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  1. Article ; Online: In Silico Screening of Natural Compounds for Candidates 5HT6 Receptor Antagonists against Alzheimer’s Disease

    Tijana Bojić / Milan Sencanski / Vladimir Perovic / Jelena Milicevic / Sanja Glisic

    Molecules, Vol 27, Iss 2626, p

    2022  Volume 2626

    Abstract: Alzheimer’s disease (AD), a devastating neurodegenerative disease, is the focus of pharmacological research. One of the targets that attract the most attention for the potential therapy of AD is the serotonin 5HT6 receptor, which is the receptor situated ...

    Abstract Alzheimer’s disease (AD), a devastating neurodegenerative disease, is the focus of pharmacological research. One of the targets that attract the most attention for the potential therapy of AD is the serotonin 5HT6 receptor, which is the receptor situated exclusively in CNS on glutamatergic and GABAergic neurons. The neurochemical impact of this receptor supports the hypothesis about its role in cognitive, learning, and memory systems, which are of critical importance for AD. Natural products are a promising source of novel bioactive compounds with potential therapeutic potential as a 5HT6 receptor antagonist in the treatment of AD dementia. The ZINC—natural product database was in silico screened in order to find the candidate antagonists of 5-HT6 receptor against AD. A virtual screening protocol that includes both short-and long-range interactions between interacting molecules was employed. First, the EIIP/AQVN filter was applied for in silico screening of the ZINC database followed by 3D QSAR and molecular docking. Ten best candidate compounds were selected from the ZINC Natural Product database as potential 5HT6 Receptor antagonists and were proposed for further evaluation. The best candidate was evaluated by molecular dynamics simulations and free energy calculations.
    Keywords molecular docking ; ligand-based virtual screening ; ADMET calculations ; FEP simulations ; Organic chemistry ; QD241-441
    Subject code 540
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: In Silico and In Vitro Inhibition of SARS-CoV-2 PL pro with Gramicidin D

    Sara Protić / Nevena Kaličanin / Milan Sencanski / Olivera Prodanović / Jelena Milicevic / Vladimir Perovic / Slobodan Paessler / Radivoje Prodanović / Sanja Glisic

    International Journal of Molecular Sciences, Vol 24, Iss 1955, p

    2023  Volume 1955

    Abstract: Finding an effective drug to prevent or treat COVID-19 is of utmost importance in tcurrent pandemic. Since developing a new treatment takes a significant amount of time, drug repurposing can be an effective option for achieving a rapid response. This ... ...

    Abstract Finding an effective drug to prevent or treat COVID-19 is of utmost importance in tcurrent pandemic. Since developing a new treatment takes a significant amount of time, drug repurposing can be an effective option for achieving a rapid response. This study used a combined in silico virtual screening protocol for candidate SARS-CoV-2 PL pro inhibitors. The Drugbank database was searched first, using the Informational Spectrum Method for Small Molecules, followed by molecular docking. Gramicidin D was selected as a peptide drug, showing the best in silico interaction profile with PL pro . After the expression and purification of PL pro , gramicidin D was screened for protease inhibition in vitro and was found to be active against PL pro . The current study’s findings are significant because it is critical to identify COVID-19 therapies that are efficient, affordable, and have a favorable safety profile.
    Keywords anti SARS-CoV-2 ; PL pro ; COVID-19 ; gramicidin D ; PL pro candidate inhibitor ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 333
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Inhibition of SARS-CoV-2 Mpro with Vitamin C, L-Arginine and a Vitamin C/L-Arginine Combination

    Ivana Đukić / Nevena Kaličanin / Milan Sencanski / Snezana B. Pajovic / Jelena Milicevic / Jelena Prljic / Slobodan Paessler / Radivoje Prodanović / Sanja Glisic

    Frontiers in Bioscience-Landmark, Vol 28, Iss 1, p

    2023  Volume 8

    Abstract: Background: Drug resistance is a critical problem in health care that affects therapy outcomes and requires new approaches to drug design. SARS-CoV-2 Mpro mutations are of concern as they can potentially reduce therapeutic efficacy. Viral infections are ... ...

    Abstract Background: Drug resistance is a critical problem in health care that affects therapy outcomes and requires new approaches to drug design. SARS-CoV-2 Mpro mutations are of concern as they can potentially reduce therapeutic efficacy. Viral infections are amongst the many disorders for which nutraceuticals have been employed as an adjunct therapy. The aim of this study was to examine the potential in vitro activity of L-arginine and vitamin C against SARS-CoV-2 Mpro. Methods: The Mpro inhibition assay was developed by cloning, expression, purification, and characterization of Mpro. Selected compounds were then screened for protease inhibition. Results: L-arginine was found to be active against SARS-CoV-2 Mpro, while a vitamin C/L-arginine combination had a synergistic antiviral action against Mpro. These findings confirm the results of our previous in silico repurposing study that showed L-arginine and vitamin C were potential Mpro inhibitors. Moreover, they suggest a possible molecular mechanism to explain the beneficial effect of arginine in COVID patients. Conclusions: The findings of the current study are important because they help to identify COVID-19 treatments that are efficient, inexpensive, and have a favorable safety profile. The results of this study also suggest a possible adjuvant nutritional strategy for COVID-19 that could be used in conjunction with pharmacological agents.
    Keywords anti sars-cov-2 ; mpro ; covid-19 ; arginine ; vitamin c/arginine combination ; mpro candidate inhibitors ; Biochemistry ; QD415-436 ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher IMR Press
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: In Silico Investigation of Selected Pesticides and Their Determination in Agricultural Products Using QuEChERS Methodology and HPLC-DAD

    Stefan Petrović / Biljana Arsić / Ivana Zlatanović / Jelena Milićević / Sanja Glišić / Milan Mitić / Rada Đurović-Pejčev / Gordana Stojanović

    International Journal of Molecular Sciences, Vol 24, Iss 8003, p

    2023  Volume 8003

    Abstract: In this study, we considered some pesticides as active substances within formulations for the protection of plant-based food in the Republic of Serbia in silico, because these pesticides have not often been investigated in this way previously, and in an ... ...

    Abstract In this study, we considered some pesticides as active substances within formulations for the protection of plant-based food in the Republic of Serbia in silico, because these pesticides have not often been investigated in this way previously, and in an analytical way, because there are not very many available fast, cheap, and easy methods for their determination in real agricultural samples. Seven pesticides were detected in selected agricultural products (tomatoes, cucumbers, peppers, and grapes) using the QuEChERS methodology and HPLC-DAD. Standard curves for the investigated pesticides (chlorantraniliprole, methomyl, metalaxyl, thiacloprid, acetamiprid, emamectin benzoate, and cymoxanil) show good linearity, with R 2 values from 0.9785 to 0.9996. The HPLC-DAD method is fast, and these pesticides can be determined in real spiked samples in less than 15 min. We further characterized the pesticides we found in food based on physicochemical properties and molecular descriptors to predict the absorption, distribution, metabolism, elimination, and toxicity (ADMET) of the compounds. We summarized the data supporting their effects on humans using various computational tools to determine their potential adverse effects. The results of our prediction study show that all of the selected pesticides considered in this study have good oral bioavailability, and those with high toxicity, therefore, could be harmful to human health. Chlorantraniliprole was shown in a molecular docking study as a good starting point for a new Alzheimer’s disease drug candidate.
    Keywords agriculture ; toxicity ; Alzheimer’s disease ; EIIP ; Mus musculus ; Homo sapiens ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Computational Studies on Selected Macrolides Active against Escherichia coli Combined with the NMR Study of Tylosin A in Deuterated Chloroform

    Biljana Arsic / Jill Barber / Ana Cikos / Manikandan Kadirvel / Emilija Kostic / Andrew J. McBain / Jelena Milicevic / Angela Oates / Andrew Regan

    Molecules, Vol 27, Iss 7280, p

    2022  Volume 7280

    Abstract: Although many antibiotics are active against Gram-positive bacteria, fewer also show activity against Gram-negative bacteria. Here, we present a combination of in silico (electron ion-interaction potential, molecular docking, ADMET), NMR, and ... ...

    Abstract Although many antibiotics are active against Gram-positive bacteria, fewer also show activity against Gram-negative bacteria. Here, we present a combination of in silico (electron ion-interaction potential, molecular docking, ADMET), NMR, and microbiological investigations of selected macrolides (14-membered, 15-membered, and 16-membered), aiming to discover the pattern of design for macrolides active against Gram-negative bacteria. Although the conformational studies of 14-membered and 15-membered macrolides are abundant in the literature, 16-membered macrolides, and their most prominent representative tylosin A, have received relatively little research attention. We therefore report the complete 1 H and 13 C NMR assignment of tylosin A in deuterated chloroform, as well as its 3D solution structure determined through molecular modelling (conformational search) and 2D ROESY NMR. Additionally, due to the degradation of tylosin A in deuterated chloroform, other species were also detected in 1D and 2D NMR spectra. We additionally studied the anti-bacterial activity of tylosin A and B against selected Gram-positive and Gram-negative bacteria.
    Keywords macrolides ; bacteria ; 2D ROESY NMR ; Organic chemistry ; QD241-441
    Subject code 540
    Language English
    Publishing date 2022-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Identification of SARS‐CoV‐2 Papain‐like Protease (PLpro) Inhibitors Using Combined Computational Approach**

    Dr. Milan Sencanski / Dr. Vladimir Perovic / Dr. Jelena Milicevic / Dr. Tamara Todorovic / Dr. Radivoje Prodanovic / Dr. Veljko Veljkovic / Dr. Slobodan Paessler / Dr. Sanja Glisic

    ChemistryOpen, Vol 11, Iss 2, Pp n/a-n/a (2022)

    2022  

    Abstract: Abstract In the current pandemic, finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID‐19 is in silico drug repurposing. The SARS‐CoV‐2 PLpro promotes viral replication and ... ...

    Abstract Abstract In the current pandemic, finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID‐19 is in silico drug repurposing. The SARS‐CoV‐2 PLpro promotes viral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and therefore is an attractive drug target. In this study, we used a combined in silico virtual screening for candidates for SARS‐CoV‐2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS‐CoV‐2 PLpro inhibitors that we propose for further experimental testing.
    Keywords drug repurposing ; ISM ; molecular docking ; Papain-like protease ; SARS-CoV-2 ; Chemistry ; QD1-999
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Wiley-VCH
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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