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Article ; Online: Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β

Sencanski, Milan / Glisic, Sanja / Kubale, Valentina / Cotman, Marko / Mavri, Janez / Vrecl, Milka

2024 Volume 14, Issue 4

Abstract: This study assessed the suitability of the complementarity-determining region 2 (CDR2) of the nanobody (Nb) as a template for the derivation of nanobody-derived peptides (NDPs) targeting active-state ... ...

Abstract	This study assessed the suitability of the complementarity-determining region 2 (CDR2) of the nanobody (Nb) as a template for the derivation of nanobody-derived peptides (NDPs) targeting active-state β
MeSH term(s)	Receptors, Adrenergic, beta-2/metabolism ; Receptors, Adrenergic, beta-2/chemistry ; Humans ; Single-Domain Antibodies/chemistry ; Single-Domain Antibodies/pharmacology ; Single-Domain Antibodies/metabolism ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/pharmacology ; Peptides/metabolism ; Complementarity Determining Regions/chemistry ; Molecular Docking Simulation ; Protein Binding ; Amino Acid Sequence ; Protein Conformation ; Cyclic AMP/metabolism
Chemical Substances	Receptors, Adrenergic, beta-2 ; Single-Domain Antibodies ; Peptides ; Complementarity Determining Regions ; Cyclic AMP (E0399OZS9N)
Language	English
Publishing date	2024-03-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom14040423
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Article ; Online: In Silico Screening of Natural Compounds for Candidates 5HT6 Receptor Antagonists against Alzheimer's Disease.

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

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 9

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.
MeSH term(s)	Alzheimer Disease/drug therapy ; Biological Products/chemistry ; Biological Products/pharmacology ; Biological Products/therapeutic use ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Neurodegenerative Diseases ; Receptors, Serotonin ; Zinc/therapeutic use
Chemical Substances	Biological Products ; Receptors, Serotonin ; serotonin 6 receptor ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2022-04-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27092626
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Article ; Online: In Silico and In Vitro Inhibition of SARS-CoV-2 PL

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

International journal of molecular sciences

2023 Volume 24, Issue 3

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
MeSH term(s)	Humans ; SARS-CoV-2 ; Gramicidin ; COVID-19 ; Molecular Docking Simulation ; Databases, Factual ; Protease Inhibitors/pharmacology ; Antiviral Agents/pharmacology
Chemical Substances	Gramicidin (1405-97-6) ; Protease Inhibitors ; Antiviral Agents
Language	English
Publishing date	2023-01-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24031955
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Article ; Online: Inhibition of SARS-CoV-2 M

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

Frontiers in bioscience (Landmark edition)

2023 Volume 28, Issue 1, Page(s) 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 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 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.
MeSH term(s)	Humans ; Arginine/pharmacology ; Ascorbic Acid/pharmacology ; COVID-19 ; Dietary Supplements ; SARS-CoV-2/drug effects ; Coronavirus 3C Proteases/antagonists & inhibitors
Chemical Substances	Arginine (94ZLA3W45F) ; Ascorbic Acid (PQ6CK8PD0R) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2023-01-31
Publishing country	Singapore
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2704569-9
ISSN	2768-6698 ; 2768-6698
ISSN (online)	2768-6698
ISSN	2768-6698
DOI	10.31083/j.fbl2801008
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Article ; Online: Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis.

Mavri, Maša / Glišić, Sanja / Senćanski, Milan / Vrecl, Milka / Rosenkilde, Mette M / Spiess, Katja / Kubale, Valentina

Cellular & molecular biology letters

2023 Volume 28, Issue 1, Page(s) 14

Abstract: Background: The viral G-protein-coupled receptor (vGPCR) BILF1 encoded by the Epstein-Barr virus (EBV) is an oncogene and immunoevasin and can downregulate MHC-I molecules at the surface of infected cells. MHC-I downregulation, which presumably occurs ... ...

Abstract	Background: The viral G-protein-coupled receptor (vGPCR) BILF1 encoded by the Epstein-Barr virus (EBV) is an oncogene and immunoevasin and can downregulate MHC-I molecules at the surface of infected cells. MHC-I downregulation, which presumably occurs through co-internalization with EBV-BILF1, is preserved among BILF1 receptors, including the three BILF1 orthologs encoded by porcine lymphotropic herpesviruses (PLHV BILFs). This study aimed to understand the detailed mechanisms of BILF1 receptor constitutive internalization, to explore the translational potential of PLHV BILFs compared with EBV-BILF1. Methods: A novel real-time fluorescence resonance energy transfer (FRET)-based internalization assay combined with dominant-negative variants of dynamin-1 (Dyn K44A) and the chemical clathrin inhibitor Pitstop2 in HEK-293A cells was used to study the effect of specific endocytic proteins on BILF1 internalization. Bioluminescence resonance energy transfer (BRET)-saturation analysis was used to study BILF1 receptor interaction with β-arrestin2 and Rab7. In addition, a bioinformatics approach informational spectrum method (ISM) was used to investigate the interaction affinity of BILF1 receptors with β-arrestin2, AP-2, and caveolin-1. Results: We identified dynamin-dependent, clathrin-mediated constitutive endocytosis for all BILF1 receptors. The observed interaction affinity between BILF1 receptors and caveolin-1 and the decreased internalization in the presence of a dominant-negative variant of caveolin-1 (Cav S80E) indicated the involvement of caveolin-1 in BILF1 trafficking. Furthermore, after BILF1 internalization from the plasma membrane, both the recycling and degradation pathways are proposed for BILF1 receptors. Conclusions: The similarity in the internalization mechanisms observed for EBV-BILF1 and PLHV1-2 BILF1 provide a foundation for further studies exploring a possible translational potential for PLHVs, as proposed previously, and provides new information about receptor trafficking.
MeSH term(s)	Animals ; Humans ; Caveolin 1/metabolism ; Clathrin/metabolism ; Endocytosis ; Epstein-Barr Virus Infections ; Herpesvirus 4, Human/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Swine ; Viral Proteins/metabolism
Chemical Substances	Caveolin 1 ; Clathrin ; Receptors, G-Protein-Coupled ; BILF1 protein, Epstein-Barr virus ; Viral Proteins
Language	English
Publishing date	2023-02-21
Publishing country	England
Document type	Letter
ZDB-ID	2108724-6
ISSN	1689-1392 ; 1689-1392
ISSN (online)	1689-1392
ISSN	1689-1392
DOI	10.1186/s11658-023-00427-y
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Article ; Online: Correction: Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis.

Mavri, Maša / Glišić, Sanja / Senćanski, Milan / Vrecl, Milka / Rosenkilde, Mette M / Spiess, Katja / Kubale, Valentina

Cellular & molecular biology letters

2023 Volume 28, Issue 1, Page(s) 94

Language	English
Publishing date	2023-11-24
Publishing country	England
Document type	Published Erratum
ZDB-ID	2108724-6
ISSN	1689-1392 ; 1689-1392
ISSN (online)	1689-1392
ISSN	1689-1392
DOI	10.1186/s11658-023-00512-2
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Article ; Online: Assessing the dispersive and electrostatic components of the selenium-aromatic interaction energy by DFT.

Senćanski, Milan / Djordjević, Ivana / Grubišić, Sonja

Journal of molecular modeling

2017 Volume 23, Issue 5, Page(s) 162

Abstract: Selenium has been increasingly recognized as an important element in biological systems, which participates in numerous biochemical processes in organisms, notably in enzyme reactions. Selenium can substitute sulfur of cysteine and methionine to form ... ...

Abstract	Selenium has been increasingly recognized as an important element in biological systems, which participates in numerous biochemical processes in organisms, notably in enzyme reactions. Selenium can substitute sulfur of cysteine and methionine to form their selenium analogues, selenocysteine (Sec) and selenomethionine (SeM). The nature of amino acid pockets in proteins is dependent on their composition and thus different non-covalent forces determine the interactions between selenium of Sec or SeM and other functional groups, resulting in specific biophysical behavior. The discrimination of selenium toward sulfur has been reported. In order to elucidate the difference between the nature of S-π and Se-π interactions, we performed extensive DFT calculations of dispersive and electrostatic contributions of Se-π interactions in substituted benzenes/hydrogen selenide (H
Language	English
Publishing date	2017-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-x
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-017-3330-z
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Article ; Online: Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel

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

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 17

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 ... ...

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
MeSH term(s)	Allosteric Site ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Betacoronavirus/pathogenicity ; COVID-19 ; Catalytic Domain ; Coronavirus 3C Proteases ; Coronavirus Infections/drug therapy ; Coronavirus Infections/enzymology ; Coronavirus Infections/virology ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/genetics ; Cysteine Endopeptidases/metabolism ; Drug Repositioning ; Gene Expression ; High-Throughput Screening Assays ; Humans ; Mezlocillin/chemistry ; Mezlocillin/pharmacology ; Molecular Docking Simulation ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/enzymology ; Pneumonia, Viral/virology ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Raltegravir Potassium/chemistry ; Raltegravir Potassium/pharmacology ; SARS-CoV-2 ; Thermodynamics ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Viral Nonstructural Proteins ; Raltegravir Potassium (43Y000U234) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Mezlocillin (OH2O403D1G)
Keywords	covid19
Language	English
Publishing date	2020-08-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25173830
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Article ; Online: Biological Rationale for the Repurposing of BCG Vaccine against SARS-CoV-2.

Glisic, Sanja / Perovic, Vladimir R / Sencanski, Milan / Paessler, Slobodan / Veljkovic, Veljko

Journal of proteome research

2020 Volume 19, Issue 11, Page(s) 4649–4654

Abstract: The Bacillus Calmette-Guerin vaccine is still widely used in the developing world. The vaccination prevents infant death not only from tuberculosis but also from unrelated infectious agents, especially respiratory tract infections and neonatal sepsis. It ...

Abstract	The Bacillus Calmette-Guerin vaccine is still widely used in the developing world. The vaccination prevents infant death not only from tuberculosis but also from unrelated infectious agents, especially respiratory tract infections and neonatal sepsis. It is proposed that these off-target protective effects of the BCG vaccine are mediated by the general long-term boosting of innate immune mechanisms, also termed "trained innate immunity". Recent studies indicate that both COVID-19 incidence and total deaths are strongly associated with the presence or absence of national mandatory BCG vaccination programs and encourage the initiation of several clinical studies with the expectation that revaccination with BCG could reduce the incidence and severity of COVID-19. Here, presented results from the bioinformatics analysis of the
MeSH term(s)	BCG Vaccine/chemistry ; BCG Vaccine/immunology ; Bacterial Proteins/chemistry ; Bacterial Proteins/immunology ; Betacoronavirus/chemistry ; Betacoronavirus/immunology ; COVID-19 ; COVID-19 Vaccines ; Coronavirus Infections/immunology ; Coronavirus Infections/prevention & control ; Drug Repositioning ; Humans ; Mycobacterium bovis/chemistry ; Mycobacterium bovis/immunology ; Pandemics/prevention & control ; Pneumonia, Viral/immunology ; Pneumonia, Viral/prevention & control ; Proteome/chemistry ; Proteome/immunology ; SARS-CoV-2 ; Viral Vaccines/chemistry ; Viral Vaccines/immunology
Chemical Substances	BCG Vaccine ; Bacterial Proteins ; COVID-19 Vaccines ; Proteome ; Viral Vaccines
Keywords	covid19
Language	English
Publishing date	2020-08-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00410
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Article ; Online: In silico study of the structurally similar ORL1 receptor agonist and antagonist pairs reveal possible mechanism of receptor activation.

Senćanski, Milan / Dosen-Mićović, Ljiljana

The protein journal

2014 Volume 33, Issue 3, Page(s) 231–242

Abstract: An opioid receptor like (ORL1) receptor is a member of a family of G-protein coupled receptors. It is anew pharmaceutical target with broad therapeutic potential in the regulation of important biological functions such as nociception, mood disorders, ... ...

Abstract	An opioid receptor like (ORL1) receptor is a member of a family of G-protein coupled receptors. It is anew pharmaceutical target with broad therapeutic potential in the regulation of important biological functions such as nociception, mood disorders, drug abuse, learning or cardiovascular control. The crystal structure of this receptor in complex with an antagonist was determined recently (PDBID: 4EA3). By removing the ligand and subjecting the empty receptor to molecular dynamics simulation in a solvated lipid membrane we obtained an optimized ORL1 receptor structure which could be used in a subsequent docking study of two structurally similar agonist–antagonist ligand pairs. Ligands were docked to the empty ORL1 receptor (with and without the third intracellular loop, IC3)in different orientations, and the resulting complexes were monitored during molecular dynamics simulation in order to see how the subtle differences in structure of agonists and antagonists might affect ligand–receptor interactions and trigger receptor activation. It was established that agonists and antagonists bound to the same, relatively large, binding site in the receptor, created by residues from transmembrane helices TM2, TM3, TM5, TM6 and TM7 and close to the extra cellular end of the receptor bundle.The key difference between these two types of ligands is interaction with residue Val283(6.55) and a flexibility of ligand molecules. Ligands that cannot easily avoid this interaction will initiate movement of the intracellular end of TM6 (by a mechanism which involves Met134(3.36) and several amino acids of TM5) and possibly activate the receptor when assisted by G-protein.
MeSH term(s)	Binding Sites ; Computer Simulation ; Molecular Dynamics Simulation ; Narcotic Antagonists/chemistry ; Narcotic Antagonists/metabolism ; Receptors, Opioid/agonists ; Receptors, Opioid/chemistry ; Receptors, Opioid/metabolism
Chemical Substances	Narcotic Antagonists ; Receptors, Opioid ; nociceptin receptor (DVO6VKD7IJ)
Language	English
Publishing date	2014-03-22
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-014-9555-0
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