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Article ; Online: Simple Theoretical Criterion for Selection of Natural Compounds with Anti-COVID-19 Activity

Veljko Veljkovic / Sanja Glisic / Vladimir Perovic / Milena Veljkovic / Slobodan Paessler

Frontiers in Bioscience-Landmark, Vol 27, Iss 5, p

2022 Volume 152

Abstract: Background: A novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the leading threat to global health. An effective antiviral could not only help those still vulnerable to the virus but could be a critical ... ...

Abstract	Background: A novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become the leading threat to global health. An effective antiviral could not only help those still vulnerable to the virus but could be a critical treatment if a virus emerges toward evading coronavirus disease 2019 (COVID-19) vaccines. Despite the significant efforts to test already-approved drugs for their potential to kill the virus, researchers found very few actually worked. Methods: The present report uses the electronic molecular descriptors, the quasi-valence number (AQVN), and the electron-ion interaction potential (EIIP), for the analysis of natural compounds with proven therapeutic activity against the COVID-19. Results: Based on the analysis of the electronic properties of natural compounds which are effective against SARS-CoV-2 virus the simple theoretical criterion for the selection of candidate compounds for the treatment of COVID-19 is proposed. Conclusions: The proposed theoretical criterion can be used for the identification and optimization of new lead compounds for the treatment of the COVID-19 disease and for the selection of the food and food supplements which could have a beneficial effect on COVID-19 patients.
Keywords	natural compounds ; secondary metabolites ; flavonoids ; coronavirus ; covid-19 ; electron-ion interaction potential ; average quasi-valence number ; Biochemistry ; QD415-436 ; Biology (General) ; QH301-705.5
Subject code	540
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	IMR Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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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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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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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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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Book ; Online: Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel in Silico Method

Milan Sencanski / Vladimir Perovic / Snezana Pajovic / Miroslav Adzic / Slobodan Paessler / Sanja Glisic

2020

Abstract: The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is in silico drug repurposing. ... ...

Abstract	The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening (VS) protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the ISM applied for Small Molecules was used for searching the Drugbank database and further followed by molecular docking. After in silico screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.
Keywords	Bioinformatics and Computational Biology ; Drug Discovery and Drug Delivery Systems ; Chemoinformatics - Computational Chemistry ; SARS-CoV-2 ; main protease Mpro ; drug repurposing applications ; Virtual Screening Tool ; ISM ; covid19
Subject code	540
Publishing date	2020-05-06T11:41:26Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel In Silico Method

Milan Sencanski / Vladimir Perovic / Snezana B. Pajovic / Miroslav Adzic / Slobodan Paessler / Sanja Glisic

Molecules, Vol 25, Iss 3830, p

2020 Volume 3830

Abstract	The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the Informational spectrum method applied for small molecules was used for searching the Drugbank database and further followed by molecular docking. After in silico screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.
Keywords	SARS-CoV-2 ; main protease M pro ; drug repurposing ; virtual screening ; ISM ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Interaction between Treg apoptosis pathways, Treg function and HLA risk evolves during type 1 diabetes pathogenesis.

Sanja Glisic / Parthav Jailwala

PLoS ONE, Vol 7, Iss 4, p e

2012 Volume 36040

Abstract: We have previously reported increased apoptosis of regulatory T cells (Tregs) in recent-onset Type 1 Diabetes subjects (RO T1D) in the honeymoon phase and in multiple autoantibody-positive (Ab+) subjects, some of which are developing T1D. We have also ... ...

Abstract	We have previously reported increased apoptosis of regulatory T cells (Tregs) in recent-onset Type 1 Diabetes subjects (RO T1D) in the honeymoon phase and in multiple autoantibody-positive (Ab+) subjects, some of which are developing T1D. We have also reported that increased Treg apoptosis was associated with High HLA risk and that it subsided with cessation of honeymoon period. In this report, we present results generated using genetics, genomics, functional cell-based assays and flow cytometry to assess cellular changes at the T-cell level during T1D pathogenesis. We measured ex vivo Treg apoptosis and Treg function, surface markers expression, expression of HLA class II genes, the influence of HLA risk on Treg apoptosis and function, and evaluated contribution of genes reported to be involved in the apoptosis process. This integrated comprehensive approach uncovered important information that can serve as a basis for future studies aimed to modulate Treg cell responsiveness to apoptotic signals in autoimmunity. For example, T1D will progress in those subjects where increased Treg apoptosis is accompanied with decreased Treg function. Furthermore, Tregs from High HLA risk healthy controls had increased Treg apoptosis levels and overexpressed FADD but not Fas/FasL. Tregs from RO T1D subjects in the honeymoon phase were primarily dying through withdrawal of growth hormones with contribution of oxidative stress, mitochondrial apoptotic pathways, and employment of TNF-receptor family members. Ab+ subjects, however, expressed high inflammation level, which probably contributed to Treg apoptosis, although other apoptotic pathways were also activated: withdrawal of growth hormones, oxidative stress, mitochondrial apoptosis and Fas/FasL apoptotic pathways. The value of these results lie in potentially different preventive treatment subjects would receive depending on disease progression stage when treated.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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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Article ; Online: Pomegranate (Punica granatum)

Veljko Veljkovic / Sanja Glisic / Vladimir Perovic / Garth L Nicolson

Functional Foods in Health and Disease, Vol 6, Iss 10, Pp 769-

a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics

2016 Volume 787

Abstract: Background: Numerous in vitro and in vivo studies, in addition to clinical data, demonstrate that pomegranate juice can prevent or slow-down the progression of some types of cancers. Despite the well-documented effect of pomegranate ingredients on ... ...

Abstract	Background: Numerous in vitro and in vivo studies, in addition to clinical data, demonstrate that pomegranate juice can prevent or slow-down the progression of some types of cancers. Despite the well-documented effect of pomegranate ingredients on neoplastic changes, the molecular mechanism(s) underlying this phenomenon remains elusive. Methods: For the study of pomegranate ingredients the electron-ion interaction potential (EIIP) and the average quasi valence number (AQVN) were used. These molecular descriptors can be used to describe the long-range intermolecular interactions in biological systems and can identify substances with strong electron-acceptor properties. In this study, candidate human proteins interacting with pomegranate flavonoids have been analyzed by the informational spectrum method (ISM). This represents a virtual spectroscopy method for studying protein molecular interactions. Results: Our analysis indicates that the anti-cancer properties of pomegranate juice can be ascribed to the strong electron-acceptor properties of its chemical ingredients. This analysis also suggests that pomegranate flavonoids inhibit the “NF-kappaB” (NF-B) pathway, which plays a critical role in the pathogenesis of cancer. Conclusion: The results offer a possible explanation for an important molecular mechanism underlying the anticancer activity of pomegranate ingredients, which could also serve as a basis for the development of new therapeutic compositions of food supplements with pomegranate-like anticancer properties.
Keywords	cancer ; pomegranate ; flavonoids ; food supplement ; informational spectrum method ; Nutrition. Foods and food supply ; TX341-641 ; Medicine (General) ; R5-920
Subject code	540
Language	English
Publishing date	2016-10-01T00:00:00Z
Publisher	Food Science Publisher
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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