Predicting Drug Resistance Using Deep Mutational Scanning.

Gur Pines,Carrie A Eckert,Reilly G Fankhauser

doi:10.3390/molecules25092265

Abstract

Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.

Highlights

In 1946, Alexander Fleming stated: “There is probably no chemotherapeutic drug to which in suitable circumstances the bacteria cannot react by in some way acquiring ‘fastness’ [resistance]” [1].Today, resistance to drugs is considered unavoidable as multi-drug resistant infections become a serious problem and possibly mark the post-antibiotic age [2,3]
This drug development cycle takes a tremendous amount of time and funds, as the resistance mechanism must be deciphered from initial anecdotal occurrences that appear spontaneously in the field (Figure 1)
Genome of anlibraries entire gene or specific targetsystems regionsasisa needed, strategy utilizing synthetic libraries may be HI-CRISPR, among others technology, we necessary. Examples of such approaches involving the genomic incorporation of synthetic libraries were able to search for point mutations in the ispC/dxr gene that confer resistance to the antimalarial utilizing CRISPR/Cas9 systems as a selection tool are CRISPR-Enabled Trackable Genome Engineering fosmidomycin (3-(N-formyl-N-hydroxyamino)propylphosphonic acid (FSM), uncovering mutations (CREATE) and HI-CRISPR, among others [35,36,37,38,39]

Summary

Introduction

In 1946, Alexander Fleming stated: “There is probably no chemotherapeutic drug to which in suitable circumstances the bacteria cannot react by in some way acquiring ‘fastness’ [resistance]” [1]. Resistance to drugs is considered unavoidable as multi-drug resistant infections become a serious problem and possibly mark the post-antibiotic age [2,3] This inevitable resistance leads to an arms race where new-generation drugs are being developed continuously, only to be rendered useless upon the development of resistance in the target system. One possible solution is to predict the resistance-conferring mutations by actively mutating the the target target gene and selecting for resistant mutants through directed evolution. We discuss various forgoperforming mutational the successfully used to predict mutationally acquired resistance mechanisms in cases relevant malaria. We go on to give examples of how these tools to have been We discuss such technologies may further advance understanding of resistance successfully used how to predict mutationally acquired resistancethe mechanisms in cases relevantand to identify drug–target pairs. We discuss how such technologies may further advance the understanding of resistance and identify drug–target pairs

Directed

Library Design

The Example of Deoxyxylulose Phosphate Reductoisomerase

The Use of Surrogate Organisms

Discussion and Future