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Article: Virtual screening of ultra-large chemical libraries identifies cell-permeable small-molecule inhibitors of a "non-druggable" target, STAT3 N-terminal domain.

Bonilla, Pedro Andrade / Hoop, Cody L / Stefanisko, Karen / Tarasov, Sergey G / Sinha, Sourav / Nicklaus, Marc C / Tarasova, Nadya I

Frontiers in oncology

2023 Volume 13, Page(s) 1144153

Abstract: STAT3 N-terminal domain is a promising molecular target for cancer treatment and modulation of immune responses. However, STAT3 is localized in the cytoplasm, mitochondria, and nuclei, and thus, is inaccessible to therapeutic antibodies. Its N-terminal ... ...

Abstract	STAT3 N-terminal domain is a promising molecular target for cancer treatment and modulation of immune responses. However, STAT3 is localized in the cytoplasm, mitochondria, and nuclei, and thus, is inaccessible to therapeutic antibodies. Its N-terminal domain lacks deep pockets on the surface and represents a typical "non-druggable" protein. In order to successfully identify potent and selective inhibitors of the domain, we have used virtual screening of billion structure-sized virtual libraries of make-on-demand screening samples. The results suggest that the expansion of accessible chemical space by cutting-edge ultra-large virtual compound databases can lead to successful development of small molecule drugs for hard-to-target intracellular proteins.
Language	English
Publishing date	2023-04-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1144153
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Article ; Online: Probing the effect of glycosaminoglycan depletion on integrin interactions with collagen I fibrils in the native extracellular matrix environment.

Roth, Jonathan / Hoop, Cody L / Williams, Jonathan K / Hayes, Robert / Baum, Jean

Protein science : a publication of the Protein Society

2022 Volume 32, Issue 1, Page(s) e4508

Abstract: Fibrillar collagen-integrin interactions in the extracellular matrix (ECM) regulate a multitude of cellular processes and cell signalling. Collagen I fibrils serve as the molecular scaffolding for connective tissues throughout the human body and are the ... ...

Abstract	Fibrillar collagen-integrin interactions in the extracellular matrix (ECM) regulate a multitude of cellular processes and cell signalling. Collagen I fibrils serve as the molecular scaffolding for connective tissues throughout the human body and are the most abundant protein building blocks in the ECM. The ECM environment is diverse, made up of several ECM proteins, enzymes, and proteoglycans. In particular, glycosaminoglycans (GAGs), anionic polysaccharides that decorate proteoglycans, become depleted in the ECM with natural aging and their mis-regulation has been linked to cancers and other diseases. The impact of GAG depletion in the ECM environment on collagen I protein interactions and on mechanical properties is not well understood. Here, we integrate ELISA protein binding assays with liquid high-resolution atomic force microscopy (AFM) to assess the effects of GAG depletion on the interaction of collagen I fibrils with the integrin α2I domain using separate rat tails. ELISA binding assays demonstrate that α2I preferentially binds to GAG-depleted collagen I fibrils in comparison to native fibrils. By amplitude modulated AFM in air and in solution, we find that GAG-depleted collagen I fibrils retain structural features of the native fibrils, including their characteristic D-banding pattern, a key structural motif. AFM fast force mapping in solution shows that GAG depletion reduces the stiffness of individual fibrils, lowering the indentation modulus by half compared to native fibrils. Together these results shed new light on how GAGs influence collagen I fibril-integrin interactions and may aid in strategies to treat diseases that result from GAG mis-regulation.
MeSH term(s)	Rats ; Humans ; Animals ; Glycosaminoglycans/analysis ; Glycosaminoglycans/chemistry ; Glycosaminoglycans/metabolism ; Extracellular Matrix/chemistry ; Proteoglycans/analysis ; Proteoglycans/metabolism ; Microscopy, Atomic Force ; Collagen/chemistry
Chemical Substances	Glycosaminoglycans ; Proteoglycans ; Collagen (9007-34-5)
Language	English
Publishing date	2022-11-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4508
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Molecular dynamics analysis of a flexible loop at the binding interface of the SARS-CoV-2 spike protein receptor-binding domain.

Williams, Jonathan K / Wang, Baifan / Sam, Andrew / Hoop, Cody L / Case, David A / Baum, Jean

Proteins

2021 Volume 90, Issue 5, Page(s) 1044–1053

Abstract: Since the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human angiotensin ... ...

Abstract	Since the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human angiotensin converting enzyme 2 (ACE2) receptor. This has provided a detailed picture of the end point structure of the RBD-ACE2 binding event, but what remains to be elucidated is the conformation and dynamics of the RBD prior to its interaction with ACE2. In this work, we utilize molecular dynamics simulations to probe the flexibility and conformational ensemble of the unbound state of the receptor-binding domain from SARS-CoV-2 and SARS-CoV. We have found that the unbound RBD has a localized region of dynamic flexibility in Loop 3 and that mutations identified during the COVID-19 pandemic in Loop 3 do not affect this flexibility. We use a loop-modeling protocol to generate and simulate novel conformations of the CoV2-RBD Loop 3 region that sample conformational space beyond the ACE2 bound crystal structure. This has allowed for the identification of interesting substates of the unbound RBD that are lower energy than the ACE2-bound conformation, and that block key residues along the ACE2 binding interface. These novel unbound substates may represent new targets for therapeutic design.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Binding Sites ; COVID-19 ; Humans ; Molecular Dynamics Simulation ; Pandemics ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26208
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Zs.A 2291: Show issues

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Article ; Online: DJ-1 Acts as a Scavenger of α-Synuclein Oligomers and Restores Monomeric Glycated α-Synuclein.

Atieh, Tamr B / Roth, Jonathan / Yang, Xue / Hoop, Cody L / Baum, Jean

Biomolecules

2021 Volume 11, Issue 10

Abstract: Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson's disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from ... ...

Abstract	Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson's disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from neurons. DJ-1, an antioxidative protein that plays a critical role in PD pathology, has been proposed to repair glycation in proteins, yet a mechanism has not been elucidated. In this study, we integrate solution nuclear magnetic resonance (NMR) spectroscopy and liquid atomic force microscopy (AFM) techniques to characterize glycated N-terminally acetylated-αSyn (glyc-ac-αSyn) and its interaction with DJ-1. Glycation of ac-αSyn by methylglyoxal increases oligomer formation, as visualized by AFM in solution, resulting in decreased dynamics of the monomer amide backbone around the Lys residues, as measured using NMR. Upon addition of DJ-1, this NMR signature of glyc-ac-αSyn monomers reverts to a native ac-αSyn-like character. This phenomenon is reversible upon removal of DJ-1 from the solution. Using relaxation-based NMR, we have identified the binding site on DJ-1 for glycated and native ac-αSyn as the catalytic pocket and established that the oxidation state of the catalytic cysteine is imperative for binding. Based on our results, we propose a novel mechanism by which DJ-1 scavenges glyc-ac-αSyn oligomers without chemical deglycation, suppresses glyc-ac-αSyn monomer-oligomer interactions, and releases free glyc-ac-αSyn monomers in solution. The interference of DJ-1 with ac-αSyn oligomers may promote free ac-αSyn monomer in solution and suppress the propagation of toxic oligomer and fibril species. These results expand the understanding of the role of DJ-1 in PD pathology by acting as a scavenger for aggregated αSyn.
MeSH term(s)	Acetylation ; Cysteine/metabolism ; Glycation End Products, Advanced/genetics ; Humans ; Magnetic Resonance Spectroscopy ; Neurons/metabolism ; Neurons/pathology ; Parkinson Disease/genetics ; Parkinson Disease/metabolism ; Parkinson Disease/pathology ; Protein Aggregation, Pathological/genetics ; Protein Aggregation, Pathological/pathology ; Protein Deglycase DJ-1/genetics ; Protein Multimerization/genetics ; alpha-Synuclein/genetics
Chemical Substances	Glycation End Products, Advanced ; SNCA protein, human ; alpha-Synuclein ; PARK7 protein, human (EC 3.1.2.-) ; Protein Deglycase DJ-1 (EC 3.1.2.-) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2021-10-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom11101466
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Article ; Online: NMR unveils an N-terminal interaction interface on acetylated-α-synuclein monomers for recruitment to fibrils.

Yang, Xue / Wang, Baifan / Hoop, Cody L / Williams, Jonathan K / Baum, Jean

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 18

Abstract: Amyloid fibril formation of α-synuclein (αS) is associated with multiple neurodegenerative diseases, including Parkinson's disease (PD). Growing evidence suggests that progression of PD is linked to cell-to-cell propagation of αS fibrils, which leads to ... ...

Abstract	Amyloid fibril formation of α-synuclein (αS) is associated with multiple neurodegenerative diseases, including Parkinson's disease (PD). Growing evidence suggests that progression of PD is linked to cell-to-cell propagation of αS fibrils, which leads to seeding of endogenous intrinsically disordered monomer via templated elongation and secondary nucleation. A molecular understanding of the seeding mechanism and driving interactions is crucial to inhibit progression of amyloid formation. Here, using relaxation-based solution NMR experiments designed to probe large complexes, we probe weak interactions of intrinsically disordered acetylated-αS (Ac-αS) monomers with seeding-competent Ac-αS fibrils and seeding-incompetent off-pathway oligomers to identify Ac-αS monomer residues at the binding interface. Under conditions that favor fibril elongation, we determine that the first 11 N-terminal residues on the monomer form a common binding site for both fibrils and off-pathway oligomers. Additionally, the presence of off-pathway oligomers within a fibril seeding environment suppresses seeded amyloid formation, as observed through thioflavin-T fluorescence experiments. This highlights that off-pathway αS oligomers can act as an auto-inhibitor against αS fibril elongation. Based on these data taken together with previous results, we propose a model in which Ac-αS monomer recruitment to the fibril is driven by interactions between the intrinsically disordered monomer N terminus and the intrinsically disordered flanking regions (IDR) on the fibril surface. We suggest that this monomer recruitment may play a role in the elongation of amyloid fibrils and highlight the potential of the IDRs of the fibril as important therapeutic targets against seeded amyloid formation.
MeSH term(s)	Amyloid/chemistry ; Amyloid/genetics ; Amyloid/ultrastructure ; Benzothiazoles/chemistry ; Benzothiazoles/metabolism ; Binding Sites/genetics ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/genetics ; Intrinsically Disordered Proteins/ultrastructure ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Nuclear Magnetic Resonance, Biomolecular ; Parkinson Disease/genetics ; Parkinson Disease/pathology ; alpha-Synuclein/chemistry ; alpha-Synuclein/genetics ; alpha-Synuclein/ultrastructure
Chemical Substances	Amyloid ; Benzothiazoles ; Intrinsically Disordered Proteins ; alpha-Synuclein ; thioflavin T (2390-54-7)
Language	English
Publishing date	2021-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2017452118
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Zs.A 1148: Show issues

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Article ; Online: Collagen I Weakly Interacts with the β-Sheets of β

Hoop, Cody L / Zhu, Jie / Bhattacharya, Shibani / Tobita, Caitlyn A / Radford, Sheena E / Baum, Jean

Journal of the American Chemical Society

2020 Volume 142, Issue 3, Page(s) 1321–1331

Abstract: Amyloidogenesis is significant in both protein function and pathology. Amyloid formation of folded, globular proteins is commonly initiated by partial or complete unfolding. However, how this unfolding event is triggered for proteins that are otherwise ... ...

Abstract	Amyloidogenesis is significant in both protein function and pathology. Amyloid formation of folded, globular proteins is commonly initiated by partial or complete unfolding. However, how this unfolding event is triggered for proteins that are otherwise stable in their native environments is not well understood. The accumulation of the immunoglobulin protein β
MeSH term(s)	Amyloid/chemistry ; Amyloid/metabolism ; Collagen Type I/metabolism ; Humans ; Protein Binding ; Protein Conformation ; beta 2-Microglobulin/metabolism
Chemical Substances	Amyloid ; Collagen Type I ; beta 2-Microglobulin
Language	English
Publishing date	2020-01-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.9b10421
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Article ; Online: CD36-Binding Amphiphilic Nanoparticles for Attenuation of Alpha Synuclein-Induced Microglial Activation.

Zhao, Nanxia / Francis, Nicola L / Song, Shuang / Kholodovych, Vladyslav / Calvelli, Hannah R / Hoop, Cody L / Pang, Zhiping P / Baum, Jean / Uhrich, Kathryn E / Moghe, Prabhas V

Advanced nanobiomed research

2022 Volume 2, Issue 6

Abstract: Neuroinflammation is one of the hallmarks contributing to Parkinson's Disease (PD) pathology, where microglial activation occurs as one of the earliest events, triggered by extracellular alpha synuclein (aSYN) binding to the CD36 receptor. Here, CD36- ... ...

Abstract	Neuroinflammation is one of the hallmarks contributing to Parkinson's Disease (PD) pathology, where microglial activation occurs as one of the earliest events, triggered by extracellular alpha synuclein (aSYN) binding to the CD36 receptor. Here, CD36-binding nanoparticles (NPs) containing synthetic tartaric acid-based amphiphilic polymers (AMs) were rationally designed to inhibit this aSYN-CD36 binding.
Language	English
Publishing date	2022-03-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	3009938-9
ISSN	2699-9307 ; 2699-9307
ISSN (online)	2699-9307
ISSN	2699-9307
DOI	10.1002/anbr.202100120
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Article ; Online: Extracellular matrix components modulate different stages in β

Benseny-Cases, Núria / Karamanos, Theodoros K / Hoop, Cody L / Baum, Jean / Radford, Sheena E

The Journal of biological chemistry

2019 Volume 294, Issue 24, Page(s) 9392–9401

Abstract: Amyloid deposition of WT human ... ...

Abstract	Amyloid deposition of WT human β
MeSH term(s)	Amyloid/chemistry ; Amyloid/metabolism ; Amyloidosis/metabolism ; Amyloidosis/pathology ; Anticoagulants/administration & dosage ; Collagen Type I/administration & dosage ; Extracellular Matrix/metabolism ; Heparin, Low-Molecular-Weight/administration & dosage ; Humans ; Mutation ; beta 2-Microglobulin/chemistry ; beta 2-Microglobulin/genetics ; beta 2-Microglobulin/metabolism
Chemical Substances	Amyloid ; Anticoagulants ; Collagen Type I ; Heparin, Low-Molecular-Weight ; beta 2-Microglobulin
Language	English
Publishing date	2019-04-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA119.008300
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Uc I Zs.108: Show issues

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Article ; Online: Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril.

Zhu, Jie / Hoop, Cody L / Case, David A / Baum, Jean

Scientific reports

2018 Volume 8, Issue 1, Page(s) 16646

Abstract: Collagen fibril interactions with cells and macromolecules in the extracellular matrix drive numerous cellular functions. Binding motifs for dozens of collagen-binding proteins have been determined on fully exposed collagen triple helical monomers. ... ...

Abstract	Collagen fibril interactions with cells and macromolecules in the extracellular matrix drive numerous cellular functions. Binding motifs for dozens of collagen-binding proteins have been determined on fully exposed collagen triple helical monomers. However, when the monomers are assembled into the functional collagen fibril, many binding motifs become inaccessible, and yet critical cellular processes occur. Here, we have developed an early stage atomic model of the smallest repeating unit of the type I collagen fibril at the fibril surface that provides a novel framework to address questions about these functionally necessary yet seemingly obstructed interactions. We use an integrative approach by combining molecular dynamics (MD) simulations with atomic force microscopy (AFM) experiments and show that reconstruction of the collagen monomers within the complex fibril play a critical role in collagen interactions. In particular, the fibril surface shows three major conformational changes, which allow cryptic binding sites, including an integrin motif involved in platelet aggregation, to be exposed. The observed dynamics and reconstruction of the fibril surface promote its role as a "smart fibril" to keep certain binding sites cryptic, and to allow accessibility of recognition domains when appropriate.
MeSH term(s)	Animals ; Binding Sites ; Collagen Type I/chemistry ; Collagen Type I/metabolism ; Extracellular Matrix/metabolism ; Fibrillar Collagens/chemistry ; Fibrillar Collagens/metabolism ; Integrins/chemistry ; Integrins/metabolism ; Molecular Dynamics Simulation ; Protein Conformation ; Rats
Chemical Substances	Collagen Type I ; Fibrillar Collagens ; Integrins
Language	English
Publishing date	2018-11-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-34616-z
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Article ; Online: Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain

Williams, Jonathan K / Wang, Baifan / Sam, Andrew / Hoop, Cody L / Case, David A / Baum, Jean

bioRxiv

Abstract	Since the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic, considerable effort has been spent characterizing the interaction between the Spike protein receptor-binding domain (RBD) and the human angiotensin converting enzyme 2 (ACE2) receptor. This has provided a detailed picture of the end point structure of the RBD-ACE2 binding event, but what remains to be elucidated is the conformation and dynamics of the RBD prior to its interaction with ACE2. In this work we utilize molecular dynamics simulations to probe the flexibility and conformational ensemble of the unbound state of the receptor-binding domain from SARS-CoV-2 and SARS-CoV. We have found that the unbound RBD has a localized region of dynamic flexibility in Loop 3 and that mutations identified during the COVID-19 pandemic in Loop 3 do not affect this flexibility. We use a loop-modeling protocol to generate and simulate novel conformations of the CoV2-RBD Loop 3 region that sample conformational space beyond the ACE2 bound crystal structure. This has allowed for the identification of interesting substates of the unbound RBD that are lower energy than the ACE2-bound conformation, and that block key residues along the ACE2 binding interface. These novel unbound substates may represent new targets for therapeutic design.
Keywords	covid19
Language	English
Publishing date	2021-01-11
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.01.08.425965
Database	COVID19

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