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  1. Article ; Online: Conformational inhibitors of protein aggregation.

    Fernández Ramírez, María Del Carmen / Afrin, Shumaila / Saelices, Lorena

    Current opinion in structural biology

    2023  Volume 83, Page(s) 102700

    Abstract: Amyloidoses are fatal conditions associated with the aggregation of proteins into amyloid fibrils that deposit systemically and/or locally. Possibly because the causal mechanism of protein aggregation and deposition is not fully understood, this group of ...

    Abstract Amyloidoses are fatal conditions associated with the aggregation of proteins into amyloid fibrils that deposit systemically and/or locally. Possibly because the causal mechanism of protein aggregation and deposition is not fully understood, this group of diseases remains uncurable. Advances in structural biology, such as the use of nuclear magnetic resonance and cryo-electron microscopy, have enabled the study of the structures and the conformational nature of the proteins whose aggregation is associated with the underlying pathogenesis of amyloidosis. As a result, the last years of research have translated into the development of directed therapeutic strategies that target the specific conformations of precursors, fibrils, and intermediary species. Current efforts include the use of small molecules, peptides, and antibodies. This review summarizes the recent progress in developing strategies that target specific protein conformations for the treatment of amyloidoses.
    MeSH term(s) Humans ; Protein Aggregates ; Cryoelectron Microscopy ; Amyloidosis/metabolism ; Amyloidosis/pathology ; Amyloid/chemistry ; Protein Conformation
    Chemical Substances Protein Aggregates ; Amyloid
    Language English
    Publishing date 2023-09-15
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2023.102700
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis.

    Nguyen, Binh An / Singh, Virender / Afrin, Shumaila / Singh, Preeti / Pekala, Maja / Ahmed, Yasmin / Pedretti, Rose / Canepa, Jacob / Lemoff, Andrew / Kluve-Beckerman, Barbara / Wydorski, Pawel / Chhapra, Farzeen / Saelices, Lorena

    bioRxiv : the preprint server for biology

    2024  

    Abstract: ATTR amyloidosis results from the conversion of transthyretin into amyloid fibrils that deposit in tissues causing organ failure and death. This conversion is facilitated by mutations in ATTRv amyloidosis, or aging in ATTRwt amyloidosis. ATTRv ... ...

    Abstract ATTR amyloidosis results from the conversion of transthyretin into amyloid fibrils that deposit in tissues causing organ failure and death. This conversion is facilitated by mutations in ATTRv amyloidosis, or aging in ATTRwt amyloidosis. ATTRv amyloidosis exhibits extreme phenotypic variability, whereas ATTRwt amyloidosis presentation is consistent and predictable. Previously, we found an unprecedented structural variability in cardiac amyloid fibrils from polyneuropathic ATTRv-I84S patients. In contrast, cardiac fibrils from five genotypically-different patients with cardiomyopathy or mixed phenotypes are structurally homogeneous. To understand fibril structure's impact on phenotype, it is necessary to study the fibrils from multiple patients sharing genotype and phenotype. Here we show the cryo-electron microscopy structures of fibrils extracted from four cardiomyopathic ATTRwt amyloidosis patients. Our study confirms that they share identical conformations with minimal structural variability, consistent with their homogenous clinical presentation. Our study contributes to the understanding of ATTR amyloidosis biopathology and calls for further studies.
    Language English
    Publishing date 2024-03-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.08.582936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Elucidating the interaction of ticlopidine with serum albumin and its role in bilirubin displacement in vitro.

    Afrin, Shumaila / Rahman, Yusra / Tabish, Mohammad

    Journal of biomolecular structure & dynamics

    2018  Volume 37, Issue 4, Page(s) 863–876

    Abstract: Ticlopidine is an anti-platelet drug that functions as a ... ...

    Abstract Ticlopidine is an anti-platelet drug that functions as a P2Y
    MeSH term(s) Animals ; Bilirubin/chemistry ; Bilirubin/metabolism ; Binding Sites ; Cattle ; Hydrophobic and Hydrophilic Interactions ; In Vitro Techniques/methods ; Models, Molecular ; Molecular Docking Simulation ; Protein Binding ; Protein Conformation ; Serum Albumin, Bovine/chemistry ; Serum Albumin, Bovine/metabolism ; Spectrometry, Fluorescence ; Thermodynamics ; Ticlopidine/chemistry ; Ticlopidine/metabolism
    Chemical Substances Serum Albumin, Bovine (27432CM55Q) ; Ticlopidine (OM90ZUW7M1) ; Bilirubin (RFM9X3LJ49)
    Language English
    Publishing date 2018-03-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2018.1449667
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Interaction of pirenzepine with bovine serum albumin and effect of β-cyclodextrin on binding: A biophysical and molecular docking approach.

    Rahman, Yusra / Afrin, Shumaila / Tabish, Mohammad

    Archives of biochemistry and biophysics

    2018  Volume 652, Page(s) 27–37

    Abstract: Studying the interaction of therapeutic molecules with serum albumin is important to understand their biopharmaceutics, pharmacokinetics and toxicity as well as their relation with the structure and function of protein. The biomolecular interaction of an ...

    Abstract Studying the interaction of therapeutic molecules with serum albumin is important to understand their biopharmaceutics, pharmacokinetics and toxicity as well as their relation with the structure and function of protein. The biomolecular interaction of an anti-spasmodic drug, pirenzepine with bovine serum albumin (BSA) was investigated using multi-spectroscopic, calorimetric and docking studies. Fluorescence quenching of BSA on interaction with pirenzepine revealed the static mode of quenching. Pirenzepine exhibited a moderate binding to serum albumin with the binding constant value in the order of 10
    MeSH term(s) Biophysical Phenomena ; Calorimetry ; Circular Dichroism ; Molecular Docking Simulation ; Muscarinic Antagonists/metabolism ; Pirenzepine/metabolism ; Protein Binding ; Serum Albumin, Bovine/chemistry ; Serum Albumin, Bovine/metabolism ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; Structure-Activity Relationship ; beta-Cyclodextrins/pharmacology
    Chemical Substances Muscarinic Antagonists ; beta-Cyclodextrins ; Serum Albumin, Bovine (27432CM55Q) ; Pirenzepine (3G0285N20N) ; betadex (JV039JZZ3A)
    Language English
    Publishing date 2018-06-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 523-x
    ISSN 1096-0384 ; 0003-9861
    ISSN (online) 1096-0384
    ISSN 0003-9861
    DOI 10.1016/j.abb.2018.06.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Author Correction: O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology.

    Balana, Aaron T / Mahul-Mellier, Anne-Laure / Nguyen, Binh A / Horvath, Mian / Javed, Afraah / Hard, Eldon R / Jasiqi, Yllza / Singh, Preeti / Afrin, Shumaila / Pedretti, Rose / Singh, Virender / Lee, Virginia M-Y / Luk, Kelvin C / Saelices, Lorena / Lashuel, Hilal A / Pratt, Matthew R

    Nature chemical biology

    2024  Volume 20, Issue 5, Page(s) 656

    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-024-01587-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology.

    Balana, Aaron T / Mahul-Mellier, Anne-Laure / Nguyen, Binh A / Horvath, Mian / Javed, Afraah / Hard, Eldon R / Jasiqi, Yllza / Singh, Preeti / Afrin, Shumaila / Pedretti, Rose / Singh, Virender / Lee, Virginia M-Y / Luk, Kelvin C / Saelices, Lorena / Lashuel, Hilal A / Pratt, Matthew R

    Nature chemical biology

    2024  Volume 20, Issue 5, Page(s) 646–655

    Abstract: Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer's and Parkinson's disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the ... ...

    Abstract Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer's and Parkinson's disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the determinants contributing to the formation of different amyloid features could open new avenues for developing disease-specific diagnostics and therapies. Here we report that O-GlcNAc modification of α-synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by cryogenic electron microscopy, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson's disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc-modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the α-synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that posttranslational modifications, such as O-GlcNAc modification, of α-synuclein are key determinants of α-synuclein amyloid strains and pathogenicity.
    MeSH term(s) alpha-Synuclein/metabolism ; alpha-Synuclein/chemistry ; Amyloid/metabolism ; Humans ; Animals ; Mice ; Parkinson Disease/metabolism ; Parkinson Disease/pathology ; Acetylglucosamine/metabolism ; Acetylglucosamine/chemistry ; Protein Processing, Post-Translational ; Cryoelectron Microscopy ; Neurons/metabolism ; Neurons/pathology
    Chemical Substances alpha-Synuclein ; Amyloid ; Acetylglucosamine (V956696549)
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-024-01551-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy.

    Nguyen, Binh An / Singh, Virender / Afrin, Shumaila / Yakubovska, Anna / Wang, Lanie / Ahmed, Yasmin / Pedretti, Rose / Fernandez-Ramirez, Maria Del Carmen / Singh, Preeti / Pękała, Maja / Cabrera Hernandez, Luis O / Kumar, Siddharth / Lemoff, Andrew / Gonzalez-Prieto, Roman / Sawaya, Michael R / Eisenberg, David S / Benson, Merrill Douglas / Saelices, Lorena

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 581

    Abstract: ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. ...

    Abstract ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies.
    MeSH term(s) Humans ; Amyloid/chemistry ; Amyloid Neuropathies, Familial/genetics ; Cryoelectron Microscopy ; Prealbumin/genetics ; Prealbumin/chemistry ; Heart ; Brain Diseases
    Chemical Substances Amyloid ; Prealbumin
    Language English
    Publishing date 2024-01-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-44820-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Biophysical insights into the binding characteristics of bovine serum albumin with dipyridamole and the influence of molecular interaction with β cyclodextrin.

    Afrin, Shumaila / Rahman, Yusra / Alhaji Isa, Mustafa / Ahmed, Shahbaz / Tabish, Mohammad

    Journal of biomolecular structure & dynamics

    2019  Volume 38, Issue 10, Page(s) 3046–3058

    Abstract: The binding characteristic of anti-platelet drug dipyridamole has been investigated with a transport protein, serum albumin. A multi-spectroscopic approach has been employed, and the results were well supported ... ...

    Abstract The binding characteristic of anti-platelet drug dipyridamole has been investigated with a transport protein, serum albumin. A multi-spectroscopic approach has been employed, and the results were well supported by
    MeSH term(s) Binding Sites ; Dipyridamole ; Molecular Docking Simulation ; Protein Binding ; Serum Albumin, Bovine/metabolism ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; Thermodynamics ; beta-Cyclodextrins
    Chemical Substances beta-Cyclodextrins ; Serum Albumin, Bovine (27432CM55Q) ; Dipyridamole (64ALC7F90C)
    Language English
    Publishing date 2019-08-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2019.1651220
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Elucidating the molecular interaction of serum albumin with nizatidine and the role of β-cyclodextrin: multi-spectroscopic and computational approach.

    Rahman, Yusra / Afrin, Shumaila / Alhaji Isa, Mustafa / Ahmed, Shahbaz / Tabish, Mohammad

    Journal of biomolecular structure & dynamics

    2019  Volume 38, Issue 5, Page(s) 1375–1387

    Abstract: Nizatidine is a histamine H2 receptor antagonist which act by inhibiting the production of stomach acid, thereby, finds its application in treating various diseases related to the gastrointestinal tract. Studying albumin-drug interaction is important for ...

    Abstract Nizatidine is a histamine H2 receptor antagonist which act by inhibiting the production of stomach acid, thereby, finds its application in treating various diseases related to the gastrointestinal tract. Studying albumin-drug interaction is important for understanding the pharmacokinetics and pharmacodynamics of therapeutic candidates. In the present work, the interaction of nizatidine with BSA was investigated by employing multi-spectroscopic and computational studies. The formation of BSA-nizatidine complex was characterised by UV-visible and fluorescence based-spectroscopic studies. Steady-state fluorescence demonstrated the static mode of quenching of BSA by nizatidine. The interaction was spontaneous and nizatidine binds to BSA with a stoichiometry of 1:1. Forster resonance energy transfer calculations revealed that there was a high possibility of energy transfer between nizatidine and BSA. The resultant secondary structural change in BSA on the addition of nizatidine was studied by circular dichroism spectroscopy. Moreover, synchronous and three-dimensional fluorescence spectroscopy was used to determine the conformational changes occurred in the structure of albumin on the binding of nizatidine. Competitive-site marker experiments suggested that nizatidine binds in the Sudlow site II of BSA. Additionally, the effect of β-cyclodextrin as an inclusion compound on the interaction was studied. Furthermore, molecular modelling and simulation studies were performed to corroborate the results obtained above.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Binding Sites ; Circular Dichroism ; Molecular Docking Simulation ; Nizatidine ; Protein Binding ; Serum Albumin ; Serum Albumin, Bovine/metabolism ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; Thermodynamics ; beta-Cyclodextrins
    Chemical Substances Serum Albumin ; beta-Cyclodextrins ; Serum Albumin, Bovine (27432CM55Q) ; Nizatidine (P41PML4GHR)
    Language English
    Publishing date 2019-04-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2019.1604265
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: O-GlcNAc modification forces the formation of an α-Synuclein amyloid-strain with notably diminished seeding activity and pathology.

    Balana, Aaron T / Mahul-Mellier, Anne-Laure / Nguyen, Binh A / Horvath, Mian / Javed, Afraah / Hard, Eldon R / Jasiqi, Yllza / Singh, Preeti / Afrin, Shumaila / Pedretti, Rose / Singh, Virender / Lee, Virginia M-Y / Luk, Kelvin C / Saelices, Lorena / Lashuel, Hilal A / Pratt, Matthew R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The process of amyloid fibril formation remains one of the primary targets for developing diagnostics and treatments for several neurodegenerative diseases (NDDs). Amyloid-forming proteins such α-Synuclein and Tau, which are implicated in the ... ...

    Abstract The process of amyloid fibril formation remains one of the primary targets for developing diagnostics and treatments for several neurodegenerative diseases (NDDs). Amyloid-forming proteins such α-Synuclein and Tau, which are implicated in the pathogenesis of Alzheimer's and Parkinson's disease, can form different types of fibril structure, or strains, that exhibit distinct structures, toxic properties, seeding activities, and pathology spreading patterns in the brain. Therefore, understanding the molecular and structural determinants contributing to the formation of different amyloid strains or their distinct features could open new avenues for developing disease-specific diagnostics and therapies. In this work, we report that O-GlcNAc modification of α-Synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by Cryo-EM, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson's disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc modified fibrils remain unclear, our
    Language English
    Publishing date 2023-03-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.07.531573
    Database MEDical Literature Analysis and Retrieval System OnLINE

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