scholarly journals A high-throughput, automated, cell-free expression and screening platform for antibody discovery

2021 ◽  
Author(s):  
Andrew C Hunt ◽  
Bastian Vogeli ◽  
Weston K. Kightlinger ◽  
Danielle J. Yoesep ◽  
Antje Kruger ◽  
...  
Keyword(s):  
High Throughput ◽  
Neutralizing Antibodies ◽  
Rapid Identification ◽  
Antibody Fragments ◽  
Free Expression ◽  
Free Dna ◽  
Antibody Discovery ◽  
Screening Platform ◽  
The Individual ◽  
Dna Template

Antibody discovery is bottlenecked by the individual expression and evaluation of antigen- specific hits. Here, we address this gap by developing an automated workflow combining cell-free DNA template generation, protein synthesis, and high-throughput binding measurements of antibody fragments in a process that takes hours rather than weeks. We apply this workflow to 119 published SARS-CoV-2 neutralizing antibodies and demonstrate rapid identification of the most potent antibody candidates.

scholarly journals A Direct-to-Biology High-Throughput Chemistry Approach to Reactive Fragment Screening

2021 ◽  
Author(s):  
Ross P. Thomas ◽  
Rachel E. Heap ◽  
Francesca Zappacosta ◽  
Emma K. Grant ◽  
Peter Pogany ◽  
...  
Keyword(s):  
High Throughput ◽  
Medicinal Chemistry ◽  
Binding Pocket ◽  
Rapid Identification ◽  
Rapid Synthesis ◽  
Iterative Design ◽  
Fragment Screening ◽  
Hit Rate ◽  
Chemical Tools ◽  
Screening Platform

<p>Methods for rapid identification of chemical tools are essential for the validation of emerging targets and to provide medicinal chemistry starting points for the development of <a>new medicines. Here, we report a screening platform that combines ‘direct-to-biology’ high-throughput chemistry (D2B-HTC) with photoreactive covalent fragments. The platform enabled the rapid synthesis of >1000 PhotoAffinity Bits (HTC-PhABits) in 384-well plates. Screening the HTC-PhABit library with </a>carbonic anhydrase I (CAI) afforded 7 hits (0.7% hit rate), which were found to covalently crosslink in the Zn<sup>2+</sup> binding pocket. A powerful advantage of the D2B-HTC screening platform is the ability to rapidly perform iterative design-make-test cycles, accelerating the development and optimisation of chemical tools and medicinal chemistry starting points with little investment of resource.</p>

scholarly journals Efficient discovery of potently neutralizing SARS-CoV-2 antibodies using LIBRA-seq with ligand blocking

2021 ◽  
Author(s):  
Andrea R Shiakolas ◽  
Nicole Johnson ◽  
Kevin J Kramer ◽  
Naveenchandra Suryadevara ◽  
Daniel Wrapp ◽  
...  
Keyword(s):  
High Throughput ◽  
Neutralizing Antibodies ◽  
High Throughput Sequencing ◽  
Therapeutic Antibody ◽  
Sequencing Platform ◽  
Large Numbers ◽  
Ligand Interactions ◽  
Antibody Discovery ◽  
Small Set

SARS-CoV-2 therapeutic antibody discovery efforts have met with notable success but have been associated with a generally inefficient process, requiring the production and characterization of exceptionally large numbers of candidates for the identification of a small set of leads. Here, we show that incorporating antibody-ligand blocking as part of LIBRA-seq, the high-throughput sequencing platform for antibody discovery, results in efficient identification of ultra-potent neutralizing antibodies against SARS-CoV-2. LIBRA-seq with ligand blocking is a general platform for functional antibody discovery targeting the disruption of antigen-ligand interactions.

scholarly journals A Direct-to-Biology High-Throughput Chemistry Approach to Reactive Fragment Screening

2021 ◽  
Author(s):  
Ross P. Thomas ◽  
Rachel E. Heap ◽  
Francesca Zappacosta ◽  
Emma K. Grant ◽  
Peter Pogany ◽  
...  
Keyword(s):  
High Throughput ◽  
Medicinal Chemistry ◽  
Binding Pocket ◽  
Rapid Identification ◽  
Rapid Synthesis ◽  
Iterative Design ◽  
Fragment Screening ◽  
Hit Rate ◽  
Chemical Tools ◽  
Screening Platform

<p>Methods for rapid identification of chemical tools are essential for the validation of emerging targets and to provide medicinal chemistry starting points for the development of <a>new medicines. Here, we report a screening platform that combines ‘direct-to-biology’ high-throughput chemistry (D2B-HTC) with photoreactive covalent fragments. The platform enabled the rapid synthesis of >1000 PhotoAffinity Bits (HTC-PhABits) in 384-well plates. Screening the HTC-PhABit library with </a>carbonic anhydrase I (CAI) afforded 7 hits (0.7% hit rate), which were found to covalently crosslink in the Zn<sup>2+</sup> binding pocket. A powerful advantage of the D2B-HTC screening platform is the ability to rapidly perform iterative design-make-test cycles, accelerating the development and optimisation of chemical tools and medicinal chemistry starting points with little investment of resource.</p>

scholarly journals Probing Specificities of Alcohol Acyltransferases for Designer Ester Biosynthesis with a High-Throughput Microbial Screening Platform

2021 ◽  
Author(s):  
Jong-Won Lee ◽  
Hyeongmin Seo ◽  
Caleb Young ◽  
Cong T Trinh
Keyword(s):  
High Throughput ◽  
Protein Design ◽  
Colorimetric Assay ◽  
Rapid Identification ◽  
Large Space ◽  
Isobutyl Acetate ◽  
Ester Biosynthesis ◽  
Microbial Screening ◽  
Screening Platform ◽  
Microbial Biosynthesis

Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CATSa) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only confirm CATSa F97W with enhanced isobutyl acetate synthesis but also identify three ATF1Sc (P348M, P348A, and P348S) variants, derived from Saccharomyces cerevisiae' s AAT and engineered by model-guided protein design, for enhanced butyl acetate production. We anticipate the high-throughput microbial screening platform is a useful tool to identify novel AATs that have important roles in nature and industrial biocatalysis for designer bioester production.

scholarly journals Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Strong Support ◽  
Gc Content ◽  
Rapid Identification ◽  
Hairpin Rna ◽  
Rna Sequences ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

High-Throughput Screening Platform for Nanoparticle-Mediated Alterations of DNA Repair Capacity

ACS Nano ◽  
2021 ◽  
Author(s):  
Sneh M. Toprani ◽  
Dimitrios Bitounis ◽  
Qiansheng Huang ◽  
Nathalia Oliveira ◽  
Kee Woei Ng ◽  
...  
Keyword(s):  
Dna Repair ◽  
High Throughput ◽  
High Throughput Screening ◽  
Repair Capacity ◽  
Dna Repair Capacity ◽  
Screening Platform

Time-Resolved Luminescent High-Throughput Screening Platform for Lysosomotropic Compounds in Living Cells

ACS Sensors ◽  
2020 ◽  
Author(s):  
Ke-Jia Wu ◽  
Chun Wu ◽  
Feng Chen ◽  
Sha-Sha Cheng ◽  
Dik-Lung Ma ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Living Cells ◽  
Time Resolved ◽  
Screening Platform

scholarly journals A High-Throughput Approach To Identify Compounds That Impair Envelope Integrity in Escherichia coli

2016 ◽  
Vol 60 (10) ◽  
pp. 5995-6002 ◽  
Author(s):  
Kristin R. Baker ◽  
Bimal Jana ◽  
Henrik Franzyk ◽  
Luca Guardabassi
Keyword(s):  
Escherichia Coli ◽  
High Throughput ◽  
High Throughput Screening ◽  
Gram Negative Bacteria ◽  
Chromogenic Substrate ◽  
Intrinsic Resistance ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Screening Platform

ABSTRACTThe envelope of Gram-negative bacteria constitutes an impenetrable barrier to numerous classes of antimicrobials. This intrinsic resistance, coupled with acquired multidrug resistance, has drastically limited the treatment options against Gram-negative pathogens. The aim of the present study was to develop and validate an assay for identifying compounds that increase envelope permeability, thereby conferring antimicrobial susceptibility by weakening of the cell envelope barrier in Gram-negative bacteria. A high-throughput whole-cell screening platform was developed to measureEscherichia colienvelope permeability to a β-galactosidase chromogenic substrate. The signal produced by cytoplasmic β-galactosidase-dependent cleavage of the chromogenic substrate was used to determine the degree of envelope permeabilization. The assay was optimized by using known envelope-permeabilizing compounds andE. coligene deletion mutants with impaired envelope integrity. As a proof of concept, a compound library comprising 36 peptides and 45 peptidomimetics was screened, leading to identification of two peptides that substantially increased envelope permeability. Compound 79 reduced significantly (from 8- to 125-fold) the MICs of erythromycin, fusidic acid, novobiocin and rifampin and displayed synergy (fractional inhibitory concentration index, <0.2) with these antibiotics by checkerboard assays in two genetically distinctE. colistrains, including the high-risk multidrug-resistant, CTX-M-15-producing sequence type 131 clone. Notably, in the presence of 0.25 μM of this peptide, both strains were susceptible to rifampin according to the resistance breakpoints (R> 0.5 μg/ml) for Gram-positive bacterial pathogens. The high-throughput screening platform developed in this study can be applied to accelerate the discovery of antimicrobial helper drug candidates and targets that enhance the delivery of existing antibiotics by impairing envelope integrity in Gram-negative bacteria.

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