1
|
Segura L, Santos N, Flores R, Sikazwe D, McGibbon M, Blay V, Cheng KH. Exploring Tau Fibril-Disaggregating and Antioxidating Molecules Binding to Membrane-Bound Amyloid Oligomers Using Machine Learning-Enhanced Docking and Molecular Dynamics. Molecules 2024; 29:2818. [PMID: 38930883 PMCID: PMC11206291 DOI: 10.3390/molecules29122818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Intracellular tau fibrils are sources of neurotoxicity and oxidative stress in Alzheimer's. Current drug discovery efforts have focused on molecules with tau fibril disaggregation and antioxidation functions. However, recent studies suggest that membrane-bound tau-containing oligomers (mTCOs), smaller and less ordered than tau fibrils, are neurotoxic in the early stage of Alzheimer's. Whether tau fibril-targeting molecules are effective against mTCOs is unknown. The binding of epigallocatechin-3-gallate (EGCG), CNS-11, and BHT-CNS-11 to in silico mTCOs and experimental tau fibrils was investigated using machine learning-enhanced docking and molecular dynamics simulations. EGCG and CNS-11 have tau fibril disaggregation functions, while the proposed BHT-CNS-11 has potential tau fibril disaggregation and antioxidation functions like EGCG. Our results suggest that the three molecules studied may also bind to mTCOs. The predicted binding probability of EGCG to mTCOs increases with the protein aggregate size. In contrast, the predicted probability of CNS-11 and BHT-CNS-11 binding to the dimeric mTCOs is higher than binding to the tetrameric mTCOs for the homo tau but not for the hetero tau-amylin oligomers. Our results also support the idea that anionic lipids may promote the binding of molecules to mTCOs. We conclude that tau fibril-disaggregating and antioxidating molecules may bind to mTCOs, and that mTCOs may also be useful targets for Alzheimer's drug design.
Collapse
Affiliation(s)
- Luthary Segura
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA;
| | - Natalia Santos
- Physics Department, Trinity University, San Antonio, TX 78212, USA;
| | - Rafael Flores
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA; (R.F.); (D.S.)
| | - Donald Sikazwe
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA; (R.F.); (D.S.)
| | - Miles McGibbon
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Vincent Blay
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Kwan H. Cheng
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA;
- Physics Department, Trinity University, San Antonio, TX 78212, USA;
| |
Collapse
|
2
|
Yazdi M, Hasanzadeh Kafshgari M, Khademi Moghadam F, Zarezade V, Oellinger R, Khosravi M, Haas S, Hoch CC, Pockley AG, Wagner E, Wollenberg B, Multhoff G, Bashiri Dezfouli A. Crosstalk Between NK Cell Receptors and Tumor Membrane Hsp70-Derived Peptide: A Combined Computational and Experimental Study. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305998. [PMID: 38298098 PMCID: PMC11005703 DOI: 10.1002/advs.202305998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Natural killer (NK) cells are central components of the innate immunity system against cancers. Since tumor cells have evolved a series of mechanisms to escape from NK cells, developing methods for increasing the NK cell antitumor activity is of utmost importance. It is previously shown that an ex vivo stimulation of patient-derived NK cells with interleukin (IL)-2 and Hsp70-derived peptide TKD (TKDNNLLGRFELSG, aa450-461) results in a significant upregulation of activating receptors including CD94 and CD69 which triggers exhausted NK cells to target and kill malignant solid tumors expressing membrane Hsp70 (mHsp70). Considering that TKD binding to an activating receptor is the initial step in the cytolytic signaling cascade of NK cells, herein this interaction is studied by molecular docking and molecular dynamics simulation computational modeling. The in silico results showed a crucial role of the heterodimeric receptor CD94/NKG2A and CD94/NKG2C in the TKD interaction with NK cells. Antibody blocking and CRISPR/Cas9-mediated knockout studies verified the key function of CD94 in the TKD stimulation and activation of NK cells which is characterized by an increased cytotoxic capacity against mHsp70 positive tumor cells via enhanced production and release of lytic granules and pro-inflammatory cytokines.
Collapse
Affiliation(s)
- Mina Yazdi
- Pharmaceutical BiotechnologyDepartment of PharmacyLudwig‐Maximilians‐Universität (LMU)81377MunichGermany
| | - Morteza Hasanzadeh Kafshgari
- Heinz‐Nixdorf‐Chair of Biomedical ElectronicsCampus Klinikum München rechts der IsarTranslaTUMTechnische Universität München81675MunichGermany
| | | | - Vahid Zarezade
- Behbahan Faculty of Medical SciencesBehbahan6361796819Iran
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional GenomicsSchool of MedicineTechnische Universität München81675MunichGermany
- Central Institute for Translational Cancer Research (TranslaTUM)School of MedicineTechnische Universität München81675MunichGermany
| | - Mohammad Khosravi
- Department of PathobiologyFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvaz6135783151Iran
| | - Stefan Haas
- Department of Radiation OncologySchool of MedicineTechnische Universität München81675MunichGermany
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Cosima C. Hoch
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Alan Graham Pockley
- John van Geest Cancer Research CentreSchool of Science and TechnologyNottingham Trent UniversityNottinghamNG11 8NSUK
| | - Ernst Wagner
- Pharmaceutical BiotechnologyDepartment of PharmacyLudwig‐Maximilians‐Universität (LMU)81377MunichGermany
| | - Barbara Wollenberg
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Gabriele Multhoff
- Central Institute for Translational Cancer Research (TranslaTUM)School of MedicineTechnische Universität München81675MunichGermany
- Department of Radiation OncologySchool of MedicineTechnische Universität München81675MunichGermany
| | - Ali Bashiri Dezfouli
- Central Institute for Translational Cancer Research (TranslaTUM)School of MedicineTechnische Universität München81675MunichGermany
- Department of Radiation OncologySchool of MedicineTechnische Universität München81675MunichGermany
- Department of OtorhinolaryngologySchool of MedicineTechnische Universität München81675MunichGermany
| |
Collapse
|
3
|
Santos N, Segura L, Lewis A, Pham T, Cheng KH. Multiscale Modeling of Macromolecular Interactions between Tau-Amylin Oligomers and Asymmetric Lipid Nanodomains That Link Alzheimer's and Diabetic Diseases. Molecules 2024; 29:740. [PMID: 38338484 PMCID: PMC10856442 DOI: 10.3390/molecules29030740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/17/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
The molecular events of protein misfolding and self-aggregation of tau and amylin are associated with the progression of Alzheimer's and diabetes, respectively. Recent studies suggest that tau and amylin can form hetero-tau-amylin oligomers. Those hetero-oligomers are more neurotoxic than homo-tau oligomers. So far, the detailed interactions between the hetero-oligomers and the neuronal membrane are unknown. Using multiscale MD simulations, the lipid binding and protein folding behaviors of hetero-oligomers on asymmetric lipid nanodomains or raft membranes were examined. Our raft membranes contain phase-separated phosphatidylcholine (PC), cholesterol, and anionic phosphatidylserine (PS) or ganglioside (GM1) in one leaflet of the lipid bilayer. The hetero-oligomers bound more strongly to the PS and GM1 than other lipids via the hydrophobic and hydrophilic interactions, respectively, in the raft membranes. The hetero-tetramer disrupted the acyl chain orders of both PC and PS in the PS-containing raft membrane, but only the GM1 in the GM1-containing raft membrane as effectively as the homo-tau-tetramer. We discovered that the alpha-helical content in the heterodimer was greater than the sum of alpha-helical contents from isolated tau and amylin monomers on both raft membranes, indicative of a synergetic effect of tau-amylin interactions in surface-induced protein folding. Our results provide new molecular insights into understanding the cross-talk between Alzheimer's and diabetes.
Collapse
Affiliation(s)
- Natalia Santos
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA; (N.S.); (L.S.); (A.L.)
| | - Luthary Segura
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA; (N.S.); (L.S.); (A.L.)
| | - Amber Lewis
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA; (N.S.); (L.S.); (A.L.)
| | - Thuong Pham
- Physics Department, Trinity University, San Antonio, TX 78212, USA;
| | - Kwan H. Cheng
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA; (N.S.); (L.S.); (A.L.)
- Physics Department, Trinity University, San Antonio, TX 78212, USA;
| |
Collapse
|
4
|
Regmi D, Shen F, Stanic A, Islam M, Du D. Effect of phospholipid liposomes on prion fragment (106-128) amyloid formation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184199. [PMID: 37454869 DOI: 10.1016/j.bbamem.2023.184199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/08/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Misfolding and aggregation of cellular prion protein (PrPc) is a major molecular process involved in the pathogenesis of prion diseases. Here, we studied the aggregation properties of a prion fragment peptide PrP(106-128). The results show that the peptide aggregates in a concentration-dependent manner in an aqueous solution and that the aggregation is sensitive to pH and the preformed amyloid seeds. Furthermore, we show that the zwitterionic POPC liposomes moderately inhibit the aggregation of PrP(106-128), whereas POPC/cholesterol (8:2) vesicles facilitate peptide aggregation likely due to the increase of the lipid packing order and membrane rigidity in the presence of cholesterol. In addition, anionic lipid vesicles of POPG and POPG/cholesterol above a certain concentration accelerate the aggregation of the peptide remarkably. The strong electrostatic interactions between the N-terminal region of the peptide and POPG may constrain the conformational plasticity of the peptide, preventing insertion of the peptide into the inner side of the membrane and thus promoting fibrillation on the membrane surface. The results suggest that the charge properties of the membrane, the composition of the liposomes, and the rigidity of lipid packing are critical in determining peptide adsorption on the membrane surface and the efficiency of the membrane in catalyzing peptide oligomeric nucleation and amyloid formation. The peptide could be used as an improved model molecule to investigate the mechanistic role of the crucial regions of PrP in aggregation in a membrane-rich environment and to screen effective inhibitors to block key interactions between these regions and membranes for preventing PrP aggregation.
Collapse
Affiliation(s)
- Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Aleksander Stanic
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA.
| |
Collapse
|
5
|
Nguyen N, Lewis A, Pham T, Sikazwe D, Cheng KH. Exploring the Role of Anionic Lipid Nanodomains in the Membrane Disruption and Protein Folding of Human Islet Amyloid Polypeptide Oligomers on Lipid Membrane Surfaces Using Multiscale Molecular Dynamics Simulations. Molecules 2023; 28:4191. [PMID: 37241931 PMCID: PMC10223233 DOI: 10.3390/molecules28104191] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The aggregation of human Islet Amyloid Polypeptide (hIAPP) on cell membranes is linked to amyloid diseases. However, the physio-chemical mechanisms of how these hIAPP aggregates trigger membrane damage are unclear. Using coarse-grained and all-atom molecular dynamics simulations, we investigated the role of lipid nanodomains in the presence or absence of anionic lipids, phosphatidylserine (PS), and a ganglioside (GM1), in the membrane disruption and protein folding behaviors of hIAPP aggregates on phase-separated raft membranes. Our raft membranes contain liquid-ordered (Lo), liquid-disordered (Ld), mixed Lo/Ld (Lod), PS-cluster, and GM1-cluster nanosized domains. We observed that hIAPP aggregates bound to the Lod domain in the absence of anionic lipids, but also to the GM1-cluster- and PS-cluster-containing domains, with stronger affinity in the presence of anionic lipids. We discovered that L16 and I26 are the lipid anchoring residues of hIAPP binding to the Lod and PS-cluster domains. Finally, significant lipid acyl chain order disruption in the annular lipid shells surrounding the membrane-bound hIAPP aggregates and protein folding, particularly beta-sheet formation, in larger protein aggregates were evident. We propose that the interactions of hIAPP and both non-anionic and anionic lipid nanodomains represent key molecular events of membrane damage associated with the pathogenesis of amyloid diseases.
Collapse
Affiliation(s)
- Ngoc Nguyen
- Physics Department, Trinity University, San Antonio, TX 78212, USA; (N.N.); (T.P.)
| | - Amber Lewis
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA;
| | - Thuong Pham
- Physics Department, Trinity University, San Antonio, TX 78212, USA; (N.N.); (T.P.)
| | - Donald Sikazwe
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA;
| | - Kwan H. Cheng
- Physics Department, Trinity University, San Antonio, TX 78212, USA; (N.N.); (T.P.)
- Neuroscience Department, Trinity University, San Antonio, TX 78212, USA;
| |
Collapse
|