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Article ; Online: Development of a rapid image-based high-content imaging screening assay to evaluate therapeutic antibodies against the monkeypox virus.

Kota, Krishna P / Ziółkowska, Natasza E / Wei, Jiayi / Peng, Junzhong / Ordonez, David / Raney, Christy / Prigge, Jon / Hooper, Jay W / Awasthi, Mayanka / Goebel, Scott J / Zabel, Brian A / Nasar, Farooq / Lederman, Seth / Bavari, Sina

Antiviral research

2022 Volume 210, Page(s) 105513

Abstract: Antibody-based therapy is emerging as a critical therapeutic countermeasure to treat acute viral infections by offering rapid protection against clinical disease. The advancements in structural biology made it feasible to rationalize monoclonal ... ...

Abstract	Antibody-based therapy is emerging as a critical therapeutic countermeasure to treat acute viral infections by offering rapid protection against clinical disease. The advancements in structural biology made it feasible to rationalize monoclonal antibodies (mAbs) by identifying key and, possibly, neutralizing epitopes of viral proteins for therapeutic purposes. A critical component in assessing mAbs during pandemics requires the development of rapid but detailed methods to detect and quantitate the neutralization activity. In this study, we developed and optimized two high-content image (HCI)-based assays: one to detect viral proteins by staining and the second to quantify cytopathic viral effects by a label-free phenotypic assay. These assays were employed to screen for therapeutic antibodies against the monkeypox virus (MPXV) using surrogate poxviruses such as vaccinia virus (VACV). Plaque-based neutralization results confirmed the HCI data. The phenotypic assay found pox virus-induced syncytia formation in various cells, and we were able to quantitate and use this phenotype to screen mAbs. The HCI identified several potent VACV-neutralizing antibodies that showed in vitro efficacy against both clades of MPXV. In addition, a combination study of ST-246/tecovirimat/TPOXX a single neutralizing antibody Ab-40, showed synergistic activity against VACV in an in-vitro neutralization assay. This rapid high-content method utilizing state-of-the-art technologies enabled the evaluation of hundreds of mAbs quickly to identify several potent anti-MPXV neutralizing mAbs for further development.
MeSH term(s)	Monkeypox virus ; Antibodies, Viral ; Antibodies, Neutralizing ; Vaccinia virus/genetics ; Viral Proteins ; Antibodies, Monoclonal/pharmacology ; Neutralization Tests
Chemical Substances	Antibodies, Viral ; Antibodies, Neutralizing ; Viral Proteins ; Antibodies, Monoclonal
Language	English
Publishing date	2022-12-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2022.105513
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Article ; Online: In vitro microtubule severing assays.

Ziółkowska, Natasza E / Roll-Mecak, Antonina

Methods in molecular biology (Clifton, N.J.)

2013 Volume 1046, Page(s) 323–334

Abstract: Microtubules are rigid and highly dynamic cellular polymers essential for intracellular transport, cell division and differentiation. Their stability is tightly regulated by a vast array of cellular factors. In vitro microtubule assays have proven to be ... ...

Abstract	Microtubules are rigid and highly dynamic cellular polymers essential for intracellular transport, cell division and differentiation. Their stability is tightly regulated by a vast array of cellular factors. In vitro microtubule assays have proven to be powerful tools for deciphering the mechanism of microtubule dynamics regulators such as molecular motors and microtubule associated proteins. In this chapter we focus on microtubule severing enzymes that use the energy of ATP hydrolysis to introduce internal breaks in the microtubule lattice. We present a detailed protocol for a light microscopy based in vitro microtubule severing assay that was instrumental in the identification and characterization of these enzymes.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Cell Differentiation/genetics ; Cell Division/genetics ; Hydrolysis ; In Vitro Techniques ; Microscopy, Polarization ; Microtubule-Associated Proteins/chemistry ; Microtubule-Associated Proteins/metabolism ; Microtubules/metabolism ; Microtubules/ultrastructure ; Molecular Biology/methods ; Polymers/chemistry
Chemical Substances	Microtubule-Associated Proteins ; Polymers ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-538-5_19
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Article ; Online: Organized living: formation mechanisms and functions of plasma membrane domains in yeast.

Ziółkowska, Natasza E / Christiano, Romain / Walther, Tobias C

Trends in cell biology

2012 Volume 22, Issue 3, Page(s) 151–158

Abstract: Plasma membrane proteins and lipids organize into lateral domains of specific composition. Domain formation is achieved by a combination of lipid-lipid and lipid-protein interactions, membrane-binding protein scaffolds and protein fences. The resulting ... ...

Abstract	Plasma membrane proteins and lipids organize into lateral domains of specific composition. Domain formation is achieved by a combination of lipid-lipid and lipid-protein interactions, membrane-binding protein scaffolds and protein fences. The resulting domains function in membrane protein turnover and homeostasis, as well as in cell signaling. We review the mechanisms generating plasma membrane domains and the functional consequences of this organization, focusing on recent findings from research on the yeast model system.
MeSH term(s)	Animals ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Homeostasis ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/metabolism ; Signal Transduction
Chemical Substances	Fungal Proteins ; Membrane Proteins
Language	English
Publishing date	2012-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2011.12.002
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Article: Organized living: formation mechanisms and functions of plasma membrane domains in yeast

Ziółkowska, Natasza E / Christiano, Romain / Walther, Tobias C

Trends in cell biology. 2012 Mar., v. 22, no. 3

2012

Abstract: Plasma membrane proteins and lipids organize into lateral domains of specific composition. Domain formation is achieved by a combination of lipid–lipid and lipid–protein interactions, membrane-binding protein scaffolds and protein fences. The resulting ... ...

Abstract	Plasma membrane proteins and lipids organize into lateral domains of specific composition. Domain formation is achieved by a combination of lipid–lipid and lipid–protein interactions, membrane-binding protein scaffolds and protein fences. The resulting domains function in membrane protein turnover and homeostasis, as well as in cell signaling. We review the mechanisms generating plasma membrane domains and the functional consequences of this organization, focusing on recent findings from research on the yeast model system.
Keywords	homeostasis ; lipids ; membrane proteins ; plasma membrane ; protein metabolism ; yeasts
Language	English
Dates of publication	2012-03
Size	p. 151-158.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2011.12.002
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Article: Structural studies of algal lectins with anti-HIV activity.

Ziółkowska, Natasza E / Wlodawer, Alexander

Acta biochimica Polonica

2006 Volume 53, Issue 4, Page(s) 617–626

Abstract: A number of antiviral lectins, small proteins that bind carbohydrates found on viral envelopes, are currently in pre-clinical trials as potential drugs for prevention of transmission of human immunodeficiency virus (HIV) and other enveloped viruses, such ...

Abstract	A number of antiviral lectins, small proteins that bind carbohydrates found on viral envelopes, are currently in pre-clinical trials as potential drugs for prevention of transmission of human immunodeficiency virus (HIV) and other enveloped viruses, such as the Ebola virus and the coronavirus responsible for severe acute respiratory syndrome (SARS). Lectins of algal origin whose antiviral properties make them candidate agents for prevention of viral transmission through topical applications include cyanovirin-N, Microcystis viridis lectin, scytovirin, and griffithsin. Although all these proteins exhibit significant antiviral activity, their structures are unrelated and their mode of binding of carbohydrates differs significantly. This review summarizes the current state of knowledge of the structures of algal lectins, their mode of binding of carbohydrates, and their potential medical applications.
MeSH term(s)	Anti-HIV Agents/chemistry ; Anti-HIV Agents/pharmacology ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Eukaryota/chemistry ; Lectins/chemistry ; Lectins/pharmacology ; Protein Binding ; Protein Conformation
Chemical Substances	Anti-HIV Agents ; Antiviral Agents ; Lectins
Keywords	covid19
Language	English
Publishing date	2006
Publishing country	Poland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	595762-x
ISSN	1734-154X ; 0001-527X
ISSN (online)	1734-154X
ISSN	0001-527X
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Article ; Online: Long-Term Real-World Outcomes and Safety of Vemurafenib and Vemurafenib + Cobimetinib Therapy in Patients with BRAF-Mutated Melanoma.

Piejko, Karolina / Cybulska-Stopa, Bożena / Ziętek, Marcin / Dziura, Robert / Galus, Łukasz / Kempa-Kamińska, Natasza / Ziółkowska, Barbara / Rutkowska, Ewa / Kopciński, Tomasz / Kubiatowski, Tomasz / Bal, Wiesław / Suwiński, Rafał / Mackiewicz, Jacek / Kamińska-Winciorek, Grażyna / Czarnecka, Anna M / Rutkowski, Piotr

Targeted oncology

2023 Volume 18, Issue 2, Page(s) 235–245

Abstract: Background: Combined treatment with BRAFi and/or MEK inhibitors (MEKi) improves outcomes in advanced melanoma patients in comparison with monotherapy.: Objective: We aim to report real-world treatment efficacy and safety of vemurafenib (V) and ... ...

Abstract	Background: Combined treatment with BRAFi and/or MEK inhibitors (MEKi) improves outcomes in advanced melanoma patients in comparison with monotherapy. Objective: We aim to report real-world treatment efficacy and safety of vemurafenib (V) and vemurafenib + cobimetinib (V + C) from 10 years of practice. Patients and methods: A total of 275 consecutive patients with unresectable or metastatic BRAF mutated melanoma started first-line V or V + C treatment between 1 October 2013 and 31 December 2020. Survival analyses were performed using the Kaplan-Meier method, and Log-rank and Chi-square tests were used for comparison between groups. Results: The estimated median overall survival (mOS) was 10.3 months in the V group, and 12.3 months in the V + C group (p = 0.0005; HR = 1.58, 95% CI 1.2-2.1), although the latter group of patients had lactate dehydrogenase elevated numerically more often. Estimated median progression-free survival (mPFS) was 5.5 months in the V group, and 8.3 months in the V + C group (p = 0.0002; HR = 1.62, 95% CI 1.3-2.1). Complete response, partial response, stable disease, and progressive disease as best responses were recorded in the V/V + C groups in 7%/10%, 52%/46%, 26%/28%, and 15%/16% of patients, respectively. The numbers of patients with any grade of adverse effects were similar in both groups. Conclusions: We confirmed significant improvement in the mOS and mPFS of unresectable and/or metastatic BRAF mutated-melanoma patients treated outside clinical trials with V + C as compared with V, with no major increase in toxicity for the combination.
MeSH term(s)	Humans ; Vemurafenib/pharmacology ; Vemurafenib/therapeutic use ; Proto-Oncogene Proteins B-raf/genetics ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Melanoma/drug therapy ; Melanoma/genetics ; Melanoma/pathology ; Skin Neoplasms/drug therapy ; Skin Neoplasms/genetics ; Mutation
Chemical Substances	Vemurafenib (207SMY3FQT) ; cobimetinib (ER29L26N1X) ; Proto-Oncogene Proteins B-raf (EC 2.7.11.1) ; BRAF protein, human (EC 2.7.11.1)
Language	English
Publishing date	2023-03-11
Publishing country	France
Document type	Journal Article
ZDB-ID	2222136-0
ISSN	1776-260X ; 1776-2596
ISSN (online)	1776-260X
ISSN	1776-2596
DOI	10.1007/s11523-023-00954-w
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Article ; Online: Eisosome-driven plasma membrane organization is mediated by BAR domains.

Ziółkowska, Natasza E / Karotki, Lena / Rehman, Michael / Huiskonen, Juha T / Walther, Tobias C

Nature structural & molecular biology

2011 Volume 18, Issue 7, Page(s) 854–856

Abstract: Plasma membranes are organized into domains of different protein and lipid composition. Eisosomes are key complexes for yeast plasma membrane organization, containing primarily Pil1 and Lsp1. Here we show that both proteins consist mostly of a banana- ... ...

Abstract	Plasma membranes are organized into domains of different protein and lipid composition. Eisosomes are key complexes for yeast plasma membrane organization, containing primarily Pil1 and Lsp1. Here we show that both proteins consist mostly of a banana-shaped BAR domain common to membrane sculpting proteins, most similar to the ones of amphiphysin, arfaptin 2 and endophilin 2. Our data reveal a previously unrecognized family of BAR-domain proteins involved in plasma membrane organization.
MeSH term(s)	Cell Membrane/metabolism ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Membrane Proteins/physiology ; Multigene Family ; Phosphoproteins/chemistry ; Phosphoproteins/metabolism ; Phosphoproteins/physiology ; Phylogeny ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; Sequence Analysis, Protein
Chemical Substances	LSP1 protein, S cerevisiae ; Membrane Proteins ; PIL1 protein, S cerevisiae ; Phosphoproteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2011-06-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.2080
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Article ; Online: New active HIV-1 protease inhibitors derived from 3-hexanol: conformation study of the free inhibitors in crystalline state and in complex with the enzyme.

Ziółkowska, Natasza E / Bujacz, Anna / Randad, Ramnarayan S / Erickson, John W / Skálová, Tereza / Hašek, Jindřich / Bujacz, Grzegorz

Chemical biology & drug design

2012 Volume 79, Issue 5, Page(s) 798–809

Abstract: Four novel linear non-peptidic HIV-1 protease inhibitors derived from 2,5-diamino-1,6-diphenyl-3-hexanol were synthesized and characterized. All of them exhibit tight binding to HIV-1 protease, with inhibition constants K(i) in the range 20 pm-5 nm. The ...

Abstract	Four novel linear non-peptidic HIV-1 protease inhibitors derived from 2,5-diamino-1,6-diphenyl-3-hexanol were synthesized and characterized. All of them exhibit tight binding to HIV-1 protease, with inhibition constants K(i) in the range 20 pm-5 nm. The investigated inhibitors were crystallized, and their crystal structures were determined by X-ray diffraction. In all cases, the conformations found in the crystalline state differ significantly from the conformations obtained by computational docking of the inhibitor in the binding cleft of native HIV-1 protease. Owing to the prevalence of hydrophobic substituents in all these inhibitors, the conformational mobility in water solution is restricted to their compact forms. The spectrum of low-energy conformations in solution dramatically changes during the formation of inhibitor crystals (phenyl ring stacking as a leading motif) or during the formation of a complex with HIV-1 protease (elongated conformation suitable to fit the enzyme pockets as a factor responsible for tight binding). High conformational flexibility and low conformational stress in the molecules of these inhibitors most likely increase their biological activity in comparison with more rigid compounds.
MeSH term(s)	Binding Sites ; Crystallography, X-Ray ; Drug Design ; HIV Infections/drug therapy ; HIV Infections/enzymology ; HIV Protease/chemistry ; HIV Protease/metabolism ; HIV Protease Inhibitors/chemistry ; HIV Protease Inhibitors/pharmacology ; HIV-1/drug effects ; HIV-1/enzymology ; Hexanols/chemistry ; Hexanols/pharmacology ; Humans ; Models, Molecular ; Molecular Conformation
Chemical Substances	HIV Protease Inhibitors ; Hexanols ; HIV Protease (EC 3.4.23.-) ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-)
Language	English
Publishing date	2012-05
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/j.1747-0285.2012.01328.x
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Article: Crystallographic studies of the complexes of antiviral protein griffithsin with glucose and N-acetylglucosamine.

Ziółkowska, Natasza E / Shenoy, Shilpa R / O'Keefe, Barry R / Wlodawer, Alexander

Protein science : a publication of the Protein Society

2007 Volume 16, Issue 7, Page(s) 1485–1489

Abstract: Crystal structures of complexes of an antiviral lectin griffithsin (GRFT) with glucose and N-acetylglucosamine were solved and refined at high resolution. In both complexes, all six monosaccharide-binding sites of GRFT were occupied and the mode of ... ...

Abstract	Crystal structures of complexes of an antiviral lectin griffithsin (GRFT) with glucose and N-acetylglucosamine were solved and refined at high resolution. In both complexes, all six monosaccharide-binding sites of GRFT were occupied and the mode of binding was similar to that of mannose. In our previous attempts to obtain a complex with N-acetylglucosamine by soaking, only a single site was occupied; thus, cocrystallization was clearly superior despite lower concentration of the ligand. Isothermal titration calorimetric experiments with N-acetylglucosamine, glucose, and mannose provided enthalpic evidence of distinct binding differences between the three monosaccharides. A comparison of the mode of binding of different monosaccharides is discussed in the context of the antiviral activity of GRFT, based on specific binding to high-mannose-containing complex carbohydrates found on viral envelopes.
MeSH term(s)	Acetylglucosamine/chemistry ; Acetylglucosamine/metabolism ; Antiviral Agents/chemistry ; Antiviral Agents/metabolism ; Crystallography, X-Ray/methods ; Glucose/chemistry ; Glucose/metabolism ; Lectins/chemistry ; Lectins/metabolism ; Mannose/chemistry ; Mannose/metabolism ; Models, Molecular ; Protein Structure, Secondary
Chemical Substances	Antiviral Agents ; Lectins ; Glucose (IY9XDZ35W2) ; Mannose (PHA4727WTP) ; Acetylglucosamine (V956696549)
Keywords	covid19
Language	English
Publishing date	2007-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1110/ps.072889407
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Article ; Online: Structural investigation of biologically active phenolic compounds isolated from European tree species.

Redzynia, Izabela / Ziółkowska, Natasza E / Majzner, Wiesław R / Willför, Stefan / Sjöholm, Rainer / Eklund, Patrik / Bujacz, Grzegorz D

Molecules (Basel, Switzerland)

2009 Volume 14, Issue 10, Page(s) 4147–4158

Abstract: X-ray structures of two compounds isolated from wood knots of coniferous trees, namely dihydrokaempferol (3,5,8,13-tetrahydroxyflavanon) and lariciresinol (3,14-dimetoxy-7,10-epoxylignan-4,15,19-triol), are presented here. Diffraction data for the ... ...

Abstract	X-ray structures of two compounds isolated from wood knots of coniferous trees, namely dihydrokaempferol (3,5,8,13-tetrahydroxyflavanon) and lariciresinol (3,14-dimetoxy-7,10-epoxylignan-4,15,19-triol), are presented here. Diffraction data for the Dihydrokaempferol crystals were collected on a CAD4 diffractometer and on a synchrotron for the lariciresinol crystal. The investigated compounds inhibit lipid peroxidation and lariciresinol is additionally a good scavenger of superoxide radicals. The structural data presented in this work provide a useful basis for designing more active compounds with potential use as antioxidants.
MeSH term(s)	Abies/chemistry ; Europe ; Flavonoids/chemistry ; Flavonoids/isolation & purification ; Furans/chemistry ; Furans/isolation & purification ; Lignans/chemistry ; Lignans/isolation & purification ; Molecular Structure ; Phenols/chemistry ; Phenols/isolation & purification ; Polyphenols ; Populus/chemistry ; X-Ray Diffraction
Chemical Substances	Flavonoids ; Furans ; Lignans ; Phenols ; Polyphenols ; lariciresinol (73XCE5OZB0) ; aromadedrin (7YA4640575)
Language	English
Publishing date	2009-10-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules14104147
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