TY  - JOUR
AU  - Senćanski, Milan
AU  - Glišić, Sanja
AU  - Kubale, Valentina
AU  - Cotman, Marko
AU  - Mavri, Janez
AU  - Vrecl, Milka
PY  - 2024
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/13222
AB  - 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 β2-adrenergic receptor (β2AR) conformation. Sequences of conformationally selective Nbs favoring the agonist-occupied β2AR were initially analyzed by the informational spectrum method (ISM). The derived NDPs in complex with β2AR were subjected to protein–peptide docking, molecular dynamics (MD) simulations, and metadynamics-based free-energy binding calculations. Computational analyses identified a 25-amino-acid-long CDR2-NDP of Nb71, designated P4, which exhibited the following binding free-energy for the formation of the β2AR:P4 complex (ΔG = −6.8 ± 0.8 kcal/mol or a Ki = 16.5 μM at 310 K) and mapped the β2AR:P4 amino acid interaction network. In vitro characterization showed that P4 (i) can cross the plasma membrane, (ii) reduces the maximum isoproterenol-induced cAMP level by approximately 40% and the isoproterenol potency by up to 20-fold at micromolar concentration, (iii) has a very low affinity to interact with unstimulated β2AR in the cAMP assay, and (iv) cannot reduce the efficacy and potency of the isoproterenol-mediated β2AR/β-arrestin-2 interaction in the BRET2-based recruitment assay. In summary, the CDR2-NDP, P4, binds preferentially to agonist-activated β2AR and disrupts Gαs-mediated signaling.
T2  - Biomolecules
T1  - Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR)
VL  - 14
IS  - 4
SP  - 423
DO  - 10.3390/biom14040423
ER  - 

@article{
author = "Senćanski, Milan and Glišić, Sanja and Kubale, Valentina and Cotman, Marko and Mavri, Janez and Vrecl, Milka",
year = "2024",
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 β2-adrenergic receptor (β2AR) conformation. Sequences of conformationally selective Nbs favoring the agonist-occupied β2AR were initially analyzed by the informational spectrum method (ISM). The derived NDPs in complex with β2AR were subjected to protein–peptide docking, molecular dynamics (MD) simulations, and metadynamics-based free-energy binding calculations. Computational analyses identified a 25-amino-acid-long CDR2-NDP of Nb71, designated P4, which exhibited the following binding free-energy for the formation of the β2AR:P4 complex (ΔG = −6.8 ± 0.8 kcal/mol or a Ki = 16.5 μM at 310 K) and mapped the β2AR:P4 amino acid interaction network. In vitro characterization showed that P4 (i) can cross the plasma membrane, (ii) reduces the maximum isoproterenol-induced cAMP level by approximately 40% and the isoproterenol potency by up to 20-fold at micromolar concentration, (iii) has a very low affinity to interact with unstimulated β2AR in the cAMP assay, and (iv) cannot reduce the efficacy and potency of the isoproterenol-mediated β2AR/β-arrestin-2 interaction in the BRET2-based recruitment assay. In summary, the CDR2-NDP, P4, binds preferentially to agonist-activated β2AR and disrupts Gαs-mediated signaling.",
journal = "Biomolecules",
title = "Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR)",
volume = "14",
number = "4",
pages = "423",
doi = "10.3390/biom14040423"
}

Senćanski, M., Glišić, S., Kubale, V., Cotman, M., Mavri, J.,& Vrecl, M.. (2024). Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR). in Biomolecules, 14(4), 423.
https://doi.org/10.3390/biom14040423

Senćanski M, Glišić S, Kubale V, Cotman M, Mavri J, Vrecl M. Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR). in Biomolecules. 2024;14(4):423.
doi:10.3390/biom14040423 .

Senćanski, Milan, Glišić, Sanja, Kubale, Valentina, Cotman, Marko, Mavri, Janez, Vrecl, Milka, "Computational Modeling and Characterization of Peptides Derived from Nanobody Complementary-Determining Region 2 (CDR2) Targeting Active-State Conformation of the β2-Adrenergic Receptor (β2AR)" in Biomolecules, 14, no. 4 (2024):423,
https://doi.org/10.3390/biom14040423 . .

TY  - JOUR
AU  - Mavri, Maša
AU  - Glišić, Sanja
AU  - Senćanski, Milan
AU  - Vrecl, Milka
AU  - Rosenkilde, Mette M.
AU  - Spiess, Katja
AU  - Kubale, Valentina
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10682
AB  - 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.
T2  - Cellular and Molecular Biology Letters
T1  - Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis
VL  - 28
IS  - 1
SP  - 14
DO  - 10.1186/s11658-023-00427-y
ER  - 

@article{
author = "Mavri, Maša and Glišić, Sanja and Senćanski, Milan and Vrecl, Milka and Rosenkilde, Mette M. and Spiess, Katja and Kubale, Valentina",
year = "2023",
abstract = "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.",
journal = "Cellular and Molecular Biology Letters",
title = "Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis",
volume = "28",
number = "1",
pages = "14",
doi = "10.1186/s11658-023-00427-y"
}

Mavri, M., Glišić, S., Senćanski, M., Vrecl, M., Rosenkilde, M. M., Spiess, K.,& Kubale, V.. (2023). Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis. in Cellular and Molecular Biology Letters, 28(1), 14.
https://doi.org/10.1186/s11658-023-00427-y

Mavri M, Glišić S, Senćanski M, Vrecl M, Rosenkilde MM, Spiess K, Kubale V. Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis. in Cellular and Molecular Biology Letters. 2023;28(1):14.
doi:10.1186/s11658-023-00427-y .

Mavri, Maša, Glišić, Sanja, Senćanski, Milan, Vrecl, Milka, Rosenkilde, Mette M., Spiess, Katja, Kubale, Valentina, "Patterns of human and porcine gammaherpesvirus-encoded BILF1 receptor endocytosis" in Cellular and Molecular Biology Letters, 28, no. 1 (2023):14,
https://doi.org/10.1186/s11658-023-00427-y . .