Drug repurposing for next-generation combination therapies against multidrug-resistant bacteria

Abstract

Antimicrobial resistance has been a global health challenge that threatens our ability to control and treat life-threatening bacterial infections. Despite ongoing efforts to identify new drugs or alternatives to antibiotics, no new classes of antibiotic or their alternatives have been clinically approved in the last three decades. A combination of antibiotics and non-antibiotic compounds that could inhibit bacterial resistance determinants or enhance antibiotic activity offers a sustainable and effective strategy to confront multidrug-resistant bacteria. In this review, we provide a brief overview of the co-evolution of antibiotic discovery and the development of bacterial resistance. We summarize drug-drug interactions and uncover the art of repurposing non-antibiotic drugs as potential antibiotic adjuvants, including discussing classification and mechanisms of action, as well as reporting novel screening platforms. A pathogen-by-pathogen approach is then proposed to highlight the critical value of drug repurposing and its therapeutic potential. Finally, general advantages, challenges and development trends of drug combination strategy are discussed.

Keywords: antibiotic adjuvants; antimicrobial resistance; combination therapies; drug repurposing; multidrug-resistant bacteria.

Figure 1

Molecular mechanisms of antimicrobial resistance in bacterial pathogens. Bacteria have evolved multifaceted strategies to counteract antibiotic killing, including (A) deactivation of antibiotics by hydrolysis or modification with resistance determinants, (B) modification of antibiotic targets by mutation or protection, and (C) prevention of intracellular accumulation of antibiotics by decreased uptake and increased activity of efflux pumps.

Figure 2

Distinguishing between three drug-drug interactions, including synergy, no interaction and antagonism. Drug-drug interactions can be evaluated by using a checkerboard assay with determination of the fractional inhibitory concentration index (FICI) or bacterial growth curves in the combination of sub-lethal (one-quarter minimal inhibitory concentration (MIC)) concentrations of drug A and B. Synergy is defined as an FICI of ≤0.5 and a significantly reduced bacterial growth curve in the presence of paired drugs. No interaction, including additive and indifference, is defined as an FICI of >0.5 and <4. Antagonism is defined as an FICI of ≥4 and an enhanced bacterial growth curve compared with monotreatment.

Figure 3

Classification, mechanisms and examples of synergistic combination in the fight against bacterial pathogens. The synergistic combinations can be divided into three types according to their modes of action. The first type (A) is the synergistic combination of two antibiotics (a and b), which target distinct essential molecular processes by way of a tandem or parallel manner. The second type (B) combination comprises an antibiotic (a) that targets an essential process and a non-antibiotic adjuvant (b) that suppresses resistance determinants or non-essential processes or enhances the host immune response. In particular, this type displays great potential in the development of novel antibiotic adjuvants. In contrast, the third combination (C) refers to two non-antibiotic agents that target non-essential but synthetically lethal gene functions.

Figure 4

Novel screening approaches for antibiotic adjuvant discovery. (A) Metabolomics-driven approach to predict novel combination antimicrobial therapies . Metabolic profiling of E. coli after 2 h of drugs treatment were analyzed by flow injection analysis in a time of flight mass spectrometer (FIA-TOFMS), while bacterial growth in the presence of drug was monitored using a plate reader over 6 h. (B) Exploring additional synergistic interactions on the basis of chemical-genetic interactions analysis , . (C) The antibiotic resistance platform (ARP) allows for the discovery of new antibiotic adjuvants . The platform consists of a cell-based library of E. coli expressing individual resistance genes. The expression of resistance genes is regulated by the utilization of two series of plasmids and two different promoters (strong P_bla promoter and the weaker P_lac promoter). Subsequently, these constructs were transformed into wild-type E. coli and/or the hyperpermeable efflux-deficient mutant E. coli BW25113 △bamB△tolC.

Figure 5

Potential colistin adjuvants against MCR-producing Enterobacterales. Four non-antimicrobial agents including food additive pterostilbene, antihistamine alternative osthole, antiprotozoal drug pentamidine and dietary supplement melatonin were found to potentiate colistin activity against MCR-producing Enterobacterales. The major mechanisms of action of these adjuvants in combination with colistin were presented next to the compounds in red font.

Figure 6

Anti-HIV agent azidothymidine potentiates tigecycline activity against Tet(X)-expressing E. coli. (A) Chemical structure of azidothymidine. (B) Checkerboard assay between tigecycline and azidothymidine against tet(X4)-positive E. coli B3-1. (C) Scheme of synergistic mechanisms of tigecycline in combination with azidothymidine. Adapted with permission from , Copyright 2020 Springer Nature.

Figure 7

Next-generation broad-spectrum combination therapies against MDR bacteria. (A) Antidiabetic drug metformin restores broad-spectrum antibiotic tetracycline activity against MDR bacteria both in vitro and in vivo by promoting intracellular accumulation of antibiotics, as well as boosting the immune response and alleviating the inflammatory response. Adapted with permission from , Copyright 2020 John Wiley & Sons, Ltd. (B) SLAP-S25 boosts the activity of multi-classes of antibiotic against MDR Gram-negative bacteria by binding to LPS in the outer membrane (OM) and phosphatidylglycerol (PG) in the cytoplasmic membrane. Adapted with permission from , Copyright 2020 Springer Nature.