Leveraging Marine Natural Products as a Platform to Tackle Bacterial Resistance and Persistence

Abstract

Antimicrobial resistance to existing antibiotics represents one of the greatest threats to human health and is growing at an alarming rate. To further complicate treatment of bacterial infections, many chronic infections are the result of bacterial biofilms that are tolerant to treatment with antibiotics because of the presence of metabolically dormant persister cell populations. Together these threats are creating an increasing burden on the healthcare system, and a "preantibiotic" age is on the horizon if significant action is not taken by the scientific and medical communities. While the golden era of antibiotic discovery (1940s-1960s) produced most of the antibiotic classes in clinical use today, followed by several decades of limited development, there has been a resurgence in antibiotic drug discovery in recent years fueled by the academic and biotech sectors. Historically, great success has been achieved by developing next-generation variants of existing classes of antibiotics, but there remains a dire need for the identification of novel scaffolds and/or antimicrobial targets to drive future efforts to overcome resistance and tolerance. In this regard, there has been no more valuable source for the identification of antibiotics than natural products, with 69-77% of approved antibiotics either being such compounds or being derived from them.Our group has developed a program centered on the chemical synthesis and chemical microbiology of marine natural products with unusual structures and promising levels of activity against multidrug-resistant (MDR) bacterial pathogens. As we are motivated by preparing and studying the biological effects of these molecules, we are not initially pursuing a biological question but instead are allowing the observed phenotypes and activities to guide the ultimate project direction. In this Account, our recent efforts on the synoxazolidinone, lipoxazolidinone, and batzelladine natural products will be discussed and placed in the context of the field's greatest challenges and opportunities. Specifically, the synoxazolidinone family of 4-oxazolidinone-containing natural products has led to the development of several chemical methods to prepare antimicrobial scaffolds and has revealed compounds with potent activity as adjuvants to treat bacterial biofilms. Bearing the same 4-oxazolidinone core, the lipoxazolidinones have proven to be potent single-agent antibiotics. Finally, our synthetic efforts toward the batzelladines revealed analogues with activity against a number of MDR pathogens, highlighted by non-natural stereochemical isomers with superior activity and simplified synthetic access. Taken together, these studies provide several distinct platforms for the development of novel therapeutics that can add to our arsenal of scaffolds for preclinical development and can provide insight into the biochemical processes and pathways that can be targeted by small molecules in the fight against antimicrobial-resistant and -tolerant infections. We hope that this work will serve as inspiration for increased efforts by the scientific community to leverage synthetic chemistry and chemical microbiology toward novel antibiotics that can combat the growing crisis of MDR and tolerant bacterial infections.

Figure 1.

(A) Shortening of the time gap between the commercial release of different antibiotics into the market and the first report of a resistant bacterial strain.^, (B) Antibacterial drugs by source. Adapted from ref . Copyright 2020 American Chemical Society and American Society of Pharmacognosy. (C) Representation of the chemical space of marine natural products (MNPs) and all approved drugs by 2016 resulting from the overlap of principal component analyses of the top 15 MNP-producing phyla and approved drugs From ref . CC BY-NC 3.0.

Figure 2.

Overview of the Pierce group’s antibiotic-focused research program presented in this Account.

Figure 3.

(A) Rapid three-component synthesis of synoxazolidinone A and B. (B) Acid dehydration approach to the synoxazolidinone core 9. (C) O vs C chemoselectivity challenge for the synthesis of the synoxazolidinone core. (D) Initial SAR profile of the 4-oxazolidinones focused on minimum inhibitory concentration (MIC) against methicillin-resistant S. aureus (MRSA). The MIC values against MRSA ATCC 33591 are shown in parentheses next to the compound numbers. (E) SAR of compounds targeting biofilms. The MIC values against MRSA ATCC BAA 44 are shown in parentheses next to the compound numbers. (F) MRSA biofilm inhibition (reported only for compounds with MIC > 64 μg/mL) and dispersion data against ATCC BAA 44. The current lead compound is presented, highlighting the dichloro motif that results in improved activity.

Figure 4.

(A) Expansion of the SAR for the synoxazolidinone analogue series targeting biofilm inhibition and dispersion. (B) Hemiaminal analogue series. (C) MIC, MBEC, and synergy activity of 59 reported against ATCC BAA 44. The images at the right are reproduced with permission from ref . Copyright 2019 Wiley-VCH. (D) The biofilm lifecycle (image created with BioRender.com)

Figure 5.

(A) Chemoselectivity switch from synoxazolidinones to 2,3-pyrrolidinediones. (B) Optimized route to 2,3-pyrrolidinediones and their synthetic application. (C) Preliminary bioactivity of 2,3-pyrrolidinediones with MIC values (in μg/mL) reported against various bacterial strains. Lead compounds 72 and 73 with their targeted bacterial strains are highlighted in red and blue, respectively. (NCCl)₃ = cyanuric chloride.

Figure 6.

(A) Total synthesis of lipoxazolidinone A (1). (B–E) Structure–activity profile of lipoxazolidinone analogues with MICs against MRSA, with MICs reported against MRSA ATCC 33591 in parentheses: (B) ent-lipoxazolidinone A; (C) eastern alkyl chain analogues; (D) analogues probing the oxazolidinone core requirements for improved antimicrobial activity; (E) western side-chain analogues. (F) Eastern aryl group analogue series. (G) MIC values (in μg/mL) reported for selected lipoxazolidinone analogues tested against Gram-positive methicillin-susceptible S. aureus (MSSA) ATCC 29213 and Gram-negative A. baumannii.

Figure 7.

Overview of our approach toward polycyclic guanidinium alkaloids.

Figure 8.

Antimicrobial evaluation MIC values (in μg/mL) of stereochemical analogues: ^aracemic batzelladine D; ^benantiopure batzelladine D (non-natural); ^cenantiopure batzelladine D (natural); ^dracemic 13-epi-batzelladine D; ^eenantiopure 13-epi-batzelladine D (non-natural); ^fenantiopure 13-epi-batzelladine D (natural); ^genantiopure elimination byproduct (non-natural); ^henantiopure elimination byproduct (natural); ⁱracemic 15-epi-batzelladine D; ^jracemic 13-epi-elimination byproduct; ^kenantiopure 13-epi-elimination byproduct (non-natural); ^lenantiopure 13-epi-elimination byproduct (natural); ^mracemic [4.6]-fused bicyclic β-lactam; ⁿracemic [4.5]-fused bicyclic β-lactam; ^oenantiopure [4.5]-fused bicyclic β-lactam; ^pLZD = linezolid (control); ^qCPL = chloramphenicol (control); ^rcolistin = CST (control).

Scheme 1.

(A) Racemic Route to Batzelladine D; (B) Synthesis of (+)-Batzelladine D; (C) Synthesis of (−)-Batzelladine D