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Brankiewicz W, Kalathiya U, Padariya M, Węgrzyn K, Prusinowski M, Zebrowska J, Zylicz-Stachula A, Skowron P, Drab M, Szajewski M, Ciesielski M, Gawrońska M, Kallingal A, Makowski M, Bagiński M. Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1. Chemistry 2023; 29:e202300970. [PMID: 37332024 DOI: 10.1002/chem.202300970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
In this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules. Our chemotherapeutic approach is based on assumption that modulation of TRF1-TIN2 interaction may be more harmful for cancer cells as cancer telomeres are more fragile than in normal cells. We have shown in vitro within SPR experiments that our modified peptide PEP1 molecule interacts with TRF1, presumably at the site originally occupied by the TIN2 protein. Disturbance of the shelterin complex by studied molecule may not in short term lead to cytotoxic effects, however blocking TRF1-TIN2 resulted in cellular senescence in cellular breast cancer lines used as a cancer model. Thus, our compounds appeared useful as starting model compounds for precise blockage of TRF proteins.
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Affiliation(s)
- Wioletta Brankiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822, Gdańsk, Poland
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822, Gdańsk, Poland
| | - Katarzyna Węgrzyn
- Intercollegiate Faculty of Biotechnology, University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
| | - Maciej Prusinowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Joanna Zebrowska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | | | - Piotr Skowron
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Marek Drab
- Unit of Nanostructural Bio-Interactions, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 Weigla-Street, 53-114, Wrocław, Poland
| | - Mariusz Szajewski
- Department of Oncological Surgery, Gdynia Oncology Centre, Gdynia, Poland
- Division of Propaedeutics of Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Maciej Ciesielski
- Department of Oncological Surgery, Gdynia Oncology Centre, Gdynia, Poland
- Division of Propaedeutics of Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Małgorzata Gawrońska
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Maciej Bagiński
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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Padariya M, Baginski M, Babak M, Kalathiya U. Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme. Biophys Chem 2022; 291:106909. [DOI: 10.1016/j.bpc.2022.106909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
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Padariya M, Kalathiya U. The Binding Specificity of PAB1 with Poly(A) mRNA, Regulated by Its Structural Folding. Biomedicines 2022; 10:biomedicines10112981. [PMID: 36428549 PMCID: PMC9687780 DOI: 10.3390/biomedicines10112981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
The poly(A)-binding protein cytoplasmic 1 (PAB1 or PABPC1) protein is associated with the long poly(A) mRNA tails, inducing stability. Herein, we investigated the dynamics of the PABPC1 protein, along with tracing its mRNA binding specificity. During molecular dynamics simulations (MDS), the R176-Y408 amino acids (RRM3-4 domains; RNA recognition motifs) initiated a folded structure that resulted in the formation of different conformations. The RRM4 domain formed high-frequency intramolecular interactions, despite such induced flexibility. Residues D45, Y54, Y56, N58, Q88, and N100 formed long-lasting interactions, and specifically, aromatic residues (Y14, Y54, Y56, W86, and Y140) gained a unique binding pattern with the poly(A) mRNA. In addition, the poly(A) mRNA motif assembled a PABPC1-specific conformation, by inducing movement of the center three nucleotides to face towards RRM1-2 domains. The majority of the high-frequency cancer mutations in PAB1 reside within the RRM4 domain and amino acids engaging in high-frequency interactions with poly(A) mRNA were found to be preserved in different cancer types. Except for the G123C variant, other studied cancer-derived mutants hindered the stability of the protein. Molecular details from this study will provide a detailed understanding of the PABPC1 structure, which can be used to modulate the activity of this gene, resulting in production of mutant peptide or neoantigens in cancer.
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Singh A, Padariya M, Faktor J, Kote S, Mikac S, Dziadosz A, Lam TW, Brydon J, Wear MA, Ball KL, Hupp T, Sznarkowska A, Vojtesek B, Kalathiya U. Identification of novel interferon responsive protein partners of human leukocyte antigen A (HLA-A) using cross-linking mass spectrometry (CLMS) approach. Sci Rep 2022; 12:19422. [PMID: 36371414 PMCID: PMC9653400 DOI: 10.1038/s41598-022-21393-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
The interferon signalling system elicits a robust cytokine response against a wide range of environmental pathogenic and internal pathological signals, leading to induction of a subset of interferon-induced proteins. We applied DSS (disuccinimidyl suberate) mediated cross-linking mass spectrometry (CLMS) to capture novel protein-protein interactions within the realm of interferon induced proteins. In addition to the expected interferon-induced proteins, we identified novel inter- and intra-molecular cross-linked adducts for the canonical interferon induced proteins, such as MX1, USP18, OAS3, and STAT1. We focused on orthogonal validation of a cohort of novel interferon-induced protein networks formed by the HLA-A protein (H2BFS-HLA-A-HMGA1) using co-immunoprecipitation assay, and further investigated them by molecular dynamics simulation. Conformational dynamics of the simulated protein complexes revealed several interaction sites that mirrored the interactions identified in the CLMS findings. Together, we showcase a proof-of-principle CLMS study to identify novel interferon-induced signaling complexes and anticipate broader use of CLMS to identify novel protein interaction dynamics within the tumour microenvironment.
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Affiliation(s)
- Ashita Singh
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK ,grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Monikaben Padariya
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Jakub Faktor
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Sachin Kote
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Sara Mikac
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Alicja Dziadosz
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Tak W. Lam
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK
| | - Jack Brydon
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK
| | - Martin A. Wear
- grid.4305.20000 0004 1936 7988School of Biological Sciences, Institute of Structural and Molecular Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | - Kathryn L. Ball
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK
| | - Ted Hupp
- grid.4305.20000 0004 1936 7988Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR Scotland, UK ,grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Alicja Sznarkowska
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Borek Vojtesek
- grid.419466.8RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Umesh Kalathiya
- grid.8585.00000 0001 2370 4076International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
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Padariya M, Kote S, Mayordomo M, Dapic I, Alfaro J, Hupp T, Fahraeus R, Kalathiya U. Corrigendum to Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations. Computational and structural biotechnology journal, 19, 5072–5091. Comput Struct Biotechnol J 2022; 20:6501-6502. [DOI: 10.1016/j.csbj.2022.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Padariya M, Jooste ML, Hupp T, Fåhraeus R, Vojtesek B, Vollrath F, Kalathiya U, Karakostis K. The Elephant evolved p53 isoforms that escape mdm2-mediated repression and cancer. Mol Biol Evol 2022; 39:6632613. [PMID: 35792674 PMCID: PMC9279639 DOI: 10.1093/molbev/msac149] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The p53 tumor suppressor is a transcription factor with roles in cell development, apoptosis, oncogenesis, aging, and homeostasis in response to stresses and infections. p53 is tightly regulated by the MDM2 E3 ubiquitin ligase. The p53–MDM2 pathway has coevolved, with MDM2 remaining largely conserved, whereas the TP53 gene morphed into various isoforms. Studies on prevertebrate ancestral homologs revealed the transition from an environmentally induced mechanism activating p53 to a tightly regulated system involving cell signaling. The evolution of this mechanism depends on structural changes in the interacting protein motifs. Elephants such as Loxodonta africana constitute ideal models to investigate this coevolution as they are large and long-living as well as having 20 copies of TP53 isoformic sequences expressing a variety of BOX-I MDM2-binding motifs. Collectively, these isoforms would enhance sensitivity to cellular stresses, such as DNA damage, presumably accounting for strong cancer defenses and other adaptations favoring healthy aging. Here we investigate the molecular evolution of the p53–MDM2 system by combining in silico modeling and in vitro assays to explore structural and functional aspects of p53 isoforms retaining the MDM2 interaction, whereas forming distinct pools of cell signaling. The methodology used demonstrates, for the first time that in silico docking simulations can be used to explore functional aspects of elephant p53 isoforms. Our observations elucidate structural and mechanistic aspects of p53 regulation, facilitate understanding of complex cell signaling, and suggest testable hypotheses of p53 evolution referencing Peto’s Paradox.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
| | - Mia-Lyn Jooste
- Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, UK
| | - Ted Hupp
- Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, UK
| | - Robin Fåhraeus
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire , Université Paris 7, Hôpital St. Louis, F-75010 Paris , France
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute , 65653 Brno , Czech Republic
- Department of Medical Biosciences, Umeå University , 90185 Umeå , Sweden
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute , 65653 Brno , Czech Republic
| | - Fritz Vollrath
- Department of Zoology, Zoology Research and Administration Building, University of Oxford , Oxford, UK
- Save the Elephants Marula Manor , Marula Lane, Karen P.O. Box 54667. Nairobi 00200. Kenya Office: +254 720 441 178
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk , ul. Kładki 24, 80-822 Gdansk , Poland
| | - Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire , Université Paris 7, Hôpital St. Louis, F-75010 Paris , France
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , 08193 Bellaterra (Barcelona) , Spain
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Padariya M, Daniels A, Tait-Burkard C, Hupp T, Kalathiya U. Self-derived peptides from the SARS-CoV-2 spike glycoprotein disrupting shaping and stability of the homotrimer unit. Biomed Pharmacother 2022; 151:113190. [PMID: 35643065 PMCID: PMC9127142 DOI: 10.1016/j.biopha.2022.113190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 01/25/2023] Open
Abstract
The structural spike (S) protein from the SARS-CoV-2 β-coronavirus is shown to make different pre- and post-fusion conformations within its homotrimer unit. To support the ongoing novel vaccine design and development strategies, we report the structure-based design approach to develop self-derived S peptides. A dataset of crucial regions from the S protein were transformed into linear motifs that could act as the blockers or stabilizers for the S protein homotrimer unit. Among these distinct S peptides, the pep02 (537-QQFGRDIAD-545) and pep07 (821-RDLICAQKFNGLTVLPPLLTDE-842) were found making stable folded binding with the S protein (550-750 and 950-1050 regions). Upon inserting SARS-CoV-2 S variants in the peptide destabilized the complexed S protein structure, resulting an allosteric effect in different functional regions of the protein. Particularly, the molecular dynamics revealed that A544D mutation in the pep02 peptide induced instability for the complexed S protein, whereas the N943K variant from pep09 exhibited an opposite behavior. An increased protein-peptide binding affinity and the stable structural folding were observed in mutated systems, compared to that of the wild type systems. The presence of mutation has induced an "up" active conformation of the spike (RBD) domain, responsible for interacting the host cell receptor. Among the lower affinity peptide datasets (e.g., pep01), the S1 and S2 subunit in the protein formed an "open" conformation, whereas with higher affinity peptides (e.g., pep07) these domains gained a "closed" conformation. These findings propose that our designed self-derived S peptides could replace a single S protein monomer, blocking the homotrimer formation or inducing stability.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland,Corresponding authors
| | - Alison Daniels
- Department of Infectious Disease, Edinburgh, Scotland EH4 2XR, United Kingdom,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland,Corresponding authors
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Padariya M, Kote S, Mayordomo M, Dapic I, Alfaro J, Hupp T, Fahraeus R, Kalathiya U. Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations. Comput Struct Biotechnol J 2021; 19:5072-5091. [PMID: 34589184 PMCID: PMC8453138 DOI: 10.1016/j.csbj.2021.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
The TAP1-TAP2 complex transports antigenic peptide substrates into the endoplasmic reticulum (ER). In ER, the peptides are further processed and loaded on the major histocompatibility class (MHC) I molecules by the peptide loading complex (PLC). The TAP transporters are linked with the PLC; a target for cancers and viral immune evasion. But the mechanisms whereby the cancer-derived mutations in TAP1-TAP2 or viral factors targeting the PLC, interfere peptide transport are only emerging. This study describes that transit of peptides through TAP can take place via two different channels (4 or 8 helices) depending on peptide length and sequence. Molecular dynamics and binding affinity predictions of peptide-transporters demonstrated that smaller peptides (8-10 mers; e.g. AAGIGILTV, SIINFEKL) can transport quickly through the transport tunnel compared to longer peptides (15-mer; e.g. ENPVVHFFKNIVTPR). In line with a regulated and selective peptide transport by TAPs, the immunopeptidome upon IFN-γ treatment in melanoma cells induced the shorter length (9-mer) peptide presentation over MHC-I that exhibit a relatively weak binding affinity with TAP. A conserved distance between N and C terminus residues of the studied peptides in the transport tunnel were reported. Furthermore, by adversely interacting with the TAP transport passage or affecting TAPNBD domains tilt movement, the viral proteins and cancer-derived mutations in TAP1-TAP2 may induce allosteric effects in TAP that block conformation of the tunnel (closed towards ER lumen). Interestingly, some cancer-associated mutations (e.g. TAP1R372Q and TAP2R373H) can specifically interfere with selective transport channels (i.e. for longer-peptides). These results provide a model for how viruses and cancer-associated mutations targeting TAP interfaces can affect MHC-I antigen presentation, and how the IFN-γ pathway alters MHC-I antigen presentation via the kinetics of peptide transport.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Marcos Mayordomo
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
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Kalathiya U, Padariya M, Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). Biomolecules 2021; 11:382. [PMID: 33806612 PMCID: PMC8001575 DOI: 10.3390/biom11030382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
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Affiliation(s)
- Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Etienne Coyaud
- Protéomique Réponse Inflammatoire Spectrométrie de Mass—PRISM, Inserm U1192, University Lille, CHU Lille, F-59000 Lille, France;
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8Z 7X8, Canada
- Genome BC Proteome Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada
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Padariya M, Kalathiya U, Mikac S, Dziubek K, Tovar Fernandez MC, Sroka E, Fahraeus R, Sznarkowska A. Viruses, cancer and non-self recognition. Open Biol 2021; 11:200348. [PMID: 33784856 PMCID: PMC8061760 DOI: 10.1098/rsob.200348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Virus-host interactions form an essential part of every aspect of life, and this review is aimed at looking at the balance between the host and persistent viruses with a focus on the immune system. The virus-host interaction is like a cat-and-mouse game and viruses have developed ingenious mechanisms to manipulate cellular pathways, most notably the major histocompatibility (MHC) class I pathway, to reside within infected cell while evading detection and destruction by the immune system. However, some of the signals sensing and responding to viral infection are derived from viruses and the fact that certain viruses can prevent the infection of others, highlights a more complex coexistence between the host and the viral microbiota. Viral immune evasion strategies also illustrate that processes whereby cells detect and present non-self genetic material to the immune system are interlinked with other cellular pathways. Immune evasion is a target also for cancer cells and a more detailed look at the interfaces between viral factors and components of the MHC class I peptide-loading complex indicates that these interfaces are also targets for cancer mutations. In terms of the immune checkpoint, however, viral and cancer strategies appear different.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Katarzyna Dziubek
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Maria C. Tovar Fernandez
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Ewa Sroka
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic
- Department of Medical Biosciences, Umeå University, Building 6M, 901 85 Umeå, Sweden
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
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Kalathiya U, Padariya M, Fahraeus R, Chakraborti S, Hupp TR. Multivalent Display of SARS-CoV-2 Spike (RBD Domain) of COVID-19 to Nanomaterial, Protein Ferritin Nanocages. Biomolecules 2021; 11:297. [PMID: 33671255 PMCID: PMC7923090 DOI: 10.3390/biom11020297] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2, or COVID-19, has a devastating effect on our society, both in terms of quality of life and death rates; hence, there is an urgent need for developing safe and effective therapeutics against SARS-CoV-2. The most promising strategy to fight against this deadly virus is to develop an effective vaccine. Internalization of SARS-CoV-2 into the human host cell mainly occurs through the binding of the coronavirus spike protein (a trimeric surface glycoprotein) to the human angiotensin-converting enzyme 2 (ACE2) receptor. The spike-ACE2 protein-protein interaction is mediated through the receptor-binding domain (RBD) of the spike protein. Mutations in the spike RBD can significantly alter interactions with the ACE2 host receptor. Due to its important role in virus transmission, the spike RBD is considered to be one of the key molecular targets for vaccine development. In this study, a spike RBD-based subunit vaccine was designed by utilizing a ferritin protein nanocage as a scaffold. Several fusion protein constructs were designed in silico by connecting the spike RBD via a synthetic linker (different sizes) to different ferritin subunits (H-ferritin and L-ferritin). The stability and the dynamics of the engineered nanocage constructs were tested by extensive molecular dynamics simulation (MDS). Based on our MDS analysis, a five amino acid-based short linker (S-Linker) was the most effective for displaying the spike RBD over the surface of ferritin. The behavior of the spike RBD binding regions from the designed chimeric nanocages with the ACE2 receptor was highlighted. These data propose an effective multivalent synthetic nanocage, which might form the basis for new vaccine therapeutics designed against viruses such as SARS-CoV-2.
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Affiliation(s)
- Umesh Kalathiya
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
| | - Monikaben Padariya
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
| | - Robin Fahraeus
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
| | | | - Ted R. Hupp
- University of Gdansk, International Centre for Cancer Vaccine Science, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (R.F.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
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Kalathiya U, Padariya M, Mayordomo M, Lisowska M, Nicholson J, Singh A, Baginski M, Fahraeus R, Carragher N, Ball K, Haas J, Daniels A, Hupp TR, Alfaro JA. Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site. J Clin Med 2020; 9:E1473. [PMID: 32422996 PMCID: PMC7290299 DOI: 10.3390/jcm9051473] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
An important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular dynamics (MD) simulation. The findings indicated that S2 subunit (heptad-repeat 1 (HR1), central helix (CH), and connector domain (CD) domains) showed low variability, low fluctuations in MD, and displayed a trimer cavity. By contrast, the receptor binding domain (RBD) domain, which is typically targeted in drug discovery programs, exhibits more sequence variability and flexibility. Interpretations from MD simulations suggest that the monomer form of spike protein is in constant motion showing transitions between an "up" and "down" state. In addition, the trimer cavity may function as a "bouncing spring" that may facilitate the homotrimer spike protein interactions with the ACE2 receptor. The feasibility of the trimer cavity as a potential drug target was examined by structure based virtual screening. Several hits were identified that have already been validated or suggested to inhibit the SARS-CoV-2 virus in published cell models. In particular, the data suggest an action mechanism for molecules including Chitosan and macrolides such as the mTOR (mammalian target of Rapamycin) pathway inhibitor Rapamycin. These findings identify a novel small molecule binding-site formed by the spike protein oligomer, that might assist in future drug discovery programs aimed at targeting the coronavirus (CoV) family of viruses.
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Affiliation(s)
- Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
| | - Marcos Mayordomo
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
| | - Małgorzata Lisowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
| | - Judith Nicholson
- Sharp Life Science (EU) Limited, Oxford Science Park, Edmund Halley Rd, Oxford OX4 4GB, UK;
| | - Ashita Singh
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland;
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
| | - Neil Carragher
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK; (N.C.); (K.B.)
| | - Kathryn Ball
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK; (N.C.); (K.B.)
| | - Juergen Haas
- Department of Infectious Disease, Edinburgh, Scotland EH4 2XR, UK; (J.H.); (A.D.)
| | - Alison Daniels
- Department of Infectious Disease, Edinburgh, Scotland EH4 2XR, UK; (J.H.); (A.D.)
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK; (N.C.); (K.B.)
| | - Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (M.P.); (M.M.); (M.L.); (A.S.); (R.F.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK; (N.C.); (K.B.)
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Padariya M, Kalathiya U, Houston DR, Alfaro JA. Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface. Cancers (Basel) 2020; 12:cancers12030737. [PMID: 32244998 PMCID: PMC7140079 DOI: 10.3390/cancers12030737] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 01/16/2023] Open
Abstract
Down regulation of the major histocompatibility class (MHC) I pathway plays an important role in tumour development, and can be achieved by suppression of HLA expression or mutations in the MHC peptide-binding pocket. The peptide-loading complex (PLC) loads peptides on the MHC-I molecule in a dynamic multi-step assembly process. The effects of cancer variants on ERp57 and tapasin components from the MHC-I pathway is less known, and they could have an impact on antigen presentation. Applying computational approaches, we analysed whether the ERp57-tapasin binding might be altered by missense mutations. The variants H408R(ERp57) and P96L, D100A, G183R(tapasin) at the protein–protein interface improved protein stability (ΔΔG) during the initial screen of 14 different variants. The H408R(ERp57) and P96L(tapasin) variants, located close to disulphide bonds, were further studied by molecular dynamics (MD). Identifying intramolecular a-a’ domain interactions, MD revealed open and closed conformations of ERp57 in the presence and absence of tapasin. In wild-type and mutant ERp57-tapasin complexes, residues Val97, Ser98, Tyr100, Trp405, Gly407(ERp57) and Asn94, Cys95, Arg97, Asp100(tapasin) formed common H-bond interactions. Moreover, comparing the H-bond networks for P96L and H408R with each other, suggests that P96L(tapasin) improved ERp57-tapasin binding more than the H408R(ERp57) mutant. During MD, the C-terminus domain (that binds MHC-I) in tapasin from the ERp57(H408R)-tapasin complex moved away from the PLC, whereas in the ERp57-tapasin(P96L) system was oppositely displaced. These findings can have implications for the function of PLC and, ultimately, for the presentation of MHC-I peptide complex on the tumour cell surface.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
- Correspondence: (M.P.); (J.A.A.)
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
| | - Douglas R. Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, UK;
| | - Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
- Correspondence: (M.P.); (J.A.A.)
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Kalathiya U, Padariya M, Baginski M. Extracting functional groups of ALLINI to design derivatives of FDA-approved drugs: Inhibition of HIV-1 integrase. Biotechnol Appl Biochem 2018; 65:594-607. [DOI: 10.1002/bab.1646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
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Padariya M, Kalathiya U, Baginski M. Structural and dynamic insights on the EmrE protein with TPP + and related substrates through molecular dynamics simulations. Chem Phys Lipids 2018; 212:1-11. [DOI: 10.1016/j.chemphyslip.2017.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/30/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022]
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Kalathiya U, Padariya M, Baginski M. The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2. Arch Biochem Biophys 2018; 642:52-62. [PMID: 29428209 DOI: 10.1016/j.abb.2018.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 01/25/2023]
Abstract
The telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results suggest that TIN2TBM is necessary to ensure the stability of TRF1TRFH homodimer but not the TRF2TRFH homodimer. In TRF1-TIN2-TRF2 complex, the peptide enhances the protein-protein interactions to yield a stable heterodimer. Both monomers in TRF1TRFH homodimer interact almost equally with the peptide, whereas in TRF2TRFH homodimer, monomer TRF2TRFH(M1) exhibits more dominant interactions than the TRF2TRFH(M2). The common residues of TRF1/2TRFH(M1) that form interactions with TIN2TBM in all peptide-bound systems originate from the H3 (helix) and L3 (loop) regions. Additionally, in the homodimer systems, residues of TRF1/2TRFH(M2) also interact with the peptide. The residue pair E71-K213 is responsible for different conformations of TRF1TRFH homodimers; specifically, this residue pair enhances the protein-peptide/protein interactions in peptide-bound/unbound systems, respectively. TRF1TRFH and TRF2TRFH proteins have a conserved but different interface responsible for the protein-protein/peptide interactions that exist in the corresponding dimers.
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Affiliation(s)
- Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland.
| | - Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland
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Kalathiya U, Padariya M, Baginski M. Molecular basis of TRF proteins and their interactions with peptides. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317093998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Padariya M, Kalathiya U, Baginski M. Structural analysis and predicting effects of natural mutations on telomerase. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s205327331709297x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Padariya M, Kalathiya U, Baginski M. Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds. Biotechnol Appl Biochem 2017; 64:810-826. [DOI: 10.1002/bab.1543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
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Padariya M, Kalathiya U. Comparative molecular dynamics study of dimeric and monomeric forms of HIV-1 protease in ligand bound and unbound state. Gen Physiol Biophys 2016; 36:141-154. [PMID: 27921997 DOI: 10.4149/gpb_2016028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/24/2016] [Indexed: 11/08/2022]
Abstract
Human immunodeficiency virus type 1 protease is a viral-encoded enzyme and it is essential for replication and assembly of the virus. Inactivation of HIV-1 protease causes production of immature, noninfectious viral particles and thus HIV-1 protease is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different ligands (COM5 - designed in our previous study, and Darunavir) and made effort to understand dynamics behaviour of our designed compound COM5. An apo form of HIV-1 protease as monomer and dimer form was also studied in order to analyze response of protein to the ligand. MD results suggest that presence of ligand in hinders the stability of HIV-1 protease and one monomer from dimer systems is dominant on other monomer in terms of interaction made with ligands. We were able to trace functional residues as well as continuous motion of opening and closing (clapping) of flap region in HIV-1 protease (apo form) during entire 1000 ns of MD simulation. COM5 showed almost similar behaviour towards HIV-1 protease enzyme as Darunavir and propose as promising lead compound for the development of new inhibitor for HIV-1 protease.
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Affiliation(s)
- Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233 Gdansk, Poland.
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Padariya M, Kalathiya U, Baginski M. Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation. Biochimica et Biophysica Acta (BBA) - Biomembranes 2015; 1848:2065-74. [DOI: 10.1016/j.bbamem.2015.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/25/2015] [Accepted: 05/18/2015] [Indexed: 01/07/2023]
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Kalathiya U, Padariya M, Baginski M. Identification of 1H-indene-(1,3,5,6)-tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach. Biotechnol Appl Biochem 2015; 63:765-778. [DOI: 10.1002/bab.1432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/06/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - M. Padariya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - M. Baginski
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
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Kalathiya U, Padariya M, Baginski M. Molecular Modeling and Evaluation of Novel Dibenzopyrrole Derivatives as Telomerase Inhibitors and Potential Drug for Cancer Therapy. IEEE/ACM Trans Comput Biol Bioinform 2014; 11:1196-1207. [PMID: 26357055 DOI: 10.1109/tcbb.2014.2326860] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
During previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central ring of acridine with pyrazole ring. These heterocyclic compounds were proposed as a new potential base for telomerase inhibitors. Obtained dibenzopyrrole structure was used as a novel scaffold structure and extension of inhibitors was done by different functional groups. Docking of newly designed compounds in the telomerase active site (telomerase catalytic subunit TERT) was carried out. All dibenzopyrrole derivatives were evaluated by three docking programs: CDOCKER, Ligandfit docking (Scoring Functions) and AutoDock. Compound C_9g, C_9k and C_9l performed best in comparison to all designed inhibitors during the docking in all methods and in interaction analysis. Introduction of pyrazole and extension of dibenzopyrrole in compounds confirm that such compound may act as potential telomerase inhibitors.
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Kalathiya U, Padariya M, Jewginski M, Baginski M. MOLECULAR DOCKING STUDIES TOWARDS DEVELOPMENT OF NOVEL GLY-PHE ANALOGS FOR POTENTIAL INHIBITION OF CATHEPSIN C (DIPEPTIDYL PEPTIDASE I). ACTA ACUST UNITED AC 2014. [DOI: 10.34040/ijcb.3.1.2014.09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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