1
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Lama D, Vosselman T, Sahin C, Liaño-Pons J, Cerrato CP, Nilsson L, Teilum K, Lane DP, Landreh M, Arsenian Henriksson M. A druggable conformational switch in the c-MYC transactivation domain. Nat Commun 2024; 15:1865. [PMID: 38424045 PMCID: PMC10904854 DOI: 10.1038/s41467-024-45826-7] [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: 01/12/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
The c-MYC oncogene is activated in over 70% of all human cancers. The intrinsic disorder of the c-MYC transcription factor facilitates molecular interactions that regulate numerous biological pathways, but severely limits efforts to target its function for cancer therapy. Here, we use a reductionist strategy to characterize the dynamic and structural heterogeneity of the c-MYC protein. Using probe-based Molecular Dynamics (MD) simulations and machine learning, we identify a conformational switch in the c-MYC amino-terminal transactivation domain (termed coreMYC) that cycles between a closed, inactive, and an open, active conformation. Using the polyphenol epigallocatechin gallate (EGCG) to modulate the conformational landscape of coreMYC, we show through biophysical and cellular assays that the induction of a closed conformation impedes its interactions with the transformation/transcription domain-associated protein (TRRAP) and the TATA-box binding protein (TBP) which are essential for the transcriptional and oncogenic activities of c-MYC. Together, these findings provide insights into structure-activity relationships of c-MYC, which open avenues towards the development of shape-shifting compounds to target c-MYC as well as other disordered transcription factors for cancer treatment.
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Affiliation(s)
- Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
| | - Thibault Vosselman
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Carmine P Cerrato
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14813, Huddinge, Sweden
| | - Kaare Teilum
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Department of Cell- and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Marie Arsenian Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, SE-221 00, Lund, Sweden.
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2
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Skriver K, Theisen FF, Kragelund BB. Conformational entropy in molecular recognition of intrinsically disordered proteins. Curr Opin Struct Biol 2023; 83:102697. [PMID: 37716093 DOI: 10.1016/j.sbi.2023.102697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023]
Abstract
Broad conformational ensembles make intrinsically disordered proteins or regions entropically intriguing. Although methodologically challenging and understudied, emerging studies into their changes in conformational entropy (ΔS°conf) upon complex formation have provided both quantitative and qualitative insight. Recent work based on thermodynamics from isothermal titration calorimetry and NMR spectroscopy uncovers an expanded repertoire of regulatory mechanisms, where ΔS°conf plays roles in partner selection, state behavior, functional buffering, allosteric regulation, and drug design. We highlight these mechanisms to display the large entropic reservoir of IDPs for the regulation of molecular communication. We call upon the field to make efforts to contribute to this insight as more studies are needed for forwarding mechanistic decoding of intrinsically disordered proteins and their complexes.
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Affiliation(s)
- Karen Skriver
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Frederik Friis Theisen
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark. https://twitter.com/@FrederikTheisen
| | - Birthe B Kragelund
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
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3
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Arar S, Haque MA, Kayed R. Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics. Proteins 2023:10.1002/prot.26561. [PMID: 37530227 PMCID: PMC10834863 DOI: 10.1002/prot.26561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.
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Affiliation(s)
- Sharif Arar
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
- Department of Chemistry, School of Science, The University of Jordan, Amman 11942, Jordan
| | - Md Anzarul Haque
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
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4
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Vendruscolo M. Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation. Expert Opin Drug Discov 2023:1-11. [PMID: 37276120 DOI: 10.1080/17460441.2023.2221024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. AREAS COVERED We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. EXPERT OPINION There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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5
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Firouzi R, Sowlati-Hashjin S, Chávez-García C, Ashouri M, Karimi-Jafari MH, Karttunen M. Identification of Catechins' Binding Sites in Monomeric A β42 through Ensemble Docking and MD Simulations. Int J Mol Sci 2023; 24:ijms24098161. [PMID: 37175868 PMCID: PMC10179585 DOI: 10.3390/ijms24098161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
The assembly of the amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline-in the framework of the ensemble docking strategy-to identify catechins' binding sites in monomeric Aβ42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ42. Additionally, it has been found that all the studied ligands, especially EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.
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Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran 1496813151, Iran
| | | | - Cecilia Chávez-García
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Mitra Ashouri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran P.O. Box 14155-6619, Iran
| | - Mohammad Hossein Karimi-Jafari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran P.O. Box 14155-6619, Iran
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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6
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Lee KY, Lee BJ. Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery. Antibiotics (Basel) 2023; 12:antibiotics12040637. [PMID: 37106997 PMCID: PMC10135005 DOI: 10.3390/antibiotics12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.
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Affiliation(s)
- Ki-Young Lee
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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7
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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8
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Zhu J, Salvatella X, Robustelli P. Small molecules targeting the disordered transactivation domain of the androgen receptor induce the formation of collapsed helical states. Nat Commun 2022; 13:6390. [PMID: 36302916 PMCID: PMC9613762 DOI: 10.1038/s41467-022-34077-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Intrinsically disordered proteins, which do not adopt well-defined structures under physiological conditions, are implicated in many human diseases. Small molecules that target the disordered transactivation domain of the androgen receptor have entered human trials for the treatment of castration-resistant prostate cancer (CRPC), but no structural or mechanistic rationale exists to explain their inhibition mechanisms or relative potencies. Here, we utilize all-atom molecular dynamics computer simulations to elucidate atomically detailed binding mechanisms of the compounds EPI-002 and EPI-7170 to the androgen receptor. Our simulations reveal that both compounds bind at the interface of two transiently helical regions and induce the formation of partially folded collapsed helical states. We find that EPI-7170 binds androgen receptor more tightly than EPI-002 and we identify a network of intermolecular interactions that drives higher affinity binding. Our results suggest strategies for developing more potent androgen receptor inhibitors and general strategies for disordered protein drug design.
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Affiliation(s)
- Jiaqi Zhu
- grid.254880.30000 0001 2179 2404Dartmouth College, Department of Chemistry, Hanover, NH 03755 USA
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, 0810 Barcelona, Spain
| | - Paul Robustelli
- grid.254880.30000 0001 2179 2404Dartmouth College, Department of Chemistry, Hanover, NH 03755 USA
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9
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Affinity of disordered protein complexes is modulated by entropy-energy reinforcement. Proc Natl Acad Sci U S A 2022; 119:e2120456119. [PMID: 35727975 PMCID: PMC9245678 DOI: 10.1073/pnas.2120456119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrinsically disordered proteins (IDPs), which are very common and essential to many biological activities, sometimes function via interaction with another IDP and form a fuzzy complex, which can be highly stable. It is unclear what the biophysical forces are that govern their thermodynamics and specificity, which are essential for de novo fuzzy complex design. Here, we explored the fuzzy complex formed between ProTα and H1, which are oppositely charged IDPs, by swapping the charges between them, generating variants that have either greater polyampholytic or polyelectrolytic nature as well as different charge patterns. Charge swapping and shuffling dramatically change the affinity of the fuzzy complex, which is contributed to by both enthalpy and entropy, where the latter is dominated by counterion release. The association between two intrinsically disordered proteins (IDPs) may produce a fuzzy complex characterized by a high binding affinity, similar to that found in the ultrastable complexes formed between two well-structured proteins. Here, using coarse-grained simulations, we quantified the biophysical forces driving the formation of such fuzzy complexes. We found that the high-affinity complex formed between the highly and oppositely charged H1 and ProTα proteins is sensitive to electrostatic interactions. We investigated 52 variants of the complex by swapping charges between the two oppositely charged proteins to produce sequences whose negatively or positively charged residue content was more homogeneous or heterogenous (i.e., polyelectrolytic or polyampholytic, having higher or lower absolute net charges, respectively) than the wild type. We also changed the distributions of oppositely charged residues within each participating sequence to produce variants in which the charges were segregated or well mixed. Both types of changes significantly affect binding affinity in fuzzy complexes, which is governed by both enthalpy and entropy. The formation of H1–ProTa is supported by an increase in configurational entropy and by entropy due to counterion release. The latter can be twice as large as the former, illustrating the dominance of counterion entropy in modulating the binding thermodynamics. Complexes formed between proteins with greater absolute net charges are more stable, both enthalpically and entropically, indicating that enthalpy and entropy have a mutually reinforcing effect. The sensitivity of the thermodynamics of the complex to net charge and the charge pattern within each of the binding constituents may provide a means to achieve binding specificity between IDPs.
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10
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Löhr T, Kohlhoff K, Heller GT, Camilloni C, Vendruscolo M. A Small Molecule Stabilizes the Disordered Native State of the Alzheimer's Aβ Peptide. ACS Chem Neurosci 2022; 13:1738-1745. [PMID: 35649268 PMCID: PMC9204762 DOI: 10.1021/acschemneuro.2c00116] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
![]()
The stabilization
of native states of proteins is a powerful drug
discovery strategy. It is still unclear, however, whether this approach
can be applied to intrinsically disordered proteins. Here, we report
a small molecule that stabilizes the native state of the Aβ42
peptide, an intrinsically disordered protein fragment associated with
Alzheimer’s disease. We show that this stabilization takes
place by a disordered binding mechanism, in which both the small molecule
and the Aβ42 peptide remain disordered. This disordered binding
mechanism involves enthalpically favorable local π-stacking
interactions coupled with entropically advantageous global effects.
These results indicate that small molecules can stabilize disordered
proteins in their native states through transient non-specific interactions
that provide enthalpic gain while simultaneously increasing the conformational
entropy of the proteins.
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Affiliation(s)
- Thomas Löhr
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Kai Kohlhoff
- Google Research, Mountain View, California 94043, United States
| | - Gabriella T. Heller
- Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
- Department of Structural and Molecular Biology, University College London, WC1E 6BT London, UK
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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11
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Robustelli P, Ibanez-de-Opakua A, Campbell-Bezat C, Giordanetto F, Becker S, Zweckstetter M, Pan AC, Shaw DE. Molecular Basis of Small-Molecule Binding to α-Synuclein. J Am Chem Soc 2022; 144:2501-2510. [PMID: 35130691 PMCID: PMC8855421 DOI: 10.1021/jacs.1c07591] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Intrinsically disordered
proteins (IDPs) are implicated in many
human diseases. They have generally not been amenable to conventional
structure-based drug design, however, because their intrinsic conformational
variability has precluded an atomic-level understanding of their binding
to small molecules. Here we present long-time-scale, atomic-level
molecular dynamics (MD) simulations of monomeric α-synuclein
(an IDP whose aggregation is associated with Parkinson’s disease)
binding the small-molecule drug fasudil in which the observed protein–ligand
interactions were found to be in good agreement with previously reported
NMR chemical shift data. In our simulations, fasudil, when bound,
favored certain charge–charge and π-stacking interactions
near the C terminus of α-synuclein but tended not to form these
interactions simultaneously, rather breaking one of these interactions
and forming another nearby (a mechanism we term dynamic shuttling). Further simulations with small molecules chosen to modify these
interactions yielded binding affinities and key structural features
of binding consistent with subsequent NMR experiments, suggesting
the potential for MD-based strategies to facilitate the rational design
of small molecules that bind with disordered proteins.
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Affiliation(s)
- Paul Robustelli
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | | | | | | | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Albert C Pan
- D. E. Shaw Research, New York, New York 10036, United States
| | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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12
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Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochem Soc Trans 2022; 50:541-554. [PMID: 35129612 DOI: 10.1042/bst20210499] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
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13
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Rizzuti B, Lan W, Santofimia-Castaño P, Zhou Z, Velázquez-Campoy A, Abián O, Peng L, Neira JL, Xia Y, Iovanna JL. Design of Inhibitors of the Intrinsically Disordered Protein NUPR1: Balance between Drug Affinity and Target Function. Biomolecules 2021; 11:biom11101453. [PMID: 34680086 PMCID: PMC8533202 DOI: 10.3390/biom11101453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are emerging as attractive drug targets by virtue of their physiological ubiquity and their prevalence in various diseases, including cancer. NUPR1 is an IDP that localizes throughout the whole cell, and is involved in the development and progression of several tumors. We have previously repurposed trifluoperazine (TFP) as a drug targeting NUPR1 and, by using a ligand-based approach, designed the drug ZZW-115 starting from the TFP scaffold. Such derivative compound hinders the development of pancreatic ductal adenocarcinoma (PDAC) in mice, by hampering nuclear translocation of NUPR1. Aiming to further improve the activity of ZZW-115, here we have used an indirect drug design approach to modify its chemical features, by changing the substituent attached to the piperazine ring. As a result, we have synthesized a series of compounds based on the same chemical scaffold. Isothermal titration calorimetry (ITC) showed that, with the exception of the compound preserving the same chemical moiety at the end of the alkyl chain as ZZW-115, an increase of the length by a single methylene group (i.e., ethyl to propyl) significantly decreased the affinity towards NUPR1 measured in vitro, whereas maintaining the same length of the alkyl chain and adding heterocycles favored the binding affinity. However, small improvements of the compound affinity towards NUPR1, as measured by ITC, did not result in a corresponding improvement in their inhibitory properties and in cellulo functions, as proved by measuring three different biological effects: hindrance of the nuclear translocation of the protein, sensitization of cells against DNA damage mediated by NUPR1, and prevention of cancer cell growth. Our findings suggest that a delicate compromise between favoring ligand affinity and controlling protein function may be required to successfully design drugs against NUPR1, and likely other IDPs.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Rende, Cosenza, Italy;
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
| | - Wenjun Lan
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France; (W.L.); (P.S.-C.)
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», 13288 Marseille, France;
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France; (W.L.); (P.S.-C.)
| | - Zhengwei Zhou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China;
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Barcelona, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», 13288 Marseille, France;
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Yi Xia
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China;
- Correspondence: (Y.X.); (J.L.I.)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France; (W.L.); (P.S.-C.)
- Correspondence: (Y.X.); (J.L.I.)
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14
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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15
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Iconaru LI, Das S, Nourse A, Shelat AA, Zuo J, Kriwacki RW. Small Molecule Sequestration of the Intrinsically Disordered Protein, p27 Kip1, Within Soluble Oligomers. J Mol Biol 2021; 433:167120. [PMID: 34197833 DOI: 10.1016/j.jmb.2021.167120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Abstract
Proteins that exhibit intrinsically disordered regions (IDRs) are prevalent in the human proteome and perform diverse biological functions, including signaling and regulation. Due to these important roles, misregulation of intrinsically disordered proteins (IDPs) is associated with myriad human diseases, including neurodegeneration and cancer. The inherent flexibility of IDPs limits the applicability of the traditional structure-based drug design paradigm; therefore, IDPs have long been considered "undruggable". Using NMR spectroscopy and other methods, we previously discovered small, drug-like molecules that bind specifically, albeit weakly, to dynamic clusters of aromatic residues within p27Kip1 (p27), an archetypal disordered protein involved in cell cycle regulation. Here, using synthetic chemistry, NMR spectroscopy and other biophysical methods, we discovered elaborated analogs of our previously reported molecules with 30-fold increased affinity for p27 (apparent Kd = 57 ± 19 μM). Strikingly, using analytical ultracentrifugation methods, we showed that the highest affinity compounds caused p27 to form soluble, disordered oligomers. Based on these observations, we propose that sequestration within soluble oligomers may represent a general strategy for therapeutically targeting disease-associated IDPs in the future.
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Affiliation(s)
- Luigi I Iconaru
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Present address: Sanofi, Waltham, MA 02451, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Molecular Interactions Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jian Zuo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE 68178, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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16
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On the specificity of protein-protein interactions in the context of disorder. Biochem J 2021; 478:2035-2050. [PMID: 34101805 PMCID: PMC8203207 DOI: 10.1042/bcj20200828] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.
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17
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Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov 2021; 20:669-688. [PMID: 34006959 DOI: 10.1038/s41573-021-00199-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.
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Affiliation(s)
- Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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18
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Biesaga M, Frigolé-Vivas M, Salvatella X. Intrinsically disordered proteins and biomolecular condensates as drug targets. Curr Opin Chem Biol 2021; 62:90-100. [PMID: 33812316 DOI: 10.1016/j.cbpa.2021.02.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022]
Abstract
Intrinsically disordered domains represent attractive therapeutic targets because they play key roles in cancer, as well as in neurodegenerative and infectious diseases. They are, however, considered undruggable because they do not form stable binding pockets for small molecules and, therefore, have not been prioritized in drug discovery. Under physiological solution conditions many biomedically relevant intrinsically disordered proteins undergo phase separation processes leading to the formation of mesoscopic highly dynamic assemblies, generally known as biomolecular condensates that define environments that can be quite different from the solutions surrounding them. In what follows, we review key recent findings in this area and show how biomolecular condensation can offer opportunities for modulating the activities of intrinsically disordered targets.
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Affiliation(s)
- Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Joint BSC-IRB Research Programme in Computational Biology, Baldiri Reixac 10, 08028, Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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19
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Wu M, Dorosh L, Schmitt-Ulms G, Wille H, Stepanova M. Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008771. [PMID: 33711010 PMCID: PMC7990313 DOI: 10.1371/journal.pcbi.1008771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/24/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization. Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST14), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST14 might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- * E-mail:
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20
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Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, Vendruscolo M. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. SCIENCE ADVANCES 2020; 6:6/45/eabb5924. [PMID: 33148639 PMCID: PMC7673680 DOI: 10.1126/sciadv.abb5924] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/22/2020] [Indexed: 05/15/2023]
Abstract
Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes.
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Affiliation(s)
- Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco Simone Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Thomas Löhr
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry. CNRS UMR 3528, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
- Department of Pharmacy, University of Naples "Federico II," 80131 Naples, Italy
| | - Isabella C Felli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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21
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Wang W, Chen Y, Xu A, Cai M, Cao J, Zhu H, Yang B, Shao X, Ying M, He Q. Protein phase separation: A novel therapy for cancer? Br J Pharmacol 2020; 177:5008-5030. [PMID: 32851637 DOI: 10.1111/bph.15242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/18/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, phase separation has been increasingly reported to play a pivotal role in a wide range of biological processes. Due to the close relationships between cancer and disorders in intracellular physiological function, the identification of new mechanisms involved in intracellular regulation has been regarded as a new direction for cancer therapy. Introducing the concept of phase separation into complex descriptions of disease mechanisms may provide many different insights. Here, we review the recent findings on the phase separation of cancer-related proteins, describing the possible relationships between phase separation and key proteins associated with cancer and indicate possible regulatory modalities, especially drug candidates for phase separation, which may provide more effective strategies for cancer therapy.
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Affiliation(s)
- Wei Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yingqian Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Aixiao Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Minyi Cai
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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22
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Drake JA, Pettitt BM. Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder. J Phys Chem B 2020; 124:4379-4390. [PMID: 32349480 PMCID: PMC7384255 DOI: 10.1021/acs.jpcb.0c02489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the last two decades it has become clear that well-defined structure is not a requisite for proteins to properly function. Rather, spectra of functionally competent, structurally disordered states have been uncovered requiring canonical paradigms in molecular biology to be revisited or reimagined. It is enticing and oftentimes practical to divide the proteome into structured and unstructured, or disordered, proteins. While function, composition, and structural properties largely differ, these two classes of protein are built upon the same scaffold, namely, the protein backbone. The versatile physicochemical properties of the protein backbone must accommodate structural disorder, order, and transitions between these states. In this review, we survey these properties through the conceptual lenses of solubility and conformational populations and in the context of protein-disorder mediated phenomena (e.g., phase separation, order-disorder transitions, allostery). Particular attention is paid to the results of computational studies, which, through thermodynamic decomposition and dissection of molecular interactions, can provide valuable mechanistic insight and testable hypotheses to guide further solution experiments. Lastly, we discuss changes in the dynamics of side chains and order-disorder transitions of the protein backbone as two modes or realizations of "entropic reservoirs" capable of tuning coupled thermodynamic processes.
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Affiliation(s)
- Justin A Drake
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, Texas, United States
- Texas Advanced Computing Center, University of Texas at Austin, Austin 78712, Texas, United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, Texas, United States
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23
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Horvath A, Miskei M, Ambrus V, Vendruscolo M, Fuxreiter M. Sequence-based prediction of protein binding mode landscapes. PLoS Comput Biol 2020; 16:e1007864. [PMID: 32453748 PMCID: PMC7304629 DOI: 10.1371/journal.pcbi.1007864] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/19/2020] [Accepted: 04/09/2020] [Indexed: 02/04/2023] Open
Abstract
Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred (http://protdyn-fuzpred.org) algorithm to predict the range of context-dependent binding modes of proteins from their amino acid sequences. As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways. Great advances have been made in the last several decades in deciphering how the behavior of proteins is encoded in their amino acid sequences. A variety of sequence-based prediction methods have been developed to estimate a wide range of properties of proteins, including secondary structure propensity, native state structures, preference for being disordered and tendency to aggregate. Much less is known, however, about the rules that regulate the conformational changes of proteins upon binding. In particular, many proteins change their binding modes upon interacting with different partners, or as a consequence of post-translational modifications or changes in the cellular milieu. Here we address the problem of how amino acid sequences can encode different binding modes depending on their binding partners, and describe the FuzPred method of predicting context-dependent binding modes.
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Affiliation(s)
- Attila Horvath
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Marton Miskei
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Viktor Ambrus
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (MV); (MF)
| | - Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
- * E-mail: (MV); (MF)
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24
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Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules 2020; 10:E743. [PMID: 32403216 PMCID: PMC7277182 DOI: 10.3390/biom10050743] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and have attracted significant interest in understanding if and how they may be targeted using small molecules for therapeutic purposes. While most existing studies have focused on extending the traditional structure-centric drug design strategies and emphasized exploring pre-existing structure features of IDPs for specific binding, several examples have also emerged to suggest that small molecules could achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. These dynamic interactions can modulate the disordered conformational ensemble and often lead to modest compaction to shield functionally important interaction sites. Much work remains to be done on further elucidation of the molecular basis of the dynamic small molecule-IDP interaction and determining how it can be exploited for targeting IDPs in practice. These efforts will rely critically on an integrated experimental and computational framework for disordered protein ensemble characterization. In particular, exciting advances have been made in recent years in enhanced sampling techniques, Graphic Processing Unit (GPU)-computing, and protein force field optimization, which have now allowed rigorous physics-based atomistic simulations to generate reliable structure ensembles for nontrivial IDPs of modest sizes. Such de novo atomistic simulations will play crucial roles in exploring the exciting opportunity of targeting IDPs through dynamic interactions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China;
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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25
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Probing Surfaces in Dynamic Protein Interactions. J Mol Biol 2020; 432:2949-2972. [DOI: 10.1016/j.jmb.2020.02.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 01/09/2023]
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26
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Abstract
Functions of intrinsically disordered proteins do not require structure. Such structure-independent functionality has melted away the classic rigid "lock and key" representation of structure-function relationships in proteins, opening a new page in protein science, where molten keys operate on melted locks and where conformational flexibility and intrinsic disorder, structural plasticity and extreme malleability, multifunctionality and binding promiscuity represent a new-fangled reality. Analysis and understanding of this new reality require novel tools, and some of the techniques elaborated for the examination of intrinsically disordered protein functions are outlined in this review.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russian Federation
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27
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Dobson CM, Knowles TPJ, Vendruscolo M. The Amyloid Phenomenon and Its Significance in Biology and Medicine. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033878. [PMID: 30936117 DOI: 10.1101/cshperspect.a033878] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The misfolding of proteins is now recognized to be the origin of a large number of medical disorders. One particularly important group of such disorders is associated with the aggregation of misfolded proteins into amyloid structures, and includes conditions ranging from Alzheimer's and Parkinson's diseases to type II diabetes. Such conditions already affect over 500 million people in the world, a number that is rising rapidly, and at present these disorders cannot be effectively treated or prevented. This review provides an overview of this field of science and discusses recent progress in understanding the nature and properties of the amyloid state, the kinetics and mechanism governing its formation, the origins of its links with disease, and the manner in which its formation may be inhibited or suppressed. This latter topic is of particular importance, both to enhance our knowledge of the maintenance of protein homeostasis in living organisms and also to address the development of therapeutic strategies through which to combat the loss of homeostasis and the associated onset and progression of disease.
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Affiliation(s)
- Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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28
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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29
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Kim MY, Na I, Kim JS, Son SH, Choi S, Lee SE, Kim JH, Jang K, Alterovitz G, Chen Y, van der Vaart A, Won HS, Uversky VN, Kim CG. Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2. SCIENCE ADVANCES 2019; 5:eaav9810. [PMID: 31799386 PMCID: PMC6867884 DOI: 10.1126/sciadv.aav9810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Although intrinsically disordered protein regions (IDPRs) are commonly engaged in promiscuous protein-protein interactions (PPIs), using them as drug targets is challenging due to their extreme structural flexibility. We report a rational discovery of inhibitors targeting an IDPR of MBD2 that undergoes disorder-to-order transition upon PPI and is critical for the regulation of the Mi-2/NuRD chromatin remodeling complex (CRC). Computational biology was essential for identifying target site, searching for promising leads, and assessing their binding feasibility and off-target probability. Molecular action of selected leads inhibiting the targeted PPI of MBD2 was validated in vitro and in cell, followed by confirming their inhibitory effects on the epithelial-mesenchymal transition of various cancer cells. Identified lead compounds appeared to potently inhibit cancer metastasis in a murine xenograft tumor model. These results constitute a pioneering example of rationally discovered IDPR-targeting agents and suggest Mi-2/NuRD CRC and/or MBD2 as a promising target for treating cancer metastasis.
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Affiliation(s)
- Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ji Sook Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Seol Eui Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Korea
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Gil Alterovitz
- Boston Children's Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Hyung-Sik Won
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk 27478, Korea
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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30
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Depicting Conformational Ensembles of α-Synuclein by Single Molecule Force Spectroscopy and Native Mass Spectroscopy. Int J Mol Sci 2019; 20:ijms20205181. [PMID: 31635031 PMCID: PMC6829300 DOI: 10.3390/ijms20205181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022] Open
Abstract
Description of heterogeneous molecular ensembles, such as intrinsically disordered proteins, represents a challenge in structural biology and an urgent question posed by biochemistry to interpret many physiologically important, regulatory mechanisms. Single-molecule techniques can provide a unique contribution to this field. This work applies single molecule force spectroscopy to probe conformational properties of α-synuclein in solution and its conformational changes induced by ligand binding. The goal is to compare data from such an approach with those obtained by native mass spectrometry. These two orthogonal, biophysical methods are found to deliver a complex picture, in which monomeric α-synuclein in solution spontaneously populates compact and partially compacted states, which are differently stabilized by binding to aggregation inhibitors, such as dopamine and epigallocatechin-3-gallate. Analyses by circular dichroism and Fourier-transform infrared spectroscopy show that these transitions do not involve formation of secondary structure. This comparative analysis provides support to structural interpretation of charge-state distributions obtained by native mass spectrometry and helps, in turn, defining the conformational components detected by single molecule force spectroscopy.
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31
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Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Konstantin Röder
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Jerelle A. Joseph
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Brooke E. Husic
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - David J. Wales
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
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32
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33
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Williams JK, Yang X, Baum J. Interactions between the Intrinsically Disordered Proteins β-Synuclein and α-Synuclein. Proteomics 2018; 18:e1800109. [PMID: 30142698 PMCID: PMC6447293 DOI: 10.1002/pmic.201800109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/18/2018] [Indexed: 12/31/2022]
Abstract
Several intrinsically disordered proteins have been implicated in the process of amyloid fibril formation in neurodegenerative disease, and developing approaches to inhibit the aggregation of these intrinsically disordered proteins is critical for establishing effective therapies against disease progression. The aggregation pathway of the intrinsically disordered protein alpha-synuclein, which is implicated in several neurodegenerative diseases known as synucleinopathies, has been extensively characterized. Less attention has been leveraged on beta-synuclein, a homologous intrinsically disordered protein that co-localizes with alpha-synuclein and is known to delay alpha-synuclein fibril formation. In this review, we focus on beta-synuclein and the molecular-level interactions between alpha-synuclein and beta-synuclein that underlie the delay of fibril formation. We highlight studies that begin to define alpha-synuclein and beta-synuclein interactions at the monomer, oligomer, and surface levels, and suggest that beta-synuclein plays a role in regulation of inhibition at many different stages of alpha-synuclein aggregation.
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Affiliation(s)
- Jonathan K Williams
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| | - Xue Yang
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
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34
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Fuxreiter M. Fold or not to fold upon binding - does it really matter? Curr Opin Struct Biol 2018; 54:19-25. [PMID: 30340123 DOI: 10.1016/j.sbi.2018.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Protein interactions are usually determined by well-defined contact patterns. In this scenario, structuring of the interface is a prerequisite, which takes place prior or coupled to binding. Recent data, however, indicate plasticity of the templated folding pathway as well as considerable variations: polymorphism or dynamics in the bound-state. Conformational fluctuations in both cases are modulated by non-native, transient contacts, which complement suboptimal binding motifs to improve affinity. Here I discuss both templated folding and fuzzy binding mechanisms and propose a uniform scheme.
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Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.
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35
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Ruan H, Sun Q, Zhang W, Liu Y, Lai L. Targeting intrinsically disordered proteins at the edge of chaos. Drug Discov Today 2018; 24:217-227. [PMID: 30278223 DOI: 10.1016/j.drudis.2018.09.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/16/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022]
Abstract
Intrinsically disordered proteins or intrinsically disordered regions (IDPs or IDRs) are those that do not fold into defined tertiary structures under physiological conditions. Given their prevalence in various diseases, IDPs are attractive therapeutic targets. However, because of the dynamic nature of the IDP structure, conventional structure-based drug design methods cannot be directly applied. Thanks to recent progress in understanding the mechanisms underlying IDP and ligand interactions, computational strategies for IDP-targeted rational drug discovery are emerging. Here, we summarize recent developments in computational IDP drug design strategies and their successful applications, analyze the typical properties of reported IDP-binding compounds (iIDPs), and discuss the major challenges ahead as well as possible solutions.
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Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qi Sun
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Weilin Zhang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying Liu
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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36
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Chen J, Kriwacki RW. Intrinsically Disordered Proteins: Structure, Function and Therapeutics. J Mol Biol 2018; 430:2275-2277. [PMID: 29906412 DOI: 10.1016/j.jmb.2018.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, United States; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN 38105, United States.
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