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Article ; Online: Discovery of Antivirals Using Phage Display.

Sokullu, Esen / Gauthier, Marie-Soleil / Coulombe, Benoit

2021 Volume 13, Issue 6

Abstract: The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of ... ...

Abstract	The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today's world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human-animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Cell Surface Display Techniques/methods ; Drug Discovery/methods ; Humans ; Peptide Library ; SARS-CoV-2/drug effects
Chemical Substances	Antiviral Agents ; Peptide Library
Language	English
Publishing date	2021-06-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13061120
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Discovery of Antivirals Using Phage Display

Sokullu, Esen / Gauthier, Marie-Soleil / Coulombe, Benoit

Viruses. 2021 June 10, v. 13, no. 6

2021

Abstract	The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today’s world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human–animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.
Keywords	COVID-19 infection ; Russia ; antibodies ; antiviral agents ; bacteriophages ; disease outbreaks ; humans ; markets ; public health ; therapeutics ; India
Language	English
Dates of publication	2021-0610
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13061120
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Analysis of the SARS-CoV-2-host protein interaction network reveals new biology and drug candidates: focus on the spike surface glycoprotein and RNA polymerase.

Sokullu, Esen / Pinard, Maxime / Gauthier, Marie-Soleil / Coulombe, Benoit

Expert opinion on drug discovery

2021 Volume 16, Issue 8, Page(s) 881–895

Abstract: ... ...

Abstract	Introduction
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; COVID-19/virology ; Drug Development ; Drug Repositioning ; Humans ; Protein Interaction Maps ; RNA-Dependent RNA Polymerase/metabolism ; SARS-CoV-2/drug effects ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Antiviral Agents ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2021-04-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2259618-5
ISSN	1746-045X ; 1746-0441
ISSN (online)	1746-045X
ISSN	1746-0441
DOI	10.1080/17460441.2021.1909566
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Article: Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics.

Sokullu, Esen / Soleymani Abyaneh, Hoda / Gauthier, Marc A

Pharmaceutics

2019 Volume 11, Issue 5

Abstract: Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides ... ...

Abstract	Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.
Language	English
Publishing date	2019-05-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics11050211
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Article ; Online: The phage display of Bacillus subtilis Lipase A significantly enhances catalytic activity due to altered nanoscale distribution in colloidal solution.

Nahar, Sharifun / Sokullu, Esen / Gauthier, Marc A

Biotechnology and bioengineering

2019 Volume 117, Issue 3, Page(s) 868–872

Abstract: Screening libraries of mutant proteins by phage display is now relatively common. However, one unknown factor is how the bacteriophage scaffold itself influences the properties of the displayed protein. This communication evaluates the effect of solution ...

Abstract	Screening libraries of mutant proteins by phage display is now relatively common. However, one unknown factor is how the bacteriophage scaffold itself influences the properties of the displayed protein. This communication evaluates the effect of solution parameters on the catalytic activity of phage displayed Bacillus subtilis Lipase A (BSLA), compared to the free enzyme in solution. While the pH- and temperature-activity profiles of BSLA were not intrinsically affected by phage display, the nanoscale distribution of BSLA within the micellar assay buffer was. This lead to a pronounced increase of activity of phage-BSLA relative to the free enzyme, owing to the accumulation of phage-BSLA at the substrate-rich micelles. Considering this result obtained for BSLA, caution is warranted and similar effects should be considered when selecting other enzymes/proteins by phage display, as the activity of the displayed protein may differ from that of the free protein.
MeSH term(s)	Bacillus subtilis/enzymology ; Bacillus subtilis/genetics ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacteriophages/genetics ; Bacteriophages/metabolism ; Cell Surface Display Techniques/methods ; Colloids/chemistry ; Enzyme Stability ; Hydrogen-Ion Concentration ; Lipase/chemistry ; Lipase/genetics ; Lipase/metabolism ; Micelles ; Nanoparticles ; Sodium Chloride
Chemical Substances	Bacterial Proteins ; Colloids ; Micelles ; Sodium Chloride (451W47IQ8X) ; Lipase (EC 3.1.1.3)
Language	English
Publishing date	2019-12-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	280318-5
ISSN	1097-0290 ; 0006-3592
ISSN (online)	1097-0290
ISSN	0006-3592
DOI	10.1002/bit.27229
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Article ; Online: Comparative study on the inactivation of MS2 and M13 bacteriophages using energetic femtosecond lasers.

Berchtikou, Aziz / Sokullu, Esen / Nahar, Sharifun / Tijssen, Peter / Gauthier, Marc A / Ozaki, Tsuneyuki

Journal of biophotonics

2020 Volume 13, Issue 10, Page(s) e202000109

Abstract: Femtosecond (fs) laser irradiation techniques are emerging tools for inactivating viruses that do not involve ionizing radiation. In this work, the inactivation of two bacteriophages representing protective capsids with different geometric constraints, ... ...

Abstract	Femtosecond (fs) laser irradiation techniques are emerging tools for inactivating viruses that do not involve ionizing radiation. In this work, the inactivation of two bacteriophages representing protective capsids with different geometric constraints, that is, the near-spherical MS2 (with a diameter of 27 nm) and the filamentous M13 (with a length of 880 nm) is compared using energetic visible and near-infrared fs laser pulses with various energies, pulse durations, and exposure times. Intriguingly, the results show that inactivation using 400 nm lasers is substantially more efficient for MS2 compared to M13. In contrast, using 800 nm lasers, M13 was slightly more efficiently inactivated. For both viruses, the genome was exposed to a harmful environment upon fs-laser irradiation. However, in addition to the protection of the genome, the metastable capsids differ in many properties required for stepwise cell entry that may explain their dissimilar behavior after (partial) disassembly. For MS2, the dominant mechanism of fs-laser inactivation was the aggregation of the viral capsid proteins, whereas aggregation did not affect M13 inactivation, suggesting that the dominant mechanism of M13 inactivation was related to breaking of secondary protein links.
MeSH term(s)	Bacteriophage M13 ; Lasers ; Light ; Proteins ; Spectrum Analysis, Raman
Chemical Substances	Proteins
Language	English
Publishing date	2020-08-10
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202000109
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Article ; Online: Plasmonic Enhancement of Two-Photon Excitation Fluorescence by Colloidal Assemblies of Very Small AuNPs Templated on M13 Phage

Sokullu, Esen / Pinsard, Maxime / Zhang, Jiawei / Plathier, Julien / Kolhatkar, Gitanjali / Blum, Amy Szuchmacher / Légaré, François / Ruediger, Andreas / Ozaki, Tsuneyuki / Gauthier, Marc A.

Biomacromolecules. 2020 June 18, v. 21, no. 7 p.2705-2713

2020

Abstract: In this study, an engineered M13 bacteriophage was examined as a biological template to create a well-defined spacing between very small gold nanoparticles (AuNPs 3–13 nm). The effect of the AuNP particle size on the enhancement of the nonlinear process ... ...

Abstract	In this study, an engineered M13 bacteriophage was examined as a biological template to create a well-defined spacing between very small gold nanoparticles (AuNPs 3–13 nm). The effect of the AuNP particle size on the enhancement of the nonlinear process of two-photon excitation fluorescence (2PEF) was investigated. Compared to conventional (one-photon) microscopy techniques, such nonlinear processes are less susceptible to scattering given that the density of background-scattered photons is too low to generate a detectable signal. Besides this, the use of very small AuNPs in 2PEF microscopy becomes more advantageous because individual “isolated” AuNPs of this size do not sufficiently enhance 2PEF to produce a detectable signal, resulting in even less background signal. To investigate the 2PEF of the AuNP–M13 assemblies, a variety of sample preparation approaches are tested, and surface-enhanced Raman spectroscopy (SERS) is employed to study the strength of plasmon coupling within the gaps of AuNPs assembled on the M13 template. Results indicate that assemblies prepared with 9–13 nm AuNP were able to clearly label Escherichia coli cells and produce a 2PEF signal that was orders of magnitude higher than the isolated AuNP (below the threshold of detection). This study thus provides a better understanding of the opportunities and limitations relevant to the use of such small AuNPs within colloidal plasmonic assemblies, for applications in biodetection or as imaging contrast agents.
Keywords	Escherichia coli ; Raman spectroscopy ; bacteriophages ; fluorescence ; microscopy ; nanogold ; particle size
Language	English
Dates of publication	2020-0618
Size	p. 2705-2713.
Publishing place	American Chemical Society
Document type	Article ; Online
Note	NAL-AP-2-clean
ISSN	1526-4602
DOI	10.1021/acs.biomac.0c00401
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Plasmonic Enhancement of Two-Photon Excitation Fluorescence by Colloidal Assemblies of Very Small AuNPs Templated on M13 Phage.

Sokullu, Esen / Pinsard, Maxime / Zhang, Jiawei / Plathier, Julien / Kolhatkar, Gitanjali / Blum, Amy Szuchmacher / Légaré, François / Ruediger, Andreas / Ozaki, Tsuneyuki / Gauthier, Marc A

Biomacromolecules

2020 Volume 21, Issue 7, Page(s) 2705–2713

Abstract: In this study, an engineered M13 bacteriophage was examined as a biological template to create a well-defined spacing between very small gold nanoparticles (AuNPs 3-13 nm). The effect of the AuNP particle size on the enhancement of the nonlinear process ... ...

Abstract	In this study, an engineered M13 bacteriophage was examined as a biological template to create a well-defined spacing between very small gold nanoparticles (AuNPs 3-13 nm). The effect of the AuNP particle size on the enhancement of the nonlinear process of two-photon excitation fluorescence (2PEF) was investigated. Compared to conventional (one-photon) microscopy techniques, such nonlinear processes are less susceptible to scattering given that the density of background-scattered photons is too low to generate a detectable signal. Besides this, the use of very small AuNPs in 2PEF microscopy becomes more advantageous because individual "isolated" AuNPs of this size do not sufficiently enhance 2PEF to produce a detectable signal, resulting in even less background signal. To investigate the 2PEF of the AuNP-M13 assemblies, a variety of sample preparation approaches are tested, and surface-enhanced Raman spectroscopy (SERS) is employed to study the strength of plasmon coupling within the gaps of AuNPs assembled on the M13 template. Results indicate that assemblies prepared with 9-13 nm AuNP were able to clearly label
MeSH term(s)	Bacteriophage M13 ; Gold ; Metal Nanoparticles ; Photons ; Spectrum Analysis, Raman
Chemical Substances	Gold (7440-57-5)
Language	English
Publishing date	2020-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/acs.biomac.0c00401
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Article ; Online: A simple cassette as point-of-care diagnostic device for naked-eye colorimetric bacteria detection.

Safavieh, Mohammadali / Ahmed, Minhaz Uddin / Sokullu, Esen / Ng, Andy / Braescu, Liliana / Zourob, Mohammed

The Analyst

2014 Volume 139, Issue 2, Page(s) 482–487

Abstract: Effective pathogen detection is necessary for treatment of infectious diseases. Point of care (POC) devices have tremendously improved the global human heath. However, design criteria for sample processing POC devices for pathogen detection in limited ... ...

Abstract	Effective pathogen detection is necessary for treatment of infectious diseases. Point of care (POC) devices have tremendously improved the global human heath. However, design criteria for sample processing POC devices for pathogen detection in limited infrastructure are challenging and can make a significant contribution to global health by providing rapid and sensitive detection of bacteria in food, water, and patient samples. In this paper, we demonstrate a novel portable POC diagnostic device that is simple to assemble for genetic detection of bacterial pathogens by isothermal DNA amplification. The device is fabricated with very low production cost, using simple methods and easy-to-access materials on a flexible ribbon polyethylene substrate. We showed that the device is capable of detection of 30 CFU mL(-1) of E. coli and 200 CFU mL(-1) of S. aureus in less than 1 hour. Through numerical simulations, we estimated that the device can be extended to high-throughput detection simultaneously performing a minimum of 36 analyses. This robust and sensitive detection device can be assembled and operated by non-specialist personnel, particularly for multiple bacterial pathogen detections in low-resource settings.
MeSH term(s)	Colorimetry/instrumentation ; Coloring Agents/chemistry ; Escherichia coli/genetics ; Escherichia coli/isolation & purification ; Fluoresceins/chemistry ; Hot Temperature ; Naphthalenesulfonates/chemistry ; Nucleic Acid Amplification Techniques ; Point-of-Care Systems ; Staphylococcus aureus/genetics ; Staphylococcus aureus/isolation & purification
Chemical Substances	Coloring Agents ; Fluoresceins ; Naphthalenesulfonates ; trisodium 3-hydroxy-4-((2Z)-2-(2-oxo-4-sulfonatonaphthalen-1-ylidene)hydrazinyl)naphthalene-2,7-disulfonate (63451-35-4) ; fluorexon (V0YM2B16TS)
Language	English
Publishing date	2014-01-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/c3an01859h
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Article ; Online: Bacteria screening, viability, and confirmation assays using bacteriophage-impedimetric/loop-mediated isothermal amplification dual-response biosensors.

Tlili, Chaker / Sokullu, Esen / Safavieh, Mohammadali / Tolba, Mona / Ahmed, Minhaz Uddin / Zourob, Mohammed

Analytical chemistry

2013 Volume 85, Issue 10, Page(s) 4893–4901

Abstract: Here, we integrate two complementary detection strategies for the identification and quantification of Escherichia coli based on bacteriophage T4 as a natural bioreceptor for living bacteria cells. The first approach involves screening and viability ... ...

Abstract	Here, we integrate two complementary detection strategies for the identification and quantification of Escherichia coli based on bacteriophage T4 as a natural bioreceptor for living bacteria cells. The first approach involves screening and viability assays, employing bacteriophage as the recognition element in label-free electrochemical impedance spectroscopy. The complementary approach is a confirmation by loop-mediated isothermal amplification (LAMP) to amplify specifically the E. coli Tuf gene after lysis of the bound E. coli cells, followed by detection using linear sweep voltammetry. Bacteriphage T4 was cross-linked, in the presence of 1,4-phenylene diisothiocyanate, on a cysteamine-modified gold electrode. The impedimetric biosensor exhibits specific and reproducible detection with sensitivity over the concentration range of 10(3)-10(9) cfu/mL, while the linear response of the LAMP approach was determined to be 10(2)-10(7) cfu/mL. The limit of detection (LOD) of 8 × 10(2) cfu/mL in less than 15 min and 10(2) cfu/mL within a response time of 40 min were achieved for the impedimetric and LAMP method, respectively. This work provides evidence that integration of the T4-bacteriophage-modified biosensor and LAMP can achieve screening, viability, and confirmation in less than 1 h.
MeSH term(s)	Bacteriophage T4 ; Biosensing Techniques/economics ; Biosensing Techniques/methods ; Dielectric Spectroscopy/economics ; Dielectric Spectroscopy/methods ; Electrochemistry ; Escherichia coli/isolation & purification ; Escherichia coli/physiology ; Escherichia coli/virology ; Microbial Viability ; Reproducibility of Results ; Time Factors
Language	English
Publishing date	2013-05-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac302699x
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