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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: Alignment-free method for functional annotation of amino acid substitutions

Branislava Gemović / Vladimir Perović / Radoslav Davidović / Tamara Drljača / Nevena Veljkovic

PLoS ONE, Vol 16, Iss 1, p e

Application on epigenetic factors involved in hematologic malignancies.

2021 Volume 0244948

Abstract: For the last couple of decades, there has been a significant growth in sequencing data, leading to an extraordinary increase in the number of gene variants. This places a challenge on the bioinformatics research community to develop and improve ... ...

Abstract	For the last couple of decades, there has been a significant growth in sequencing data, leading to an extraordinary increase in the number of gene variants. This places a challenge on the bioinformatics research community to develop and improve computational tools for functional annotation of new variants. Genes coding for epigenetic regulators have important roles in cancer pathogenesis and mutations in these genes show great potential as clinical biomarkers, especially in hematologic malignancies. Therefore, we developed a model that specifically focuses on these genes, with an assumption that it would outperform general models in predicting the functional effects of amino acid substitutions. EpiMut is a standalone software that implements a sequence based alignment-free method. We applied a two-step approach for generating sequence based features, relying on the biophysical and biochemical indices of amino acids and the Fourier Transform as a sequence transformation method. For each gene in the dataset, the machine learning algorithm-Naïve Bayes was used for building a model for prediction of the neutral or disease-related status of variants. EpiMut outperformed state-of-the-art tools used for comparison, PolyPhen-2, SIFT and SNAP2. Additionally, EpiMut showed the highest performance on the subset of variants positioned outside conserved functional domains of analysed proteins, which represents an important group of cancer-related variants. These results imply that EpiMut can be applied as a first choice tool in research of the impact of gene variants in epigenetic regulators, especially in the light of the biomarker role in hematologic malignancies. EpiMut is freely available at https://www.vin.bg.ac.rs/180/tools/epimut.php.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
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: 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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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: The first insight into the genetic structure of the population of modern Serbia

Tamara Drljaca / Branka Zukic / Vladimir Kovacevic / Branislava Gemovic / Kristel Klaassen-Ljubicic / Vladimir Perovic / Mladen Lazarevic / Sonja Pavlovic / Nevena Veljkovic

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 12

Abstract: Abstract The complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses ... ...

Abstract	Abstract The complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses fine-scale genetic diversity. Despite significant efforts in recent years, uneven representation still characterizes genomic resources and among the underrepresented European populations are the Western Balkans including the Serbian population. Our research addresses this gap and presents the first ever targeted sequencing dataset of variants in clinically relevant genes. By measuring population differentiation and applying the Principal Component and Admixture analysis we demonstrated that the Serbian population differs little from other European populations, yet we identified several novel and more frequent variants that appear as its unique genetic determinants. We explored thoroughly the functional impact of frequent variants and its correlation with the health burden of the population of Serbia based on a sample of 144 individuals. Our variants catalogue improves the understanding of genetics of modern Serbia, contributes to research on ancestry, and aids in improvements of well-being and health equity. In addition, this resource may also be applicable in neighboring regions and valuable in worldwide functional analyses of genetic variants in individuals of European descent.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Colonization with Multidrug-Resistant Bacteria in the First Week of Life among Hospitalized Preterm Neonates in Serbia

Marija Milic / Marina Siljic / Valentina Cirkovic / Milos Jovicevic / Vladimir Perovic / Milos Markovic / Jelena Martic / Maja Stanojevic / Vera Mijac

Microorganisms, Vol 9, Iss 2613, p

Risk Factors and Outcomes

2021 Volume 2613

Abstract: The aim of this prospective cohort study was to determine the prevalence of gut colonization with multidrug-resistant (MDR) bacteria, risk factors for colonization, infection risk, and outcomes among preterm neonates hospitalized at a tertiary-care ... ...

Abstract	The aim of this prospective cohort study was to determine the prevalence of gut colonization with multidrug-resistant (MDR) bacteria, risk factors for colonization, infection risk, and outcomes among preterm neonates hospitalized at a tertiary-care center in Serbia. During the period from December 2017 to April 2018, 103 neonates were screened for rectal carriage at admission and on the seventh day of life. Characterization of MDR strains was done by conventional microbiology and molecular methods. Out of 61 (59.2%) colonized neonates, 12 (11.6%) were found colonized at admission, while 49 (47.6%) became colonized at the study site. Among a total of 72 MDR isolates, extended-spectrum beta-lactamase (ESBL)-producing enterobacteria prevailed (56/72, 77%), followed by Acinetobacter baumannii (14/72, 19%). The majority of ESBL-producing strains carried multiple genes ( bla TEM/ bla CTX-M-15 or bla TEM/ bla SHV). Longer previous hospitalization and delivery by cesarean section were associated with MDR colonization, while mechanical ventilation was a risk factor for colonization at the study site. Infections due to MDR bacteria were more frequent among colonized than non-colonized neonates, but not significantly, and mortality was low (1%) in the studied neonates. These results indicate that hospitalized preterm neonates in Serbia are rapidly colonized with a diversity of MDR species and resistance phenotypes/genotypes.
Keywords	preterm neonates ; multidrug-resistant bacteria ; gut colonization ; risk factors ; infection ; outcome ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 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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