Cross-variant immune shield: computational multiepitope vaccine design against B.617.2 to Omicron sub-lineages in SARS-CoV-2 Jinal M. Thakor, Unnati V. Panchal, Dhaval Patel, Slawomir Filipek, Urszula Orzeł, Ramasamy Paulmurugan, Katja Hanack, Dorian Liepmann, Venkatesan Renugopalakrishnan, Chaitanya G. Joshi, Madhvi Joshi Journal of Biomolecular Structure and Dynamics, 2026 The COVID-19 pandemic had a profound impact on global health. This study focuses on an in-depth analysis of the structural proteins (Spike (S), Nucleocapsid (N), Membrane (M), and Envelope (E) protein) of SARS-CoV-2 and its variants, aiming to develop a multiepitope vaccine construct that targets the virus independently of its variants. The analysis began by examining genetic variations in viral proteins relative to the reference strain Wuhan-Hu2, particularly in the S, M, N, and E proteins. T-cell epitope predictions for MHC Class-I and Class-II binding were conducted, shedding light on potential cytotoxic and helper T lymphocyte recognition. Identification of linear B-cell epitopes laid the groundwork for antibody-based humoral immune responses. The safety and efficacy of these epitopes were assessed for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy. Population coverage analysis indicated promising global effectiveness of the designed vaccine construct. By incorporating 28 epitopes, we validated that was designed vaccine construct for stability through structural analysis. Molecular dynamics simulations and docking studies revealed its robust interaction with Toll-like receptor 4 (TLR4). Immune simulation studies suggested that the vaccine construct could induce a potent immune response by enhancing antibody titers, B-cell proliferation, memory cell development, and activation of T cells and natural killer cells upon administration. This comprehensive approach offers a promising multiepitope vaccine against SARS-CoV-2, with the potential for broad global coverage and strong immunogenicity. Further experimental validation holds the prospect of introducing a novel candidate vaccine to aid in the ongoing battle against the COVID-19 pandemic.
Structural Characterization and AI-Enhanced Modeling of a Broadly Neutralizing Camelid Antibody Against SARS-CoV-2 Variants Katja Hanack, Urszula Orzeł, Anja Schlör, Sourabh Mehta, Anandi Krishnan, Slawomir Filipek, Rushika Patel, Madhvi Joshi, Markus Hoffmann, Stefan Pöhlmann, Chaitanya Joshi, Dorian Liepmann, Ramasamy Paulmurugan, Venkatesan Renugopalakrishnan Advanced Therapeutics, 2026 The Omicron variants of SARS‐CoV‐2 are characterized by their high transmissibility and immune evasion. Existing treatments using neutralizing antibodies have shown different effectiveness due to variants with mutations occurring mainly in the RBD and NTD regions. In this study, the functional neutralizing ability of a camelid full‐length antibody (hcAb‐B10) and its corresponding VHH fragment (VHH‐B10) is investigated. Experimental binding studies demonstrated clear recognition and neutralization of Wild‐type (WT) and Omicron variants, but not Delta. Epitope mapping, peptide fragment inhibition, and neutralization studies using pseudovirus expressing respective SARS‐CoV‐2 Spike variants, along with in silico molecular docking studies and AI‐directed structural design, reveal that the B10 antibody interacts effectively with the Spike trimer in a closed position of both WT and Omicron, by targeting the RBD region. This newly generated B10 antibody shows a wide coverage, including the currently dominant Omicron variants, and demonstrates its potential to efficiently neutralize SARS‐CoV‐2.
Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways David Aranda-García, Tomasz Maciej Stepniewski, Mariona Torrens-Fontanals, Adrian García-Recio, Marta Lopez-Balastegui, Brian Medel-Lacruz, Adrián Morales-Pastor, Alejandro Peralta-García, Miguel Dieguez-Eceolaza, David Sotillo-Nuñez, Tianyi Ding, Matthäus Drabek, Célien Jacquemard, Jakub Jakowiecki, Willem Jespers, Mireia Jiménez-Rosés, Víctor Jun-Yu-Lim, Alessandro Nicoli, Urszula Orzel, Aida Shahraki, Johanna K. S. Tiemann, Vicente Ledesma-Martin, Francho Nerín-Fonz, Sergio Suárez-Dou, Oriol Canal, Gáspár Pándy-Szekeres, Jiafei Mao, David E. Gloriam, Esther Kellenberger, Dorota Latek, Ramon Guixà-González, Hugo Gutiérrez-de-Terán, Irina G. Tikhonova, Peter W. Hildebrand, Marta Filizola, M. Madan Babu, Antonella Di Pizio, Slawomir Filipek, Peter Kolb, Arnau Cordomi, Toni Giorgino, Maria Marti-Solano, Jana Selent Nature Communications, 2025 G protein-coupled receptors (GPCRs) constitute a functionally diverse protein family and are targets for a broad spectrum of pharmaceuticals. Technological progress in X-ray crystallography and cryogenic electron microscopy has enabled extensive, high-resolution structural characterisation of GPCRs in different conformational states. However, as highly dynamic events underlie GPCR signalling, a complete understanding of GPCR functionality requires insights into their conformational dynamics. Here, we present a large dataset of molecular dynamics simulations covering 60% of currently available GPCR structures. Our analysis reveals extensive local "breathing" motions of the receptor on a nano- to microsecond timescale and provides access to numerous previously unexplored receptor conformational states. Furthermore, we reveal that receptor flexibility impacts the shape of allosteric drug binding sites, which frequently adopt partially or completely closed states in the absence of a molecular modulator. We demonstrate that exploring membrane lipid dynamics and their interaction with GPCRs is an efficient approach to expose such hidden allosteric sites and even lateral ligand entrance gateways. The obtained insights and generated dataset on conformations, allosteric sites and lateral entrance gates in GPCRs allows us to better understand the functionality of these receptors and opens new therapeutic avenues for drug-targeting strategies.
GPCR oligomerization across classes: A2AR-mediated regulation of mGlu5R activation Urszula Orzeł, Carlos A.V. Barreto, Sławomir Filipek, Irina S. Moreira International Journal of Biological Macromolecules, 2025 The adenosine A 2A receptor (A 2A R), a class A GPCR, is a known player in neurological diseases, including Parkinson's disease and Alzheimer's disease, and is also implicated in SARS-CoV-2 infection. Recent studies have revealed its oligomerization with metabotropic glutamate receptor type 5 (mGlu 5 R), a class C G protein coupled receptor (GPCR) that exists in the homodimeric form. Simultaneous activation of both receptors synergistically enhances mGlu 5 R-mediated effects in the hippocampus. Despite their importance, the molecular mechanisms governing these interactions remain unclear. In this study, we used molecular modelling techniques, including molecular docking, extensive molecular dynamics (MD) simulations, and detailed analysis, to elucidate the interactions between mGlu 5 R and A 2A R in the inactive and active states. Our findings provide molecular-level insights into the permissive role of A 2A R in mGlu 5 R activation, demonstrating that the inactive A 2A R interface within the oligomer blocks the mGlu 5 R transmembrane helix 6 (TM6), which is crucial for activation. Upon A 2A R activation, the oligomer interface undergoes conformational rearrangement, exposing mGlu 5 R-TM6 and allowing for mGlu 5 R activation. Furthermore, we identified a pivotal role of the mGlu 5 R-TM4:A 2A R-TM4 interface in facilitating mGlu 5 R activation. These results highlight the intricate architecture of the mGlu 5 R:A 2A R oligomer, advancing our understanding of GPCR oligomerization and its regulatory mechanisms on receptor activity.
Conformational Changes and Unfolding of β-Amyloid Substrates in the Active Site of γ-Secretase Jakub Jakowiecki, Urszula Orzeł, Przemysław Miszta, Krzysztof Młynarczyk, Sławomir Filipek International Journal of Molecular Sciences, 2024 Alzheimer’s disease (AD) is the leading cause of dementia and is characterized by a presence of amyloid plaques, composed mostly of the amyloid-β (Aβ) peptides, in the brains of AD patients. The peptides are generated from the amyloid precursor protein (APP), which undergoes a sequence of cleavages, referred as trimming, performed by γ-secretase. Here, we investigated conformational changes in a series of β-amyloid substrates (from less and more amyloidogenic pathways) in the active site of presenilin-1, the catalytic subunit of γ-secretase. The substrates are trimmed every three residues, finally leading to Aβ40 and Aβ42, which are the major components of amyloid plaques. To study conformational changes, we employed all-atom molecular dynamics simulations, while for unfolding, we used steered molecular dynamics simulations in an implicit membrane-water environment to accelerate changes. We have found substantial differences in the flexibility of extended C-terminal parts between more and less amyloidogenic pathway substrates. We also propose that the positively charged residues of presenilin-1 may facilitate the stretching and unfolding of substrates. The calculated forces and work/energy of pulling were exceptionally high for Aβ40, indicating why trimming of this substrate is so infrequent.
Investigation of Peptides for Molecular Recognition of C-Reactive Protein-Theoretical and Experimental Studies Katarzyna Szot-Karpińska, Patryk Kudła, Urszula Orzeł, Magdalena Narajczyk, Martin Jönsson-Niedziółka, Barbara Pałys, Sławomir Filipek, Andreas Ebner, Joanna Niedziółka-Jönsson Analytical Chemistry, 2023 We investigate the interactions between C-reactive protein (CRP) and new CRP-binding peptide materials using experimental (biological and physicochemical) methods with the support of theoretical simulations (computational modeling analysis). Three specific CRP-binding peptides (P2, P3, and P9) derived from an M13 bacteriophage have been identified using phage-display technology. The binding efficiency of the peptides exposed on phages toward the CRP protein was demonstrated via biological methods. Fibers of the selected phages/peptides interact differently due to different compositions of amino acid sequences on the exposed peptides, which was confirmed by transmission electron microscopy. Numerical and experimental studies consistently showed that the P3 peptide is the best CRP binder. A combination of theoretical and experimental methods demonstrates that identifying the best binder can be performed simply, cheaply, and fast. Such an approach has not been reported previously for peptide screening and demonstrates a new trend in science where calculations can replace or support laborious experimental techniques. Finally, the best CRP binder─the P3 peptide─was used for CRP recognition on silicate-modified indium tin oxide-coated glass electrodes. The obtained electrodes exhibit a wide range of operation (1.0–100 μg mL–1) with a detection limit (LOD = 3σ/S) of 0.34 μg mL–1. Moreover, the dissociation constant Kd of 4.2 ± 0.144 μg mL–1 (35 ± 1.2 nM) was evaluated from the change in the current. The selectivity of the obtained electrode was demonstrated in the presence of three interfering proteins. These results prove that the presented P3 peptide is a potential candidate as a receptor for CRP, which can replace specific antibodies.
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex Urszula Orzeł, Paweł Pasznik, Przemysław Miszta, Marcin Lorkowski, Szymon Niewieczerzał, Jakub Jakowiecki, Sławomir Filipek Nucleic Acids Research, 2023 Despite recent advances in research, the mechanism of Alzheimer's disease is not fully understood yet. Understanding the process of cleavage and then trimming of peptide substrates, can help selectively block γ-secretase (GS) to stop overproduction of the amyloidogenic products. Our GS-SMD server (https://gs-smd.biomodellab.eu/) allows cleaving and unfolding of all currently known GS substrates (more than 170 peptide substrates). The substrate structure is obtained by threading of the substrate sequence into the known structure of GS complex. The simulations are performed in an implicit water-membrane environment so they are performed rather quickly, 2–6 h per job, depending on the mode of calculations (part of GS complex or the whole structure). It is also possible to introduce mutations to the substrate and GS and pull any part of the substrate in any direction using the steered molecular dynamics (SMD) simulations with constant velocity. The obtained trajectories are visualized and analyzed in the interactive way. One can also compare multiple simulations using the interaction frequency analysis. GS-SMD server can be useful for revealing mechanisms of substrate unfolding and role of mutations in this process.
Cross-variant immune shield: computational multiepitope vaccine design against B. 617.2 to Omicron sub-lineages in SARS-CoV-2 JM Thakor, UV Panchal, D Patel, S Filipek, U Orzeł, R Paulmurugan, ... Journal of Biomolecular Structure and Dynamics 44 (2), 983-1002 , 2026 2026.0 Citations: 1
Cover Feature: Structural Characterization and AI‐Enhanced Modeling of a Broadly Neutralizing Camelid Antibody Against SARS‐CoV‐2 Variants (Adv. Therap. 1/2026) K Hanack, U Orzeł, A Schlör, S Mehta, A Krishnan, S Filipek, R Patel, ... Advanced Therapeutics 9 (1), e70113 , 2026 2026.0
Structural Characterization and AI‐Enhanced Modeling of a Broadly Neutralizing Camelid Antibody Against SARS‐CoV‐2 Variants K Hanack, U Orzeł, A Schlör, S Mehta, A Krishnan, S Filipek, R Patel, ... Advanced Therapeutics 9 (1), e00244 , 2026 2026.0
Artificial intelligence in rare diseases: toward clinical impact AMB Amorim, U Orzeł, AB Caniceiro, N Rosário-Ferreira, IS Moreira Trends in Pharmacological Sciences , 2025 2025.0 Citations: 5
GPCR oligomerization across classes: A2AR-mediated regulation of mGlu5R activation U Orzeł, CAV Barreto, S Filipek, IS Moreira International Journal of Biological Macromolecules 299, 139880 , 2025 2025.0 Citations: 2
Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways D Aranda-García, TM Stepniewski, M Torrens-Fontanals, A García-Recio, ... Nature communications 16 (1), 2020 , 2025 2025.0 Citations: 52
Leveraging artificial intelligence in GPCR activation studies: computational prediction methods as key drivers of knowledge AB Caniceiro, U Orzeł, N Rosário-Ferreira, S Filipek, IS Moreira Protein Supersecondary Structures: Methods and Protocols, 183-220 , 2024 2024.0 Citations: 9
Conformational changes and unfolding of β-amyloid substrates in the active site of γ-secretase J Jakowiecki, U Orzeł, P Miszta, K Młynarczyk, S Filipek International Journal of Molecular Sciences 25 (5), 2564 , 2024 2024.0 Citations: 2
Investigation of peptides for molecular recognition of C-reactive protein–theoretical and experimental studies K Szot-Karpinska, P Kudła, U Orzeł, M Narajczyk, M Jönsson-Niedziółka, ... Analytical Chemistry 95 (38), 14475-14483 , 2023 2023.0 Citations: 15
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex U Orzeł, P Pasznik, P Miszta, M Lorkowski, S Niewieczerzał, J Jakowiecki, ... Nucleic Acids Research 51 (W1), W251-W262 , 2023 2023.0 Citations: 3
Specificities of Protein Homology Modeling for Allosteric Drug Design J Jakowiecki, U Orzeł, A Gliździnska, M Możajew, S Filipek Homology Modeling: Methods and Protocols, 339-348 , 2023 2023.0
The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex U Orzeł, J Jakowiecki, K Młynarczyk, S Filipek Biomolecules 11 (7), 935 , 2021 2021.0 Citations: 10
Allosteric modulation of the CB1 cannabinoid receptor by cannabidiol—A molecular modeling study of the N-terminal domain and the allosteric-orthosteric coupling J Jakowiecki, R Abel, U Orzeł, P Pasznik, R Preissner, S Filipek Molecules 26 (9), 2456 , 2021 2021.0 Citations: 52
The hydrophobic ligands entry and exit from the GPCR binding site-SMD and SUMD simulations J Jakowiecki, U Orzeł, S Chawananon, P Miszta, S Filipek Molecules 25 (8), 1930 , 2020 2020.0 Citations: 17
Computational methods to study the structure and dynamics of biomolecules and biomolecular processes D Latek, B Trzaskowski, S Niewieczerzał, P Miszta, K Młynarczyk, ... Springer , 2019 2019.0 Citations: 10
Modeling of Membrane Proteins W Puławski, S Yuan, A Sztyler, U Orzeł Computational Methods to Study the Structure and Dynamics of Biomolecules … , 2018 2018.0
Modeling of membrane proteins D Latek, B Trzaskowski, S Niewieczerzał, P Miszta, K Młynarczyk, ... Computational Methods to Study the Structure and Dynamics of Biomolecules … , 2018 2018.0 Citations: 10
OC12–Urszula Orzeł U Orzeł, B Bueshbell, C Baretto, S Flipek, IS Moreira 3D-BIOINFO-PT, 29 , 0
MOST CITED SCHOLAR PUBLICATIONS
Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways D Aranda-García, TM Stepniewski, M Torrens-Fontanals, A García-Recio, ... Nature communications 16 (1), 2020 , 2025 2025.0 Citations: 52
Allosteric modulation of the CB1 cannabinoid receptor by cannabidiol—A molecular modeling study of the N-terminal domain and the allosteric-orthosteric coupling J Jakowiecki, R Abel, U Orzeł, P Pasznik, R Preissner, S Filipek Molecules 26 (9), 2456 , 2021 2021.0 Citations: 52
The hydrophobic ligands entry and exit from the GPCR binding site-SMD and SUMD simulations J Jakowiecki, U Orzeł, S Chawananon, P Miszta, S Filipek Molecules 25 (8), 1930 , 2020 2020.0 Citations: 17
Investigation of peptides for molecular recognition of C-reactive protein–theoretical and experimental studies K Szot-Karpinska, P Kudła, U Orzeł, M Narajczyk, M Jönsson-Niedziółka, ... Analytical Chemistry 95 (38), 14475-14483 , 2023 2023.0 Citations: 15
The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex U Orzeł, J Jakowiecki, K Młynarczyk, S Filipek Biomolecules 11 (7), 935 , 2021 2021.0 Citations: 10
Computational methods to study the structure and dynamics of biomolecules and biomolecular processes D Latek, B Trzaskowski, S Niewieczerzał, P Miszta, K Młynarczyk, ... Springer , 2019 2019.0 Citations: 10
Modeling of membrane proteins D Latek, B Trzaskowski, S Niewieczerzał, P Miszta, K Młynarczyk, ... Computational Methods to Study the Structure and Dynamics of Biomolecules … , 2018 2018.0 Citations: 10
Leveraging artificial intelligence in GPCR activation studies: computational prediction methods as key drivers of knowledge AB Caniceiro, U Orzeł, N Rosário-Ferreira, S Filipek, IS Moreira Protein Supersecondary Structures: Methods and Protocols, 183-220 , 2024 2024.0 Citations: 9
Artificial intelligence in rare diseases: toward clinical impact AMB Amorim, U Orzeł, AB Caniceiro, N Rosário-Ferreira, IS Moreira Trends in Pharmacological Sciences , 2025 2025.0 Citations: 5
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex U Orzeł, P Pasznik, P Miszta, M Lorkowski, S Niewieczerzał, J Jakowiecki, ... Nucleic Acids Research 51 (W1), W251-W262 , 2023 2023.0 Citations: 3
GPCR oligomerization across classes: A2AR-mediated regulation of mGlu5R activation U Orzeł, CAV Barreto, S Filipek, IS Moreira International Journal of Biological Macromolecules 299, 139880 , 2025 2025.0 Citations: 2
Conformational changes and unfolding of β-amyloid substrates in the active site of γ-secretase J Jakowiecki, U Orzeł, P Miszta, K Młynarczyk, S Filipek International Journal of Molecular Sciences 25 (5), 2564 , 2024 2024.0 Citations: 2
Cross-variant immune shield: computational multiepitope vaccine design against B. 617.2 to Omicron sub-lineages in SARS-CoV-2 JM Thakor, UV Panchal, D Patel, S Filipek, U Orzeł, R Paulmurugan, ... Journal of Biomolecular Structure and Dynamics 44 (2), 983-1002 , 2026 2026.0 Citations: 1
Cover Feature: Structural Characterization and AI‐Enhanced Modeling of a Broadly Neutralizing Camelid Antibody Against SARS‐CoV‐2 Variants (Adv. Therap. 1/2026) K Hanack, U Orzeł, A Schlör, S Mehta, A Krishnan, S Filipek, R Patel, ... Advanced Therapeutics 9 (1), e70113 , 2026 2026.0
Structural Characterization and AI‐Enhanced Modeling of a Broadly Neutralizing Camelid Antibody Against SARS‐CoV‐2 Variants K Hanack, U Orzeł, A Schlör, S Mehta, A Krishnan, S Filipek, R Patel, ... Advanced Therapeutics 9 (1), e00244 , 2026 2026.0
Specificities of Protein Homology Modeling for Allosteric Drug Design J Jakowiecki, U Orzeł, A Gliździnska, M Możajew, S Filipek Homology Modeling: Methods and Protocols, 339-348 , 2023 2023.0
Modeling of Membrane Proteins W Puławski, S Yuan, A Sztyler, U Orzeł Computational Methods to Study the Structure and Dynamics of Biomolecules … , 2018 2018.0
OC12–Urszula Orzeł U Orzeł, B Bueshbell, C Baretto, S Flipek, IS Moreira 3D-BIOINFO-PT, 29 , 0
