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      Density functional theory and molecular docking study to lutein molecule for COVID-19 protease inhibitors

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          Abstract

          Since the beginning of the corona pandemic, numerous scientific projects have been conducted worldwide to investigate how the new virus can be combated. Researchers are developing various vaccines and drugs at full speed – with varying degrees of success. In this work, silico screening (molecular docking analysis) is performed on twenty natural compounds, which are expected to provide valuable lead molecules and medication to treat a new condition SARS-CoV-2. Our results indicate that out of the 20 compounds on the candidate list, lutein and Polydatin, natural components of fruits and vegetables (especially egg yolk and maize) have shown an excellent performance in our docking studies through a minimum binding energy of − 9.8 kcal/mol also − 7.4 kcal/mol, separately. This indicates their potential for the inhibitory molecular interactions against COVID-19. The main intent of the research is to analyse the protein components and investigate the molecules.

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          Is Open Access

          Pandemics, tourism and global change: a rapid assessment of COVID-19

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            The COVID-19 vaccine development landscape

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              Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules.

              Epik is a computer program for predicting pK(a) values for drug-like molecules. Epik can use this capability in combination with technology for tautomerization to adjust the protonation state of small drug-like molecules to automatically generate one or more of the most probable forms for use in further molecular modeling studies. Many medicinal chemicals can exchange protons with their environment, resulting in various ionization and tautomeric states, collectively known as protonation states. The protonation state of a drug can affect its solubility and membrane permeability. In modeling, the protonation state of a ligand will also affect which conformations are predicted for the molecule, as well as predictions for binding modes and ligand affinities based upon protein-ligand interactions. Despite the importance of the protonation state, many databases of candidate molecules used in drug development do not store reliable information on the most probable protonation states. Epik is sufficiently rapid and accurate to process large databases of drug-like molecules to provide this information. Several new technologies are employed. Extensions to the well-established Hammett and Taft approaches are used for pK(a) prediction, namely, mesomer standardization, charge cancellation, and charge spreading to make the predicted results reflect the nature of the molecule itself rather just for the particular Lewis structure used on input. In addition, a new iterative technology for generating, ranking and culling the generated protonation states is employed.
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                Author and article information

                Contributors
                dhkh77@yahoo.com
                sc.adil_nameh78@uoanbar.edu.iq
                Journal
                Appl Nanosci
                Appl Nanosci
                Applied Nanoscience
                Springer International Publishing (Cham )
                2190-5509
                2190-5517
                19 January 2023
                : 1-12
                Affiliations
                [1 ]GRID grid.497428.4, Department of Medical Physics, College of Applied Science, , University of Fallujah, ; Baghdad, Iraq
                [2 ]GRID grid.440827.d, ISNI 0000 0004 1771 7374, Department of Physics, , College of Science, University of Anbar, ; Ramadi, Iraq
                Author information
                http://orcid.org/0000-0003-1505-4020
                Article
                2735
                10.1007/s13204-022-02735-9
                9850325
                36691520
                e870dda9-a410-4219-a9c1-2b5bd09e22b8
                © King Abdulaziz City for Science and Technology 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 25 August 2022
                : 9 December 2022
                Categories
                Original Article

                covid-19,polyphenols,molecular docking,active sites.lutein

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