Bogado L, Forli S, Olson A, Peruchena N. Flap-site Fragment Restores Back Wild-type Behaviour in Resistant Form of HIV Protease. Mol Inform 2018; 37:e1800053. [PMID: 30051611 DOI: 10.1002/minf.201800053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/11/2018] [Indexed: 11/09/2022]
Abstract
HIV-1 protease (HIV-PR) performs a vital step in the virus life cycle which makes it an excellent target for drug therapy. However, due to the error-prone of HIV reverse transcriptase, mutations in HIV-PR often occur, inducing drug-resistance to inhibitors. Some HIV-PR mutations can make the flaps of the enzyme more flexible thus increasing the flaps opening rate and inhibitor releasing. It has been shown that by targeting novel binding sites on HIV-PR with small molecules, it is possible to alter the equilibrium of flap conformational states. A previous fragment-based crystallographic screen have found two novel binding sites for small fragments in the inhibited, closed form of HIV-PR, termed flap and exo sites. While these experiments were performed in wild type HIV-PR, it still remains to be proven whether these small fragments can stabilize the closed conformation of flaps in resistant forms of the enzyme. Here we performed Molecular Dynamics simulations of wild type and mutant form of HIV-PR bound to inhibitor TL-3. Simulations show that on going from wild type to 6X mutant the equilibrium shifts from closed to semi-open conformation of flaps. However, when fragment Br6 is placed at flap site of mutant form, the enzyme is restored back to closed conformation. This finding supports the hypothesis that allosteric inhibitors, together with active site inhibitors could increase the number of point mutations necessary for appreciable clinical resistance to AIDS therapy.
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Affiliation(s)
- Adriano Luchi
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FACENA, Av. Libertad 5470, Corrientes, 3400, Argentina
| | - Emilio Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FACENA, Av. Libertad 5470, Corrientes, 3400, Argentina
| | - Lucrecia Bogado
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FACENA, Av. Libertad 5470, Corrientes, 3400, Argentina
| | - Stefano Forli
- Molecular Graphics Lab, Department of Integrative Structural and Computational Biology, MB-112, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037-1000
| | - Arthur Olson
- Molecular Graphics Lab, Department of Integrative Structural and Computational Biology, MB-112, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037-1000
| | - Nélida Peruchena
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FACENA, Av. Libertad 5470, Corrientes, 3400, Argentina
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15
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Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis. J Comput Aided Mol Des 2018; 32:781-791. [DOI: 10.1007/s10822-018-0129-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/02/2018] [Indexed: 11/27/2022]
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16
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Kesharwani MK, Manna D, Sylvetsky N, Martin JML. The X40×10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n–1)d Subvalence Correlation. J Phys Chem A 2018; 122:2184-2197. [DOI: 10.1021/acs.jpca.7b10958] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Debashree Manna
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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17
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The σ and π Holes. The Halogen and Tetrel Bondings: Their Nature, Importance and Chemical, Biological and Medicinal Implications. ChemistrySelect 2017. [DOI: 10.1002/slct.201701676] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Tetrahydroisoquinolines functionalized with carbamates as selective ligands of D2 dopamine receptor. J Mol Model 2017; 23:273. [DOI: 10.1007/s00894-017-3441-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 08/15/2017] [Indexed: 01/11/2023]
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19
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Vettorazzi M, Angelina E, Lima S, Gonec T, Otevrel J, Marvanova P, Padrtova T, Mokry P, Bobal P, Acosta LM, Palma A, Cobo J, Bobalova J, Csollei J, Malik I, Alvarez S, Spiegel S, Jampilek J, Enriz RD. An integrative study to identify novel scaffolds for sphingosine kinase 1 inhibitors. Eur J Med Chem 2017; 139:461-481. [PMID: 28822281 DOI: 10.1016/j.ejmech.2017.08.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/02/2017] [Accepted: 08/05/2017] [Indexed: 10/19/2022]
Abstract
Sphingosine kinase 1 (SphK1), the enzyme that produces the bioactive sphingolipid metabolite, sphingosine-1-phosphate, is a promising new molecular target for therapeutic intervention in cancer and inflammatory diseases. In view of its importance, the main objective of this work was to find new and more potent inhibitors for this enzyme possessing different structural scaffolds than those of the known inhibitors. Our theoretical and experimental study has allowed us to identify two new structural scaffolds (three new compounds), which could be used as starting structures for the design and then the development of new inhibitors of SphK1. Our study was carried out in different steps: virtual screening, synthesis, bioassays and molecular modelling. From our results, we propose a new dihydrobenzo[b]pyrimido[5,4-f]azepine and two alkyl{3-/4-[1-hydroxy-2-(4-arylpiperazin-1-yl)ethyl]phenyl}carbamates as initial structures for the development of new inhibitors. In addition, our molecular modelling study using QTAIM calculations, allowed us to describe in detail the molecular interactions that stabilize the different Ligand-Receptor complexes. Such analyses indicate that the cationic head of the different compounds must be refined in order to obtain an increase in the binding affinity of these ligands.
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Affiliation(s)
- Marcela Vettorazzi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Santiago Lima
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA
| | - Tomas Gonec
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic
| | - Jan Otevrel
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic
| | - Pavlina Marvanova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic
| | - Tereza Padrtova
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic
| | - Petr Mokry
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic
| | - Pavel Bobal
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic
| | - Lina M Acosta
- Laboratorio de Síntesis Orgánica, Escuela de Química, Universidad Industrial de Santander, Carrera 27, Calle 9, A.A 678, Bucaramanga, Colombia
| | - Alirio Palma
- Laboratorio de Síntesis Orgánica, Escuela de Química, Universidad Industrial de Santander, Carrera 27, Calle 9, A.A 678, Bucaramanga, Colombia
| | - Justo Cobo
- Inorganic and Organic Department, University of Jaén, Campus Las Lagunillas s/n, 23071, Jaén, Spain
| | - Janette Bobalova
- Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i., Veveri 97, 602 00 Brno, Czech Republic
| | - Jozef Csollei
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1, 612 42 Brno, Czech Republic; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojarov 10, 83232 Bratislava, Slovakia
| | - Ivan Malik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojarov 10, 83232 Bratislava, Slovakia
| | - Sergio Alvarez
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA
| | - Josef Jampilek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojarov 10, 83232 Bratislava, Slovakia
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina.
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20
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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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