scholarly journals A curcumin direct protein (DiPro) biosensor for cell-free prototyping

2021 ◽  
Author(s):  
Agata Lesniewska ◽  
Guy Griffin ◽  
Paul K Freemont ◽  
Karen M Polizzi ◽  
Simon J Moore
Keyword(s):  
Synthetic Biology ◽  
Small Molecules ◽  
Detection System ◽  
Reaction Parameters ◽  
Enhanced Fluorescence ◽  
Liquid Handling ◽  
A Cell ◽  
Double Bond Reductase ◽  
Fine Tune ◽  
Synthetic Biology Approach

In synthetic biology, biosensors are routinely coupled to a gene expression cascade for detecting small molecules and physical signals. We posit that an alternative direct protein (DiPro) biosensor mechanism, could provide a new opportunity for rapid detection of specific chemicals. Herein, we reveal a fluorescent curcumin DiPro biosensor, based on the Escherichia coli double bond reductase (EcCurA) as a detection system. We characterise the curcumin DiPro biosensor and propose enhanced fluorescence is generated through π-π stacking between protein and ligand. Using a cell-free synthetic biology approach, we use the DiPro biosensor to fine-tune 10 reaction parameters (cofactor, substrate, and enzyme levels), assisted through acoustic liquid handling robotics. Overall, we increase curcumin DiPro biosensor fluorescence by 80-fold. We propose a generic DiPro biosensor fluorescence mechanism that can be further exploited for a wider range of chemicals that share intrinsic fluorescence and have a suitable binding protein.

scholarly journals A Synthetic Biology Approach Using Engineered Bacteria to Detect Perfluoroalkyl Substance (PFAS) Contamination in Water

2021 ◽  
Vol 186 (Supplement_1) ◽  
pp. 801-807
Author(s):  
Nathaniel A Young ◽  
Ryan L Lambert ◽  
Angela M Buch ◽  
Christen L Dahl ◽  
Jackson D Harris ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Dna Sequences ◽  
Detection System ◽  
The United States ◽  
Detection Methods ◽  
Health Concern ◽  
Contaminated Water ◽  
Engineered Bacteria ◽  
Synthetic Biology Approach ◽  
Rhodococcus Jostii

ABSTRACT Introduction Per- and polyfluoroalkyl substances (PFAS) are a class of synthetic compounds used industrially for a wide variety of applications. These PFAS compounds are very stable and persist in the environment. The PFAS contamination is a growing health issue as these compounds have been reported to impact human health and have been detected in both domestic and global water sources. Contaminated water found on military bases poses a potentially serious health concern for active duty military, their families, and the surrounding communities. Previous detection methods for PFAS in contaminated water samples require expensive and time-consuming testing protocols that limit the ability to detect this important global pollutant. The main objective of this work was to develop a novel detection system that utilizes a biological reporter and engineered bacteria as a way to rapidly and efficiently detect PFAS contamination. Materials and Methods The United States Air Force Academy International Genetically Engineered Machine team is genetically engineering Rhodococcus jostii strain RHA1 to contain novel DNA sequences composed of a propane 2-monooxygenase alpha (prmA) promoter and monomeric red fluorescent protein (mRFP). The prmA promoter is activated in the presence of PFAS and transcribes the mRFP reporter. Results The recombinant R. jostii containing the prmA promoter and mRFP reporter respond to exposure of PFAS by activating gene expression of the mRFP. At 100 µM of perfluorooctanoic acid, the mRFP expression was increased 3-fold (qRT-PCR). Rhodococcus jostii without exposure to PFAS compounds had no mRFP expression. Conclusions This novel detection system represents a synthetic biology approach to more efficiently detect PFAS in contaminated samples. With further refinement and modifications, a similar system could be readily deployed in the field around the world to detect this critical pollutant.

scholarly journals Fine-tuning of a generative neural network for designing multi-target compounds

2021 ◽  
Author(s):  
Thomas Blaschke ◽  
Jürgen Bajorath
Keyword(s):  
Neural Network ◽  
Small Molecules ◽  
De Novo ◽  
Pharmaceutical Research ◽  
Generative Models ◽  
Fine Tuning ◽  
Data Sets ◽  
Single Target ◽  
Fine Tune ◽  
Target Activity

AbstractExploring the origin of multi-target activity of small molecules and designing new multi-target compounds are highly topical issues in pharmaceutical research. We have investigated the ability of a generative neural network to create multi-target compounds. Data sets of experimentally confirmed multi-target, single-target, and consistently inactive compounds were extracted from public screening data considering positive and negative assay results. These data sets were used to fine-tune the REINVENT generative model via transfer learning to systematically recognize multi-target compounds, distinguish them from single-target or inactive compounds, and construct new multi-target compounds. During fine-tuning, the model showed a clear tendency to increasingly generate multi-target compounds and structural analogs. Our findings indicate that generative models can be adopted for de novo multi-target compound design.

How To Make a Glycopeptide: A Synthetic Biology Approach To Expand Antibiotic Chemical Diversity

2016 ◽  
Vol 2 (9) ◽  
pp. 642-650 ◽  
Author(s):  
Grace Yim ◽  
Wenliang Wang ◽  
Maulik N. Thaker ◽  
Stephanie Tan ◽  
Gerard D. Wright
Keyword(s):  
Synthetic Biology ◽  
Chemical Diversity ◽  
Synthetic Biology Approach

scholarly journals Understanding Cell Interactions Using Modular Nanoparticle Libraries

2019 ◽  
Vol 72 (8) ◽  
pp. 595 ◽  
Author(s):  
Georgina K. Such ◽  
Angus P. R. Johnston
Keyword(s):  
Immune Responses ◽  
Small Molecules ◽  
Active Form ◽  
Reticuloendothelial System ◽  
Endosomal Escape ◽  
Biological Interactions ◽  
Nanoparticle Delivery ◽  
A Cell ◽  
Nanoparticle Structure ◽  
The Right

Nanoparticle delivery systems have significant potential to facilitate the delivery of novel therapeutics, such as proteins, DNA or small molecules. However, there are multiple biological barriers that need to be overcome to deliver the cargo in an active form. These challenges include evading clearance by the reticuloendothelial system, minimising adverse immune responses, targeting specific cells and tissues, and trafficking into the right compartment of the cell. In this account, we will discuss how nanoparticle structure can be tuned to optimise biological interactions and thus improve the ability of nanoparticles to overcome these barriers. The focus of this article will be on controlling cell targeting and trafficking within a cell, e.g. endosomal escape.

scholarly journals A sustainable synthetic biology approach for the control of the invasive golden mussel (Limnoperna fortunei)

2018 ◽  
Author(s):  
Mauro F Rebelo ◽  
Luana F Afonso ◽  
Juliana A Americo ◽  
Lucas da Silva ◽  
José L B Neto ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Control Method ◽  
Economic Feasibility ◽  
South American ◽  
Gene Drive ◽  
Limnoperna Fortunei ◽  
Invasive Mussel ◽  
Golden Mussel ◽  
And Control ◽  
Synthetic Biology Approach

The recent development of the CRISPR-Cas9-based gene drive has created the conditions to seriously consider this technology to solve one of the major environmental challenges in biodiversity conservation i.e. the control of invasive species. There is no efficient control method for golden mussel infestation available so far. Here we discuss the technical and economic feasibility of using a synthetic biology based approach to fight and control the invasive mussel Limnoperna fortunei in South American rivers and reservoirs.

scholarly journals Cell-Permeable, Small-Molecule Activators of the Insulin-Degrading Enzyme

2012 ◽  
Vol 17 (10) ◽  
pp. 1348-1361 ◽  
Author(s):  
Sayali S. Kukday ◽  
Surya P. Manandhar ◽  
Marissa C. Ludley ◽  
Mary E. Burriss ◽  
Benjamin J. Alper ◽  
...  
Keyword(s):  
Small Molecules ◽  
Biologically Active ◽  
Small Peptides ◽  
Insulin Degrading Enzyme ◽  
Potential Therapeutic Target ◽  
Aβ Peptides ◽  
Degrading Enzyme ◽  
Enzyme Substrate ◽  
A Cell

The insulin-degrading enzyme (IDE) cleaves numerous small peptides, including biologically active hormones and disease-related peptides. The propensity of IDE to degrade neurotoxic Aβ peptides marks IDE as a potential therapeutic target for Alzheimer disease. Using a synthetic reporter based on the yeast a-factor mating pheromone precursor, which is cleaved by multiple IDE orthologs, we identified seven small molecules that stimulate rat IDE activity in vitro. Half-maximal activation of IDE by the compounds is observed in vitro in the range of 43 to 198 µM. All compounds decrease the Km of IDE. Four compounds activate IDE in the presence of the competing substrate insulin, which disproportionately inhibits IDE activity. Two compounds stimulate rat IDE activity in a cell-based assay, indicating that they are cell permeable. The compounds demonstrate specificity for rat IDE since they do not enhance the activities of IDE orthologs, including human IDE, and they appear specific for a-factor–based reporters since they do not enhance rat IDE-mediated cleavage of Aβ-based reporters. Our results suggest that IDE activators function in the context of specific enzyme-substrate pairs, indicating that the choice of substrate must be considered in addition to target validation in IDE activator screens.

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