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Meador WE, Kapusta K, Owolabi I, Autry SA, Saloni J, Kolodziejczyk W, Hammer NI, Flynt AS, Hill GA, Delcamp JH. Ultra Bright Near‐Infrared Sulfonate‐Indolizine Cyanine‐ and Squaraine‐Albumin Chaperones: Record Quantum Yields and Applications. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- William E. Meador
- University of Mississippi Department of Chemistry and Biochemistry 38677 University UNITED STATES
| | - Karina Kapusta
- Jackson State University Department of Chemistry, Physics and Atmospheric Sciences 39217 Jackson UNITED STATES
| | - Iyanuoluwani Owolabi
- University of Southern Mississippi Department of Biological Sciences 39406 UNITED STATES
| | - Shane A. Autry
- University of Mississippi Department of Chemistry and Biochemistry 38677 UNITED STATES
| | - Julia Saloni
- Jackson State University Department of Chemistry, Physics and Atmospheric Sciences 39217 UNITED STATES
| | - Wojciech Kolodziejczyk
- Jackson State University Department of Chemistry, Physics and Atmospheric Sciences 39217 UNITED STATES
| | - Nathan I. Hammer
- University of Mississippi Department of Chemistry and Biochemistry 38677 UNITED STATES
| | - Alex S. Flynt
- University of Southern Mississippi Department of Biological Sciences 39406 UNITED STATES
| | - Glake A. Hill
- Jackson State University Department of Chemistry, Physics and Atmospheric Sciences 39217 UNITED STATES
| | - Jared Heath Delcamp
- University of Mississippi Chemistry 405 Coulter Hall 38677 University UNITED STATES
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Toledo EJL, Ramalho TC. Controversies about hydrogen bonds in water molecules on the influence of high magnetic fields: implications on structural and electronic parameters. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1957883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Teodorico C. Ramalho
- Chemistry Department, Federal University of Lavras, Lavras, Brazil
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, Hradec Kralove, Czech Republic
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Kuz’min V, Artemenko A, Ognichenko L, Hromov A, Kosinskaya A, Stelmakh S, Sessions ZL, Muratov EN. Simplex representation of molecular structure as universal QSAR/QSPR tool. Struct Chem 2021; 32:1365-1392. [PMID: 34177203 PMCID: PMC8218296 DOI: 10.1007/s11224-021-01793-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/07/2021] [Indexed: 10/24/2022]
Abstract
We review the development and application of the Simplex approach for the solution of various QSAR/QSPR problems. The general concept of the simplex method and its varieties are described. The advantages of utilizing this methodology, especially for the interpretation of QSAR/QSPR models, are presented in comparison to other fragmentary methods of molecular structure representation. The utility of SiRMS is demonstrated not only in the standard QSAR/QSPR applications, but also for mixtures, polymers, materials, and other complex systems. In addition to many different types of biological activity (antiviral, antimicrobial, antitumor, psychotropic, analgesic, etc.), toxicity and bioavailability, the review examines the simulation of important properties, such as water solubility, lipophilicity, as well as luminescence, and thermodynamic properties (melting and boiling temperatures, critical parameters, etc.). This review focuses on the stereochemical description of molecules within the simplex approach and details the possibilities of universal molecular stereo-analysis and stereochemical configuration description, along with stereo-isomerization mechanism and molecular fragment "topography" identification.
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Affiliation(s)
- Victor Kuz’min
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Anatoly Artemenko
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Luidmyla Ognichenko
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Alexander Hromov
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Anna Kosinskaya
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
- Department of Medical Chemistry, Odessa National Medical University, Odessa, 65082 Ukraine
| | - Sergij Stelmakh
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Zoe L. Sessions
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Eugene N. Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, PB 58059 Brazil
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Mamede R, de-Almeida BS, Chen M, Zhang Q, Aires-de-Sousa J. Machine Learning Classification of One-Chiral-Center Organic Molecules According to Optical Rotation. J Chem Inf Model 2020; 61:67-75. [PMID: 33350814 DOI: 10.1021/acs.jcim.0c00876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, machine learning algorithms were investigated for the classification of organic molecules with one carbon chiral center according to the sign of optical rotation. Diverse heterogeneous data sets comprising up to 13,080 compounds and their corresponding optical rotation were retrieved from Reaxys and processed independently for three solvents: dichloromethane, chloroform, and methanol. The molecular structures were represented by chiral descriptors based on the physicochemical and topological properties of ligands attached to the chiral center. The sign of optical rotation was predicted by random forests (RF) and artificial neural networks for independent test sets with an accuracy of up to 75% for dichloromethane, 82% for chloroform, and 82% for methanol. RF probabilities and the availability of structures in the training set with the same spheres of atom types around the chiral center defined applicability domains in which the accuracy is higher.
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Affiliation(s)
- Rafael Mamede
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Bruno Simões de-Almeida
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Mengyao Chen
- Henan Engineering Research Center of Industrial Circulating Water Treatment, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, Henan University, Kaifeng 475004, PR China
| | - Qingyou Zhang
- Henan Engineering Research Center of Industrial Circulating Water Treatment, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, Henan University, Kaifeng 475004, PR China
| | - Joao Aires-de-Sousa
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
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Computer-aided molecular and processes design based on quantum chemistry: current status and future prospects. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2019.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Kapusta K, Sizochenko N, Anderson ML, Kolodziejczyk W, Voronkov EO, Saloni J, Leszczynski J, Hill GA. N-arylnaphthylamines as inhibitors of human immunodeficiency virus integrase - lens epithelium-derived growth factor interactions: theoretical studies. J Biomol Struct Dyn 2020; 39:867-880. [PMID: 31965914 DOI: 10.1080/07391102.2020.1719203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Presented work reports a comprehensive theoretical study on the inhibitory nature of N-arylnaphthylamines in Human Immunodeficiency Virus Integrase (HIV IN) - Lens Epithelium-Derived Growth Factor (LEDGF/p75) complexes. Factors influencing the inhibition efficiency in AlphaScreen% assay are evaluated and explained through the structure- and ligand-based studies; including molecular docking, molecular dynamics calculations, and quantitative structure-activity relationship (QSAR) approach. It has been shown that N-arylnaphthylamines possess a wide variety of binding poses. Three QSAR models have been developed using structural descriptors and descriptors derived from docking calculations. The activity of untested N-arylnaphthylamines have been predicted using the most successful model. Proposed here technique could become a useful tool for ligand selection, accelerating the development of a new generation of anti-HIV medications. [Formula: see text] Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karina Kapusta
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
| | | | - Micah L Anderson
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
| | - Wojciech Kolodziejczyk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
| | | | - Julia Saloni
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
| | - Glake A Hill
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS, USA
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Light-dependent isomeric effects of polycyclic aromatic hydrocarbons on the predication of DNA cleavage factor efficiency. Struct Chem 2018. [DOI: 10.1007/s11224-018-1196-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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