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  - Senćanski, Milan V.
AU  - Glišić, Sanja
AU  - Šnajder, Marko
AU  - Veljković, Nevena V.
AU  - Poklar Ulrih, Nataša
AU  - Mavri, Janez
AU  - Vrecl, Milka
PY  - 2019
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8648
AB  - This study aimed to design and functionally characterize peptide mimetics of the nanobody (Nb) related to the β2-adrenergic receptor (β2-AR) (nanobody-derived peptide, NDP). We postulated that the computationally derived and optimized complementarity-determining region 3 (CDR3) of Nb is sufficient for its interaction with receptor. Sequence-related Nb-families preferring the agonist-bound active conformation of β2-AR were analysed using the informational spectrum method (ISM) and β2-AR:NDP complexes studied using protein-peptide docking and molecular dynamics (MD) simulations in conjunction with metadynamics calculations of free energy binding. The selected NDP of Nb71, designated P3, was 17 amino acids long and included CDR3. Metadynamics calculations yielded a binding free energy for the β2-AR:P3 complex of ΔG = (−7.23 ± 0.04) kcal/mol, or a Kd of (7.9 ± 0.5) μM, for T = 310 K. In vitro circular dichroism (CD) spectropolarimetry and microscale thermophoresis (MST) data provided additional evidence for P3 interaction with agonist-activated β2-AR, which displayed ~10-fold higher affinity for P3 than the unstimulated receptor (MST-derived EC50 of 3.57 µM vs. 58.22 µM), while its ability to inhibit the agonist-induced interaction of β2-AR with β-arrestin 2 was less evident. In summary, theoretical and experimental evidence indicated that P3 preferentially binds agonist-activated β2-AR. © 2019, The Author(s).
T2  - Scientific Reports
T1  - Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR)
VL  - 9
IS  - 1
SP  - 16555
DO  - 10.1038/s41598-019-52934-8
ER  - 

@article{
author = "Senćanski, Milan V. and Glišić, Sanja and Šnajder, Marko and Veljković, Nevena V. and Poklar Ulrih, Nataša and Mavri, Janez and Vrecl, Milka",
year = "2019",
abstract = "This study aimed to design and functionally characterize peptide mimetics of the nanobody (Nb) related to the β2-adrenergic receptor (β2-AR) (nanobody-derived peptide, NDP). We postulated that the computationally derived and optimized complementarity-determining region 3 (CDR3) of Nb is sufficient for its interaction with receptor. Sequence-related Nb-families preferring the agonist-bound active conformation of β2-AR were analysed using the informational spectrum method (ISM) and β2-AR:NDP complexes studied using protein-peptide docking and molecular dynamics (MD) simulations in conjunction with metadynamics calculations of free energy binding. The selected NDP of Nb71, designated P3, was 17 amino acids long and included CDR3. Metadynamics calculations yielded a binding free energy for the β2-AR:P3 complex of ΔG = (−7.23 ± 0.04) kcal/mol, or a Kd of (7.9 ± 0.5) μM, for T = 310 K. In vitro circular dichroism (CD) spectropolarimetry and microscale thermophoresis (MST) data provided additional evidence for P3 interaction with agonist-activated β2-AR, which displayed ~10-fold higher affinity for P3 than the unstimulated receptor (MST-derived EC50 of 3.57 µM vs. 58.22 µM), while its ability to inhibit the agonist-induced interaction of β2-AR with β-arrestin 2 was less evident. In summary, theoretical and experimental evidence indicated that P3 preferentially binds agonist-activated β2-AR. © 2019, The Author(s).",
journal = "Scientific Reports",
title = "Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR)",
volume = "9",
number = "1",
pages = "16555",
doi = "10.1038/s41598-019-52934-8"
}

Senćanski, M. V., Glišić, S., Šnajder, M., Veljković, N. V., Poklar Ulrih, N., Mavri, J.,& Vrecl, M.. (2019). Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR). in Scientific Reports, 9(1), 16555.
https://doi.org/10.1038/s41598-019-52934-8

Senćanski MV, Glišić S, Šnajder M, Veljković NV, Poklar Ulrih N, Mavri J, Vrecl M. Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR). in Scientific Reports. 2019;9(1):16555.
doi:10.1038/s41598-019-52934-8 .

Senćanski, Milan V., Glišić, Sanja, Šnajder, Marko, Veljković, Nevena V., Poklar Ulrih, Nataša, Mavri, Janez, Vrecl, Milka, "Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR)" in Scientific Reports, 9, no. 1 (2019):16555,
https://doi.org/10.1038/s41598-019-52934-8 . .