Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics

Emerging antibiotic resistance by various novel proteins/enzymes

BACKGROUND

The emergence and dissemination of antibiotic resistance represents a significant and ever-increasing global threat to human, animal, and environmental health. The explosive proliferation of resistance has ultimately been seen in all clinically used antibiotics. Infections caused by antibiotic-resistant bacteria have been associated with an estimated 4,950,000 deaths annually, with extremely limited therapeutic options and only a few new antibiotics under development. To combat this silent pandemic, a better understanding of the molecular mechanisms of antibiotic resistance is immensely needed, which not only helps to improve the efficacy of current drugs in clinical use but also design new antimicrobial agents that are less susceptible to resistance.

RESULTS

The past few years have witnessed a number of new advances in revealing the molecular mechanisms of AMR. Following five sophisticated mechanisms (efflux pump, antibiotics inactivation by enzymes, alteration of membrane permeability, target modification, and target protection), the roles of various novel proteins/enzymes in the acquisition of antibiotic resistance are constantly being described. They are widely used by clinical bacterial strains, playing a key role in the emergence of resistance.

CONCLUSION

While most of these have so far received less attention, expanding our understanding of these emerging resistance mechanisms is of crucial importance to combat the antibiotic resistance crisis in the world. This review summarizes recent advances in our knowledge of emerging resistance mechanisms in bacteria, providing an update on the current antibiotic resistance threats and encouraging researchers to develop critical strategies for overcoming the resistance.

Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism

Microbiota-mediated drug metabolism can affect pharmacological efficacy. Here we conducted a systematic comparative metabolomics investigation of drug metabolism modes by evaluating the impacts of human gut commensal bacteria on 127 G-protein-coupled receptor (GPCR)-targeted drugs. For the most extensively metabolized drugs in our screen, we elucidated both conventional and unconventional drug transformations and the corresponding activities of generated metabolites. Comparisons of drug metabolism by a gut microbial community versus individual species revealed both taxon intrinsic and collaborative processes that influenced the activity of the metabolized drugs against target GPCRs. We also observed iloperidone inactivation by generating unconventional metabolites. The human gut commensal bacteria mixture incorporated sulfur in the form of a thiophene motif, whereas Morganella morganii used a cascade reaction to incorporate amino-acid-derived tricyclic systems into the drug metabolites. Our results reveal a broad impact of human gut commensal bacteria on GPCR-targeted drug structures and activities through diverse microbiota-mediated biotransformations.

Naturally Occurring and Widespread Resistance to Bioactive Natural Products

Naturally occurring resistances diminish the effectiveness of antibiotics, and present significant challenges to human health. Human activities are usually considered as the main drivers of the dissemination of antibiotic resistance, however, the origin of the clinical antibiotic resistance can be traced to the environmental microbes, and the clinically relevant resistance determinants have already pre-existed in nature before the antibiotics come into clinic. In this concept, we present the naturally occurring and widespread resistance determinants recently discovered during the biosynthesis study of bioactive compounds. These widely prevalent resistances in environmental microbes, including antibiotic producers and non-producers, advance the understanding of the origin of resistance, and provide prediction for the clinically relevant resistance to aid in the rational design of more effective drug analogues to combat resistance.

An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity

The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.

Newly Discovered Mechanisms of Antibiotic Self-Resistance with Multiple Enzymes Acting at Different Locations and Stages

Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions catalyzed by these proteins. However, as more examples of self-resistance have been reported, it has been revealed that the enzymatic reactions contribute to self-protection are not confined to the cellular location where the final toxic compounds are present. In this review, we summarize representative examples of self-resistance mechanisms for bioactive natural products functional at different cell locations to explore the models of resistance strategies involved. Moreover, we also highlight those resistance determinants that are widespread in nature and describe the applications of self-resistance genes in natural product mining to interrogate the landscape of self-resistance genes in drug resistance-related new drug discovery.

Deciphering a novel chloramphenicols resistance mechanism: Oxidative inactivation of the propanediol pharmacophore

Expanding knowledge about new types of antibiotic resistance genes is of great significance in dealing with the global antibiotic resistance crisis. Herein, a novel oxidoreductase capO was discovered to be responsible for oxidative inactivation of chloramphenicol and thiamphenicol. The antibiotic resistance mechanism was comprehensively deciphered using multi-omics and multiscale computational approaches. A 66,383 bp DNA fragment carrying capO was shared among four chloramphenicol-resistant strains, and the co-occurrence of capO with a mobile genetic element cluster revealed its potential mobility among different taxa. Metagenomic analysis of 772 datasets indicated that chloramphenicol was the crucial driving factor for the development and accumulation of capO in activated sludge bioreactors treating antibiotic production wastewater. Therefore, we should pay sufficient attention to its possible prevalence and transfer to pathogens, especially in some hotspot environments contaminated with high concentrations of chloramphenicols. This finding significantly expands our knowledge boundary about chloramphenicols resistance mechanisms.

Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis

Dihydrofolate reductase (DHFR), a housekeeping enzyme in primary metabolism, has been extensively studied as a model of acid-base catalysis and a clinic drug target. Herein, we investigated the enzymology of a DHFR-like protein SacH in safracin (SAC) biosynthesis, which reductively inactivates hemiaminal pharmacophore-containing biosynthetic intermediates and antibiotics for self-resistance. Furthermore, based on the crystal structure of SacH-NADPH-SAC-A ternary complexes and mutagenesis, we proposed a catalytic mechanism that is distinct from the previously characterized short-chain dehydrogenases/reductases-mediated inactivation of hemiaminal pharmacophore. These findings expand the functions of DHFR family proteins, reveal that the common reaction can be catalyzed by distinct family of enzymes, and imply the possibility for the discovery of novel antibiotics with hemiaminal pharmacophore.

Influence of cationic groups on the antibacterial behavior of cationic nano-sized hyperbranched polymers to enhance bacteria-infected wound healing

With the continuous emergence of drug-resistant pathogens, new strategies with high antibacterial efficacy are urgently needed. Herein, five cationic nano-sized hyperbranched polymers (CNHBPs) with cationic functional groups have been constructed, and their antibacterial mechanism has been studied in detail. CNHBPs bearing secondary ammonium salt groups and long alkyl chains (S₁₂-CNHBP) exhibited weak antibacterial and antibiofilm ability, while CNHBPs bearing quaternary ammonium salt groups and long alkyl chains (Q₁₂-CNHBP) showed the highest antimicrobial and strongest antibiofilm activities. ζ potential and isothermal titration microcalorimetry (ITC) results suggest that the negatively charged surfaces of bacterial cells provided Q₁₂-CNHBP with a higher intrinsic electrostatic driving force for bacterial killing than that with S₁₂-CNHBP. Fluorescent tracing and morphological observations indicate that the bacterial genome might be another antibacterial target for S₁₂-CNHBP in addition to the cell wall and membrane, which are mainly antibacterial targets for Q₁₂-CNHBP, making it less likely to induce bacterial resistance. Surprisingly, Q₁₂-CNHBP exhibited superior in vivo therapeutic efficacy in a mouse wound model of methicillin-resistant Staphylococcus aureus (MRSA) infection with low toxicity during treatment. These advantages and ease of preparation will undoubtedly distinguish Q₁₂-CNHBP as a new class of suitable candidates to combat multidrug-resistant pathogen infections. This study opens up a new avenue for exploiting antibacterial biomaterials to treat infections caused by drug-resistant bacteria.

Potent Antibiotic Lemonomycin: A Glimpse of Its Discovery, Origin, and Chemical Synthesis

Lemonomycin (1) was first isolated from the fermentation broth of Streptomyces candidus in 1964. The complete chemical structure was not elucidated until 2000 with extensive spectroscopic analysis. Lemonomycin is currently known as the only glycosylated tetrahydroisoquinoline antibiotic. Its potent antibacterial activity against Staphylococcus aureus and Bacillus subtilis and complex architecture make it an ideal target for total synthesis. In this short review, we summarize the research status of lemonomycin for biological activity, biosynthesis, and chemical synthesis. The unique deoxy aminosugar-lemonose was proposed to play a crucial role in biological activity, as shown in other antibiotics, such as arimetamycin A, nocathiacin I, glycothiohexide α, and thiazamycins. Given the self-resistance of the original bacterial host, the integration of biosynthesis and chemical synthesis to pursue efficient synthesis and further derivatization is in high demand for the development of novel antibiotics to combat antibiotic-resistant infections.