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Drug Discovery Today Aug 2022Phage display technology can be used for the discovery of antibodies for research, diagnostic, and therapeutic purposes. In this review, we present and discuss key... (Review)
Review
Phage display technology can be used for the discovery of antibodies for research, diagnostic, and therapeutic purposes. In this review, we present and discuss key parameters that can be optimized when performing phage display selection campaigns, including the use of different antibody formats and advanced strategies for antigen presentation, such as immobilization, liposomes, nanodiscs, virus-like particles, and whole cells. Furthermore, we provide insights into selection strategies that can be used for the discovery of antibodies with complex binding requirements, such as targeting a specific epitope, cross-reactivity, or pH-dependent binding. Lastly, we provide a description of specialized phage display libraries for the discovery of bispecific antibodies and pH-sensitive antibodies. Together, these methods can be used to improve antibody discovery campaigns against all types of antigens.
Topics: Antibodies; Bacteriophages; Epitopes; Peptide Library; Technology
PubMed: 35550436
DOI: 10.1016/j.drudis.2022.05.002 -
ELife Jul 2016In vitro selection of antibodies allows to obtain highly functional binders, rapidly and at lower cost. Here, we describe the first fully synthetic phage display library...
In vitro selection of antibodies allows to obtain highly functional binders, rapidly and at lower cost. Here, we describe the first fully synthetic phage display library of humanized llama single domain antibody (NaLi-H1: Nanobody Library Humanized 1). Based on a humanized synthetic single domain antibody (hs2dAb) scaffold optimized for intracellular stability, the highly diverse library provides high affinity binders without animal immunization. NaLi-H1 was screened following several selection schemes against various targets (Fluorescent proteins, actin, tubulin, p53, HP1). Conformation antibodies against active RHO GTPase were also obtained. Selected hs2dAb were used in various immunoassays and were often found to be functional intrabodies, enabling tracking or inhibition of endogenous targets. Functionalization of intrabodies allowed specific protein knockdown in living cells. Finally, direct selection against the surface of tumor cells produced hs2dAb directed against tumor-specific antigens further highlighting the potential use of this library for therapeutic applications.
Topics: Animals; Antibodies, Monoclonal, Humanized; Camelids, New World; Humans; Molecular Biology; Peptide Library; Single-Domain Antibodies
PubMed: 27434673
DOI: 10.7554/eLife.16228 -
Advanced Drug Delivery Reviews Feb 2017Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no... (Review)
Review
Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors.
Topics: Animals; Combinatorial Chemistry Techniques; Humans; Ligands; Neoplasms; Peptide Library; Peptides; Protein Binding
PubMed: 27210583
DOI: 10.1016/j.addr.2016.05.009 -
International Journal of Molecular... Dec 2019Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves... (Review)
Review
Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.
Topics: Animals; Drug Design; Drug Discovery; Humans; Peptide Library; Peptides; Recombinant Proteins
PubMed: 31892275
DOI: 10.3390/ijms21010215 -
Molecules (Basel, Switzerland) Jun 2021Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common... (Review)
Review
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
Topics: Cyclization; Humans; Peptide Library; Peptide Synthases; Peptides, Cyclic; Two-Hybrid System Techniques
PubMed: 34206124
DOI: 10.3390/molecules26113338 -
Nature Biotechnology Dec 2021MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA...
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.
Topics: Peptide Library; Proteome; Proteomics; Software
PubMed: 34239088
DOI: 10.1038/s41587-021-00968-7 -
BMC Bioinformatics May 2022Computational methods based on initial screening and prediction of peptides for desired functions have proven to be effective alternatives to lengthy and expensive...
BACKGROUND
Computational methods based on initial screening and prediction of peptides for desired functions have proven to be effective alternatives to lengthy and expensive biochemical experimental methods traditionally utilized in peptide research, thus saving time and effort. However, for many researchers, the lack of expertise in utilizing programming libraries, access to computational resources, and flexible pipelines are big hurdles to adopting these advanced methods.
RESULTS
To address the above mentioned barriers, we have implemented the peptide design and analysis under Galaxy (PDAUG) package, a Galaxy-based Python powered collection of tools, workflows, and datasets for rapid in-silico peptide library analysis. In contrast to existing methods like standard programming libraries or rigid single-function web-based tools, PDAUG offers an integrated GUI-based toolset, providing flexibility to build and distribute reproducible pipelines and workflows without programming expertise. Finally, we demonstrate the usability of PDAUG in predicting anticancer properties of peptides using four different feature sets and assess the suitability of various ML algorithms.
CONCLUSION
PDAUG offers tools for peptide library generation, data visualization, built-in and public database peptide sequence retrieval, peptide feature calculation, and machine learning (ML) modeling. Additionally, this toolset facilitates researchers to combine PDAUG with hundreds of compatible existing Galaxy tools for limitless analytic strategies.
Topics: Algorithms; Machine Learning; Peptide Library; Peptides; Software
PubMed: 35643441
DOI: 10.1186/s12859-022-04727-6 -
Methods in Molecular Biology (Clifton,... 2022There is increasing interest in expanding an antibody beyond high affinity and specificity. One such feature is custom regulation of the binding event, such as...
There is increasing interest in expanding an antibody beyond high affinity and specificity. One such feature is custom regulation of the binding event, such as pH-dependent control. Here, we provide a methodology for generating single-domain antibodies (sdAbs) that bind their antigen in a pH-dependent fashion. As each sdAb is unique, we start by providing the conceptual framework for designing a combinatorial histidine scanning library within a sdAb-antigen-binding interface. Methods are provided to create a phage display library, containing up to 1 × 10 unique members where each permutation of histidine substitution is sampled within the confines of the specified interface region(s). Finally, we describe phage display protocols for the selection and analysis of unique pH-dependent sdAb clones.
Topics: Antibodies; Antigens; Cell Surface Display Techniques; Hydrogen-Ion Concentration; Peptide Library; Single-Domain Antibodies
PubMed: 35157278
DOI: 10.1007/978-1-0716-2075-5_13 -
Therapeutic Innovation & Regulatory... Mar 2020Phage display (PD) is a technology based on the presentation of functional exogenous peptides on the capsid surface of bacteriophages. PD is performed by introducing a... (Review)
Review
Phage display (PD) is a technology based on the presentation of functional exogenous peptides on the capsid surface of bacteriophages. PD is performed by introducing a DNA sequence of interest at a specific position within a functional viral gene. In addition, peptide phage libraries are powerful tools for expressing a wide range of random peptides and for specific peptide screening. Specifically, PD applications include the analysis of binding and interactions between proteins, the identification of bioactive peptides that bind to receptors, the identification of disease-associated antigens, and the identification of cell-specific peptides. Since its emergence, PD technology has revolutionized several fields in the biological sciences, such as oncology, cell biology, and pharmacology, the innumerable applications for which will be described throughout this review.
Topics: Bacteriophages; Peptide Library; Peptides
PubMed: 32072579
DOI: 10.1007/s43441-019-00059-5 -
Viruses Jun 2021The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The... (Review)
Review
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.
Topics: Antiviral Agents; Cell Surface Display Techniques; Drug Discovery; Humans; Peptide Library; SARS-CoV-2; COVID-19 Drug Treatment
PubMed: 34200959
DOI: 10.3390/v13061120