Antibacterials with Novel Chemical Scaffolds in Clinical Development

Abstract

The rise of antimicrobial resistance represents a significant global health threat, driven by the diminishing efficacy of existing antibiotics, a lack of novel antibacterials entering the market, and an over- or misuse of existing antibiotics, which accelerates the evolution of resistant bacterial strains. This review focuses on innovative therapies by highlighting 19 novel antibacterials in clinical development as of June 2024. These selected compounds are characterized by new chemical scaffolds, novel molecular targets, and/or unique mechanisms of action, which render their potential to break antimicrobial resistance particularly high. A detailed analysis of the scientific foundations behind each of these compounds is provided, including their pharmacodynamic profiles, current development state, and potential for overcoming existing limitations in antibiotic therapy. By presenting this subset of chemically novel antibacterials, the review highlights the ability to innovate in antibiotic drug development to counteract bacterial resistance and improve treatment outcomes.

Key Points

The antibacterial pipeline is dominated by improved derivatives of known antibiotic classes, but it also contains novel chemical scaffolds addressing novel mechanisms of action, which are the focus of this review.

Antibiotics with novel chemical scaffolds address new targets for outer membrane biosynthesis, protein secretion, membrane integrity, or virulence factors. In addition, existing targets such as gyrase, RNA polymerase or β-lactamases are addressed with new chemistry.

The antibacterial pipeline shows the ability to innovate, but it is too small overall.

Introduction

The discovery and widespread utilization of antibiotics—compounds that eradicate bacteria or inhibit their growth—heralded the advent of modern medicine. Antibiotics are indispensable not only for treating existing infections but also for enabling modern medical procedures. For example, they play a critical role in managing neutropenia [1], frequently induced by chemotherapy [2], and are essential for infection prophylaxis following invasive surgeries like Caesarean section [3] as well as during immunosuppressive therapy after organ or bone marrow transplantation [4].

Increasing antimicrobial resistance (AMR), arising from the survival of pathogenic microorganisms in the presence of antimicrobials, represents one of the most significant global health challenges of the 21st century. In 2021 alone, despite a notable decrease in non-COVID-related infections during the coronavirus pandemic, there were an estimated 1.14 million global deaths directly attributable to bacterial drug resistance, and this burden is estimated to increase to 1.91 million deaths by 2050 [5]. The 2022 World Health Organization (WHO) “Global Antimicrobial Resistance and Use Surveillance System (GLASS)” report disclosed alarming levels of resistance worldwide that substantiate the need for concerted action [6]. The rise of AMR is further exacerbated by the misuse of antibiotics in agriculture (e.g., as feed additives for infection prevention or for growth promotion), and aqua- or crop culture [7] inducing an increasing prevalence of resistant pathogens in these environments. Beyond its direct health implications, AMR poses a severe threat to the global economy with wide-ranging effects on international trade and overall productivity [8].

To effectively address AMR, an integrated approach has been proclaimed that encompasses, among other elements, improved surveillance to monitor resistance, the development of new vaccines, the implementation of rapid diagnostics to reduce unnecessary antibiotic use, and continued research and development efforts for novel antimicrobials [9]. To streamline these efforts, the WHO has categorized bacterial pathogens into critical, high and medium priority for the year 2024 [10]. The group of critical pathogens, including Carbapenem-resistant Acinetobacter baumannii (CRAB) as well as carbapenem-resistant (CRE) and third-generation cephalosporin-resistant (3GCRE) Enterobacterales exemplify the urgent need for novel therapeutic strategies as they exhibit resistance to last-resort antibiotics, leaving limited treatment options. Investment in the development of innovative and effective antibacterial agents is crucial to outpace the rapid evolution of resistant pathogens [10]. However, the pharmaceutical industry has mostly abandoned antibiotic development, because its economic profitability is unclear or non-existent given the current market environment [9].

To fill the void, several funding initiatives have been established, including Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator (CARB-X) in Boston [11], the INCubator for Antibacterial Therapies in Europe (INCATE) [12], the Replenishing and Enabling the Pipeline for Anti-Infective Resistance (REPAIR) Impact Fund established by the Novo Holdings in Denmark [13], the AMR Action Fund [14, 15] and the Global Antibiotic Research & Development Partnership (GARDP). Despite all these efforts, the WHO concludes in its recent reports that antibacterial agents in the clinical pipeline combined with those approved between 2018–2023 are still insufficient to combat the threat of the emergence and spread of drug-resistant infections [8, 10].

This review aims to shed light on small-molecule antibacterial agents currently in clinical development to stimulate future research. A tabular overview of the complete pipeline (Table 1) was compiled using existing reviews [16, 17], the Global AMR R&D Hub's Dynamic Dashboard funded by the German Federal Ministry of Health (cut-off date July 2022) [18], and the WHO's report "2023 Antibacterial agents in clinical and preclinical development: an overview and analysis" (cut-off date December 2023) [8], followed by a supplementary search for Phase I-III studies started, first posted, updated, or completed between January 2022 and June 10th 2024 on ClinicalTrials.gov with the keywords “infection” or “bacterial infection”. Rather than commenting on all pipeline entries, we focus this review on particularly innovative new antibacterials represented by compounds with novel chemical scaffolds. The presence of a novel scaffold is not a sufficient criterion for efficacy against a pathogen that has developed resistance to approved antibiotics or even for achieving clinically relevant innovation. However, we hypothesize that the new chemical classes have more likelihood of distinct pre-existing therapeutic potential for overcoming resistance than the new derivatives of existing chemical classes. This is because the latter, despite all newly acquired advantages, are unlikely to completely overcome resistance mechanisms or fundamentally alter the properties of the drug class. We have selected 19 antibacterials with new chemical scaffolds, a new target, and/or a novel mechanism of action (MoA) and discuss their scientific background and current development state. The presented examples do not cover all novel concepts and have been selected based on the authors' discretion. Compounds were excluded from this analysis that exclusively targeted Clostridium difficile as well as Mycobacteria including Mycobacterium tuberculosis, or non-traditional approaches such as antibodies, other proteins, live biotherapeutic products (LBPs) such as bacteriophages, microbiome-modulating or immune-modulating agents.

Table 1.

Global pipeline of small-molecule antibiotics with reported clinical trials

Name	Cmpd. class	Developer/sponsor	Mechanism (target)	Indication: trial number (phase)	References
Phase III
Benapenem	Carbapenem	Sihuan Pharmaceutical Holdings Group Ltd.	Cell wall (PBP)	cUTI or AP: NCT04505683 (II/III)	[234]
Epetraborole (GSK2251052, AN3365, BRII-658)	Oxaborole	AN2 Therapeutics, Brii Biosciences	Protein synthesis (leucyl-tRNA synthetase, LeuRS)	MAC Lung Disease: NCT05327803 (II/III)	[235]
Funobactam (XNW4107) + imipenem + cilastin	DBO BLI + carbapenem + degradation inhibitor	Evopoint Biosciences	Cell wall (PBP)	cUTI: NCT05204368 (III) HABP/VABP: NCT05204563 (III)	[236]
Gepotidacin (GSK2140944)	Triazaacenaphthylene	GSK	DNA organization (DNA gyrase, GyrA)	uUTI: NCT04020341 (III), NCT05630833 (III), NCT04010539 (III), NCT04187144 (III) Gonorrhea: NCT04010539 (III)	[34]
Nacubactam (OP0595, FPI-1459, RG6080, RO7079901) + cefepime or aztreonam (OP0595)	DBO BLI + cephalosporin or monobactam	Meiji Seika Pharma Co.	Cell wall (PBP)	cUTI, AP, HABP, VABP, cIAI: NCT05905055 (III), NCT05887908 (III)	[237]
Nafithromycin (WCK 4873)	Macrolide (Ketolide)	Wockhardt Limited	Protein synthesis (50S ribosomal subunit)	CABP: CTRI/2019/11/021964 (III)	[238]
Reltecimod (AB103)	Peptide mimetic	Atox Bio	Immunomodulating (T-lymphocyte receptor mimetic)	Necrotizing Soft-Tissue Infections: NCT02469857 (III)	[239]
Rifasutenizol (TNP-2198)	Rifamycin-nitroimidazole hybrid	TenNor Therapeutics	DNA-dependent RNA synthesis (RNA polymerase) + Formation of reactive radicals	H. pylori infections: NCT05857163 (III)	[240]
Solithromycin (T-4288)	Macrolide (Ketolide)	FUJIFILM Toyama Chemical Co.	Protein synthesis (50S ribosomal subunit)	CABP: NCT01968733 (III), NCT01756339 (III), NCT02605122 (II/III) Gonorrhea: NCT02210325 (III)	[241]
Sudapyridine (WX-081)	Diarylquinoline	Shanghai Jiatan Pharmatech Co.	ATP production (mycobacterial ATP synthase)	TB: NCT05824871 (III), NCT04608955 (II)	[242]
Sulopenem (CP-65,207) Sulopenem etzadroxil (PF-03709270) (+ probenecid)	Penem	Iterum Therapeutics	Cell wall (PBP)	cIAI: NCT03358576 (III) cUTI: NCT03357614 (III) uUTI: NCT03354598 (III), NCT05584657 (III)	[243]
Taniborbactam (VNRX-5133) + cefepime	Bicyclic boronate BLI + cephalosporin	VenatoRx Pharmaceuticals	Cell wall (PBP)	cUTI: NCT03840148 (III) VABP, HABP: NCT06168734 (III)	[244]
Zoliflodacin (ETX0914, AZD0914)	Spiropyrimidinetrione	Innoviva; Global Antibiotics Research and Development Partnership	DNA organization (DNA gyrase, GyrB)	Gonorrhea: NCT03959527 (III)	[245]
Phase II
ACG-701 (ARV-1801, sodium fusidate, fusidic acid) + ceftazidime or meropenem	Steroid antibiotic	Aceragen	Protein synthesis (elongation factor G)	Melioidosis: NCT05105035 (II)	[246]
Afabicin (Debio 1450, AFN-1270)	Benzofuran naphthyridine	Debiopharm	Cell wall / fatty acid biosynthesis (Enoyl-acyl carrier protein reductase, FabI)	S. aureus Bone or Joint Infection: NCT03723551 (II) Staphylococcal ABSSSI: NCT02426918 (II)	[247]
Alpibectir (BVL-GSK098, GSK3729098) + ethionamide or isoniazid	Amido piperidine spiroisoxazoline	BioVersys AG, GSK	Cell wall / fatty acid biosynthesis (transcriptional regulators of Mtb; NAD+)	Pulmonary TB: NCT05473195 (II)	[248]
Brilacidin (PMX-30063)	Aryl amide foldamer	Innovation Pharmaceuticals	Cell wall (Host defense protein mimetic)	ABSSSI: NCT02052388 (II) ABSSSI: NCT01211470 (II)	[135]
BTZ-043 (+ bedaquiline + delamanid) or (+ GSK3036656 + bedaquiline) or (+ delamanid + bedaquiline)	Benzothiazinone	Ludwig-Maximilians-Universität in Munich	Cell wall (DprE1)	TB: NCT05926466 (II), NCT06114628 (II), NCT05382312 (II), NCT05807399 (II), NCT04044001 (I/II)	[249]
CRS3123 (REP3123)	Diaryldiamine	Crestone	Protein synthesis (Methionyl-tRNA synthetase)	CDI: NCT04781387 (II)	[250]
Cannabidiol (BTX 1801, BTX 1503, BTX 1204)	Cannabinoid	Botanix Pharmaceuticals	Cell wall	Nasal S. aureus decolonization: ACTRN12620000456954 (II) Acne: NCT03573518 (II) Atopic Dermatitis: NCT03824405 (II)	[251]
Delpazolid (RMX2001, LCB01-0371) + bedaquiline + delamanid + moxifloxacin; delpazolid + vancomycin	Oxazolidinone	LigaChem Biosciences	Protein synthesis (50S ribosomal subunit)	Pulmonary TB: NCT04550832 (II), NCT02836483 (II) MRSA bacteraemia: NCT05225558 (II)	[252]
Dovramilast (CC-11050, AMR-634) + isoniazid + rifampicin + pyrazinamide + ethambutol	3-Oxo-1H-isoindol-4-yl	Medicines Development for Global Health	Anti-inflammatory (PDE4)	Leprosy: NCT03807362 (II) TB: NCT02968927 (II)	[253]
Exeporfinium chloride (XF-73)	Porphyrin	Destiny Pharma	Cell wall	Post-Op nasal S. aureus decolonization: NCT03915470 (II)	[254]
Finafloxacin	Fluoroquinolone	MerLion Pharmaceuticals	DNA organization (DNA gyrase, GyrA)	cUTI and AP: NCT01928433 (II) uUTI: NCT00722735 (II) H. pylori infections: NCT00723502 (II)	[255]
Fobrepodacin (SPR720, pVXc-486) SPR719 (active metabolite)	Aminobenzimidazole	Spero Therapeutics	DNA organization (DNA gyrase, GyrB)	MAC Lung Disease: NCT05496374 (II), NCT04553406 (II)	[256]
Ftortiazinon (fluorothiazinone, CL-55) + cefepime	Thyazinone + cephalosporin	Gamaleya Research Institute of Epidemiology and Microbiology	Bacterial virulence (Bacterial type III secretion system, T3SS) + Cell wall (PBP)	Nosocomial G-ve: NCT06135350 (II) cUTI: NCT03638830 (II)	[194]
Gallium citrate (AR501)	Organic metal salt	Aridis Pharmaceuticals	Disruption of bacterial iron metabolism	Pseudomonal cystic fibrosis: NCT03669614 (I/II)	[257]
Gallium nitrate (Ganite)	Inorganic metal salt	University of Washington	Disruption of bacterial iron metabolism	Pseudomonal cystic fibrosis: NCT02354859 (II)	[258]
Ganfeborole (GSK3036656, GSK656, GSK070)	Oxaborole	GSK	Protein synthesis (leucyl-tRNA synthetase, LeuRS)	TB: NCT05382312 (II), NCT03557281 (II), NCT06114628 (II) MAC Lung Disease: NCT05327803 (II/III)	[259]
Ibezapolstat (ACX-362E)	Dichlorobenzyl guanine	Acurx Pharmaceuticals	DNA synthesis (DNA polymerase IIIC)	CDI: NCT04247542 (II)	[260]
JDB0131 besylate	Undisclosed	Beijing Chest Hospital	–	Pulmonary TB: NCT06224036 (II)	–
MGB-BP-3	Distamycin	MGB Biopharma	DNA (Minor groove binding)	CDAD: NCT03824795 (II) CDI: NCT02518607 (I)	[261]
Niclosamide (ATx201)	Salicylanilide	UNION therapeutics	Bacterial growth (Proton motive force, PMF)	Atopic Dermatitis: NCT04339985 (II), NCT03009734 (I/II), NCT03304470 Impetigo: NCT03429595 (II)	[262]
Nilofabicin (CG-549, CG400549)	Pyridone	CrystalGenomics	Cell wall / fatty acid biosynthesis (Enoyl-acyl carrier protein reductase, FabI)	ABSSSI: NCT01593761 (II)	[263]
OMN6	Antimicrobial cyclic peptide (40 amino acids)	Omnix Medical	Cell wall / Bacterial membrane	HABP, VABP: NCT06087536 (II), CS0379-200475 Omnix (I)	[132]
Peceleganan (PL-5, V681)	Cationic peptide	Jiangsu ProteLight Pharmaceutical & Biotechnology Co.	Cell wall / Bacterial membrane	Wound infections: ChiCTR2000033334 (II)	[114]
Pravibismane (MBN-101, BisEDT)	Bismuth thiol	Microbion Corporation	Cellular bioenergetics via membrane potential	DFI: NCT05174806 (II) Orthopedic-implant infection: NCT02436876 (II)	[264]
Pyrifazimine (TBI-166)	Riminophenazine	Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College	Bacterial proliferation (DNA)	TB: NCT04670120 (II)	[265]
Quabodepistat (opc-167832) (+ delamanid + bedaquiline + sutezolid + pretomanid)	Carbostyril Derivative	Otsuka Pharmaceutical Development and Commercialization	Cell wall (DprE1)	Pulmonary TB: NCT05971602 (II), NCT05221502 (II), NCT03678688 (I/II)	[266]
Recce 327 (R327)	Acrolein polymer	Recce Pharmaceuticals	Cellular bioenergetics via membrane potential and/or ATP synthesis	Burn wound infections: ACTRN12621000412831 (I/II) DFI: ACTRN12623000056695 (I/II) UTI: ACTRN12623000448640 (I/II) Serious bacterial infections: ACTRN12621001313820 (I)	[267]
Rifabutin (BV100)	Rifamycin	BioVersys AG	DNA-dependent RNA synthesis (RNA polymerase)	VABP: NCT05685615	[268]
Sanfetrinem cilexetil (GV-104326)	Trinem	GSK	Cell wall (PBP)	Pulmonary TB: NCT05388448 (II)	[269]
Sutezolid (PF-2341272, PNU-100480) (+ bedaquiline + delamanid + moxifloxacin) (+ bedaquiline + pretomanid)	Oxazolidinone	TB Alliance	Protein synthesis (50S ribosomal subunit)	TB: NCT05686356 (II/III), NCT01225640 (II), NCT03959566 (II)	[270]
TBA-7371	Azaindole	TB Alliance	Cell wall (DprE1)	TB: NCT04176250 (II)	[271]
TBAJ-876	Diarylquinoline	TB Alliance	ATP production (mycobacterial ATP synthase)	TB: NCT06058299 (II)	[272]
Telacebec (Q-203)	Imidazopyridine amide	Qurient Co., Infectex	Cellular energy production (Respiratory cytochrome bc1 complex)	Pulmonary TB: NCT03563599 (II)	[273]
TNP-2092 (CBR-2092)	Rifamycin-quinolizinone hybrid	TenNor Therapeutics	DNA-dependent RNA synthesis; DNA organization (RNA polymerase; DNA gyrase, GyrA; Topoisomerase IV, ParC)	ABSSSI: NCT03964493 (II) PJI: NCT04294862 (I)	[274]
Voxvoganan (LTX-109)	Antimicrobial peptide	Pharma Holdings AS	Cell wall / Bacterial membrane	Nasal S. aureus decolonization: NCT05889351 (II), NCT04767321 (I/II)	[110]
Phase I
ALS-4	Undisclosed	Aptorum Therapeutics	Bacterial virulence (4,4ʹ-diapophytoene desaturase, CrtN)	NCT05274802 (I)	[275]
ANT3310 + meropenem	DBO BLI + carbapenem	Antabio	Cell wall (PBP)	NCT05905913 (I)	[276]
Apramycin (EBL-1003)	Aminoglycoside	Juvabis	Protein synthesis (30S ribosomal subunit)	NCT04105205 (I), NCT05590728 (I)	[277]
Avibactam (NXL104) + Meropenem (combination: TQD3606)	DBO BLI + carbapenem	Chia Tai Tianqing Pharmaceutical Group Co.	Cell wall (PBP)	NCT05340530 (I)	[278]
Avibactam tomilopil (PF-07338233, ARX-1796, AV-006, AVP, AVI-ARX) + ceftibuten (PF-06264006, CTB)	DBO BLI + cephalosporin	Pfizer	Cell wall (PBP)	cUTI: NCT05554237 (I) NCT03931876 (I)	[160]
BWC0977	Oxazolidinone containing NBTI	Bugworks	DNA organization (DNA gyrase, GyrA; Topoisomerase IV)	NCT05088421 (I)	[279]
EQ-778	Undisclosed	Vedic Lifesciences	–	RTI: NCT05835375	–
ETX0282 + cefpodoxime proxetil (combination: ETX0282CPDP)	DBO BLI + cephalosporin	Entasis Therapeutics	Cell wall (PBP)	NCT03491748 (I)	[280]
GSK2556286 (GSK286)	Uracil aryloxypiperidine	GSK	Bacterial growth (Adenylyl cyclase Rv1625c)	TB: NCT04472897 (I)	[281]
GSK3882347	Mannose derivative	GSK, Fimbrion Therapeutics	Bacterial virulence (Type 1 fimbrin D-mannose specific adhesin, FimH)	uUTI: NCT05138822 (I) NCT04488770 (I)	[214] [216]
KSP-1007 + meropenem	Bicyclic boronate BLI + carbapenem	Sumitomo Dainippon Pharma	Cell wall (PBP)	NCT05226923 (I)	[186]
Ledaborbactam etzadroxil (VNRX-7145) + ceftibuten	Bicyclic boronate BLI + cephalosporin	VenatoRx Pharmaceuticals	Cell wall (PBP)	NCT05527834 (I), NCT05488678 (I), NCT04243863 (I), NCT04877379 (I)	[166]
Macozinone (PBTZ-169)	Benzothiazinone	Innovative Medicines for Tuberculosis Foundation, Nearmedic Plus	Cell wall (DprE1)	TB: NCT03776500 (I), NCT03423030 (I), NCT03036163 (I)	[282]
MK-7762 (TBD09)	Oxazolidinone	Bill & Melinda Gates Medical Research Institute	Protein synthesis (50S ribosomal subunit)	TB: NCT05824091 (I)	[283]
MRX-8	Polymyxin	MicuRx Pharmaceuticals	Cell wall / Bacterial membrane	NCT04649541 (I)	[284]
Murepavadin (POL7080, RG7929)	Protegrin I	Spexis	Cell wall (LPS-assembly protein LptD)	Pseudomonal cystic fibrosis (I)	[66]
Nacubactam (OP0595, FPI-1459, RG6080, RO7079901) + meropenem	DBO BLI + carbapenem	Meiji Seika, Roche	Cell wall (PBP)	NCT02134834 (I), NCT02975388 (I), NCT03182504 (I), NCT02972255 (I), NCT03174795 (I)	[237]
PL-18	Cationic peptide	Jiangsu ProteLight Pharmaceutical and Biotechnology	Cell wall / Bacterial membrane	Bacterial vaginosis: NCT05340790 (I)	[114]
PLG0206 (WLBU2)	Cationic peptide	Peptilogics	Cell wall / Bacterial membrane	PJI: NCT05137314 (I)	[118]
QPX9003 (F365, BRII-693)	Polymyxin	Brii Biosciences	Cell wall / Bacterial membrane	NCT04808414 (I)	[285]
RG6436 (GDC-0829)	Arylomycin	Genentech	Cell wall (Type I signal peptidase LepB)	ISRCTN18049481 (I)	–
SZEY-2108	Monobactam	Suzhou Erye Pharmaceutical Co.	Cell wall (PBP)	CRE: NCT06055777 (I)	–
TBAJ-587	Diarylquinoline	TB Alliance	ATP production (mycobacterial ATP synthase)	TB: NCT04890535 (I)	[286]
TBI-223	Oxazolidinone	TB Alliance	Protein synthesis (50S ribosomal subunit)	TB: NCT03758612 (I), NCT04865536 (I)	[287]
TXA709	Benzamide	TAXIS Pharmaceuticals	Cell wall (Cell division protein FtsZ)	S. aureus	[95]
Upleganan (SPR206)	Polymyxin	Spero Therapeutics	Cell wall / Bacterial membrane	NCT03792308 (I), NCT04868292 (I), NCT04865393 (I)	[288]
Ursodeoxycholic acid (ursodiol)	Steroid	Nottingham University Hospitals NHS Trust	–	CDI: NCT05526807 (I)	–
Xeruborbactam (QPX7728) or prodrug (QPX7831) (+ QPX2014) (+ ceftibuten/QPX2015)	Bicyclic boronate BLI + (undisclosed) BL	Qpex Biopharma	Cell wall (PBP)	NCT04380207 (I), NCT05072444 (I), NCT04578873 (I), NCT03939429 (I)	[179]
Zidebactam (WCK 5107) + cefepime (combination: WCK 5222, FEP-ZID) zidebactam + ertapenem (WCK 6777)	DBO BLI + cephalosporin or carbapenem	Wockhardt	Cell wall (PBP)	cUTI and AP: NCT05645757 (I)	[289]
Zifanocycline (KBP-7072)	Tetracycline	KBP BioSciences Pharmaceutical Technical Co. Ltd.	Protein synthesis (30S ribosomal subunit)	NCT02454361(I), NCT02654626 (I), NCT04532957 (I), NCT05507463 (I)	[290]
Zosurabalpin (RG6006, RO7223280, Abx MCP)	Macrocyclic peptide	Roche	Cell wall (LptB2FGC complex)	NCT05614895 (I), NCT04605718 (I), BP43532	[62]

Compounds categorized by the WHO as “agents not under active development” are not listed [8]

ABSSSI acute bacterial skin and skin structure infections, ADC antibody drug conjugate, AP acute pyelonephritis, BL β-lactam, BLI β-lactamase inhibitor, CABP community-acquired bacterial pneumonia, CDAD Clostridium difficile-associated diarrhea, CDI Clostridium difficile infections, cIAI complicated intra-abdominal infections, CRE carbapenem-resistant Enterobacteriaceae, cUTI complicated urinary tract infections, DBO diazabicyclooctane, DFI diabetic foot infections, G-ve Gram-negative, HABP hospital-acquired bacterial pneumonia, MAC Mycobacterium avium complex, NBTI novel bacterial topoisomerase inhibitor, PBP penicillin binding protein, PJI prosthetic joint infections, RTI respiratory tract infection, TB tuberculosis, UTI urinary tract infections, uUTI uncomplicated urinary tract infections, VABP ventilator-associated bacterial pneumonia

Antibiotics with New Chemical Scaffolds

DNA Gyrase and Topoisomerase IV Inhibitors

Type IIa topoisomerases, including DNA gyrase and topoisomerase IV (TI IV), play critical roles in the control of bacterial DNA topology (3D configuration). The DNA gyrase introduces negative supercoils into DNA [19], facilitating essential processes such as replication and transcription, whereas TI IV primarily resolves DNA entanglements [20] and decatenates replicated chromosomes [21, 22]. Both enzymes create transient double-strand breaks in the DNA helix, allowing the passage of another DNA segment before resealing the breaks, and have a heterotetramer structure: DNA gyrase comprises two GyrA and two GyrB subunits [23], while TI IV consists of two ParC and two ParE subunits [24]. Novobiocin, the sole approved aminocoumarin antibiotic, binds to the GyrB (gyrase) and ParE (TI IV) subunits [25, 26]. It was indicated for the treatment of serious Staphylococcus aureus infections. However, the oral formulation of the drug has been discontinued from the market due to lack of effectiveness and safety concerns [27]. In contrast, the quinolone antibiotics, dual gyrase and topoisomerase inhibitors, span a major class of antibiotics that has been widely used over decades, until safety concerns have limited their use [28]. Two quinolones bind to the GyrA (gyrase) or ParC (TI IV) subunits in the presence of DNA, forming a ternary complex immediately after the DNA double strand break was introduced, thereby inhibiting DNA relegation. The inhibition ultimately results in irreversible double-strand breaks, leading to DNA fragmentation, eventually causing cell death [29, 30]. The ‘Novel Bacterial Topoisomerase Inhibitors’ (NBTI) represent a new, chemically heterogeneous class following a similar MoA, yet with distinct binding sites (Fig. 1) [31].

Fig. 1.

Overlay of the crystal structures of moxifloxacin (green), zoliflodacin (yellow) and gepotidacin (pink) in a ternary complex with S. aureus DNA gyrase (GyrA: beige; GyrB: coral) and doubly nicked DNA (blue) with magnesium (purple) (PDB: 5CDQ, 8BP2, and 6QTK) [32–34]

Gepotidacin (GSK2140944)

Gepotidacin is a triazaacenaphthylene (Fig. 2) developed by GlaxoSmithKline [35]. Although gepotidacin binds to the same subunits (GyrA and ParC) as the quinolones, it occupies a different binding pocket (Fig. 1), thereby conferring a lower potential for cross-resistance [36, 37]. Nevertheless, the simultaneous binding of quinolones and gepotidacin to the complex is not possible [30, 34]. Within the topoisomerase cleavage-complex, a gepotidacin molecule interacts with the DNA between the two staggered cleavage sites of the topoisomerase, inducing single-strand breaks that culminate in a bactericidal effect [30]. The in vitro activity spectrum includes Gram-positives such as methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA), Streptococcus pneumoniae, S. pyrogenes and Gram-negatives such as Haemophilus influenzae, Moraxella catarrhalis, Escherichia coli and Neisseria gonorrhoeae with MIC₉₀ values ranging from ≤ 0.06–2 μg/mL [38, 39]. In Phase III studies for uncomplicated urinary tract infections (uUTIs), the compound showed non-inferiority (NCT04020341) or superiority (NCT04187144) after 1.5 g peroral (po) twice daily administration against nitrofurantoin 100 mg po twice daily [40]. Additionally, non-inferiority was shown in a Phase III study for 3 g gepotidacin administered po twice daily compared to ceftriaxone 500 mg intramuscular (IM) plus azithromycin 1 g po as comparative therapy (NCT04010539) in patients with uncomplicated urogenital gonorrhea [41].

Fig. 2.

Structure of gepotidacin

Zoliflodacin (ETX0914, AZD0914)

Zoliflodacin is another member of the NBTIs featuring a spiropyrimidinetrione core (Fig. 3), commonly known as barbituric acid [42]. It was originally developed by AstraZeneca and its spin-off Entasis, which was acquired by Innoviva Specialty Therapeutics in 2022 [43]. Although the compound shares a similar binding pocket with the quinolone antibiotics (Fig. 1), zoliflodacin does not interact with GyrA but with the GyrB subunits. As a result, it is less susceptible to GyrA mutations that lead to quinolone resistance [33, 44]. The in vitro spectrum includes S. aureus (MSSA and MRSA), Enterococcus faecalis, Streptococci including S. pneumoniae, N. gonorrhoeae, Helicobacter pylori and atypical bacteria with MIC₉₀ values ranging from 0.125–1 μg/mL, while the activity against E. faecium shows high variability with MIC values between ≤ 0.06-128 μg/mL [44–46]. In partnership with GARDP, zoliflodacin is currently under development against uncomplicated gonorrhea infections [47]. Similar to gepotidacin, a non-inferiority Phase III study on uncomplicated urogenital gonorrhae patients with 3 g zoliflodacin po compared to ceftriaxone 500 mg IM plus azithromycin 1 g po in the comparator arm was successful (NCT03959527).

Fig. 3.

Structure of zoliflodacin

BWC0977

BWC0977 is an oxazolidinone NBTI (Fig. 4) under development by Bugworks with support of GARDP [48]; a backup program is supported by CARB-X [49]. The compound shows very high in vitro activity against all members of the ESKAPE panel (E. faecium, S. aureus, E. coli, Klebsiella pneumoniae, A. baumannii, Pseudomonas aeruginosa and Enterobacter cloacae) with MIC₉₀ values ranging from ≤ 0.5–2 μg/mL as well as N. gonorrhoeae, independent of their resistance against marketed drug classes [50, 51]. Thus, in contrast to the NBTIs mentioned above, BWC0977 has potential for a broad-spectrum antibiotic. The data also indicate an overlapping binding pocket with gepotidacin and the same MoA [30, 52, 53]. First Phase I safety and tolerability studies of intravenous (IV) infusions have been completed (NCT05088421).

Fig. 4.

Structure of BWC0977

RNA Polymerase Inhibitor

DSTA4637S

DSTA4637S is the first antibody-antibiotic conjugate (AAC) in clinical development. The conjugate comprises the small molecule rifamycin analog dmDNA31 (named ‘rifalogue’) that is coupled to the monoclonal immunoglobulin G1 (IgG1) antibody MSTA3852A [54] via a cathepsin-cleavable valine-citrulline linker (Fig. 5) [55]. Isolated from human blood and engineered by the THIOMAB™ [56] technology, the antibody targets β-O-linked N-acetylglucosamine modifications on bacterial wall-teichoic acids (WTAs) [54]. The AAC is developed for the treatment of bacteremia caused by S. aureus within host phagocytic cells, such as neutrophils and macrophages [54, 57, 58]. While the Fab region of the antibody directs binding of the conjugate to the cell wall of S. aureus, the Fc region mediates uptake of the opsonized bacteria into immune cells, where the active agent rifalogue is enzymatically released in the phagolysosomes and thus eliminates bacteria intracellularly. Advantages of this approach, apart from an increase in intracellular efficacy and minimization of toxicity through targeted drug delivery, are the extension of the half-life from 3–4 h (free rifalogue) to four days (conjugate) in mice [59].

Fig. 5.

Structure of DSTA4637S

Safety, pharmacokinetics (PK) and tolerability (immunogenicity) were determined in a first single-ascending dose (5–150 mg/kg) Phase I study (NCT02596399) in 20 healthy volunteers [60]. Besides one infusion-related moderate adverse event, no serious side effects were observed and no significant changes in laboratory parameters or vital signs occurred. Anti-drug antibodies (ADAs) induced by DSTA4637S conjugate were not observed. In a multiple-ascending dose Phase Ib study (NCT03162250), patients who tested positive for S. aureus were administered a low, intermediate or high dose of DSTA4637S via IV infusion, followed by up to five additional doses every seven days in combination with anti-staphylococcal standard of care antibiotics. Since this study, development has been suspended [8].

Small Molecules and Peptides Affecting Cell Wall Integrity

Zosurabalpin (Abx MCP, RG6006, RO7223280)

The outer membrane (OM) of Gram-negative bacteria is difficult to penetrate for xenobiotics due to its specific structure, consisting of an asymmetric bilayer with phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. The latter are transported to the cell surface by a multiprotein complex (LPS transporter), which extends from the inner membrane through the periplasm to the OM (Fig. 6). Zosurabalpin belongs to a novel class of synthetic cyclic tripeptides with a non-peptidic tether [61, 62]. By blocking LptB₂FGC, the inner membrane component of the LPS transporter, zosurabalpin traps an LPS-bound conformation (Fig. 6c) [61]. This ternary complex disrupts LPS transport to the OM, leading to toxic accumulation of LPS biosynthetic intermediates with relatively slow in vitro killing kinetics (≥ 12 h) in Acinetobacter spp., including carbapenem-resistant Acinetobacter baumannii-calcoaceticus (ABC) complex [63, 64]. The selectivity for Acinetobacter spp. (MICs: ≤ 0.06–1 mg/L) is attributed to the significant variation in the protein sequences of the target LptFG across different Gram-negative species. Zosurabalpin's zwitterionic character, imparted by the carboxylic acid, reduced the formation of aggregated low-density lipoprotein (LDL)/high-density lipoprotein (HDL) vesicles and enhanced the tolerability in rats significantly, compared to more basic progenitors [62]. In addition to in vivo activity in a neutropenic mouse thigh infection model and in an immunocompetent mouse sepsis model, a > 5 log reduction in colony-forming units (CFUs) at a total daily dose of 360 mg/kg could be demonstrated in a murine pneumonia model with a pan-drug–resistant contemporary clinical isolate (A. baumannii ACC01073). In two Phase I studies in healthy volunteers (NCT04605718, ISRCTN37043682), a single IV infusion of 10–2000 mg was found to be safe and well tolerated [65]. Moreover, approximately dose-proportional plasma exposure (C_max and AUC_inf) up to 1000 mg and more than dose-proportional plasma exposure at > 1000 mg was observed.

Fig. 6.

a Structure of zosurabalpin. b Schematic structure of the lipopolysaccharide (LPS) transporter. Adapted from [61]. c Cryo-EM structure of zosurabalpin (green) with Acinetobacter baylyi LptB₂FG (F: blue; G: red) and Acinetobacter LPS (grey) (PDB: 8FRN) [61]

Murepavadin (POL7080, RG7929)

Murepavadin is a synthetic, cyclic 14-amino-acid cationic peptide (Fig. 7) based on the membranolytic host-defense peptide Protegin I, whose d-proline-l-proline scaffold facilitates the stabilization of a β-hairpin conformation [66]. By binding to the OM-embedded β-barrel protein LptD of the LPS transporter (Fig. 6b), which resides in a complex with the lipoprotein LptE [67], murepavadin inhibits the transport of LPS to their final location on the cell surface of Pseudomonas spp. in the nanomolar range (MIC₉₀ = 0.25 mg/L) [68–70]. This leads to changes in the OM [71] and ultimately to bacterial cell death. Photolabeling experiments indicated a binding site at the N-terminal periplasmic segment of LptD, which contains an additional 100 amino acids in Pseudomonas spp., thereby explaining murepavadin's high selectivity for these bacteria over other Gram-negative species [68, 71]. Following the observation of elevated serum creatinine levels [72], indicative of higher-than-anticipated incidences of acute kidney injury post-IV murepavadin administration [73], Phase III trials NCT03409679 and NCT03582007 for the treatment of ventilator-associated bacterial pneumonia (VABP)/hospital-acquired bacterial pneumonia were terminated, despite the absence of increased mortality in the murepavadin arm relative to the control arm [74]. To mitigate those nephrotoxic side effects [75, 76], an inhalation of single doses ranging from 12.5–300 mg in healthy volunteers was explored in a first-in-human Phase I study (POL7080-201-01) [71, 77]. At the highest dose level, a systemic bioavailability of just 5% was observed, while a murepavadin concentration that inhibits the growth of 90% of P. aeruginosa isolates (MIC₉₀) obtained from people with cystic fibrosis (CF) was still detected in the epithelial lining fluid after 24 hours [78]. In a future Phase II clinical trial, Spexis intends to investigate the treatment of P. aeruginosa infections in patients with CF and non-CF bronchiectasis. A detailed review about murepavadin was published in 2018 [79].

Fig. 7.

Structure of murepavadin

Afabicin (Debio 1450, AFN-1270)

The benzofuran napthyridinone afabicin is a prodrug of afabicin desphosphono (Debio 1452, AFN-1252), an enoyl-acyl carrier protein (ACP) reductase (FabI) inhibitor developed by Debiopharm (Fig. 8) [81]. Debiopharm acquired Affinium Pharmaceuticals in the year 2014, who had owned the license for the lead compound, originally discovered by GSK [82, 83]. The target FabI catalyzes the final step of the bacterial fatty acid biosynthesis cycle, the reduction of the double bond in the enoyl-ACP intermediate [84]. Inhibition of FabI disrupts this process, preventing the bacteria from synthesizing fatty acids for membrane assembly (Fig. 9) [85].

Fig. 8.

a Structure of afabicin. The cleavage site to give the active agent afabicin dephospho is indicated by a dotted line. b Crystal structure of afabicin (green) with S. aureus FabI (beige) and the unnatural substrate 3´NADPH (pink) (PDB: 4FS4). Besides interactions with the target, the carbonyl of afabicin desphospho cis-amide can interact with NADPH [80]

Fig. 9.

Bacterial fatty acid biosynthesis and the inhibition of the FabI-catalyzed step by afabicin desphospho. Adapted from [85]

This mechanism is particularly effective for species such as Staphylococci (MIC₉₀ = 0.008–0.06 mg/L) [86], which have not developed salvage pathways. After oral or IV administration of afabicin, dephosphorylation and cleavage of the resulting hemiaminal lead to the formation of the active species, showing selective and potent antibacterial activity against Staphylococcus spp., including MRSA [87]. In a Phase II study against acute bacterial skin and skin structure infections (ABSSSI) (NCT02426918), IV-to-oral afabicin (low-dose: 80 mg IV followed by 120 mg po twice a day and high-dose: 160 mg IV followed by 240 mg po twice a day) showed non-inferiority to a combination of vancomycin (1 g or 15 mg/kg IV) followed by linezolid (600 mg po twice a day). Most frequent treatment-emergent adverse events were mild headache and nausea [87]. In another, ongoing Phase II trial, afabicin is evaluated using an IV-to-oral switch strategy for the treatment of S. aureus bone or joint infections (NCT03723551).

TXA709

The cell division protein filamenting temperature-sensitive mutant Z (FtsZ) is a new, potentially broad-spectrum target for the inhibition of bacterial cytokinesis, the process by which a bacterial cell divides into two daughter cells (Fig. 10) [90]. Its structure and function are comparable to that of mammalian β-tubulin [91]. Filamenting temperature-sensitive mutant Z forms a ring-like, inner cytoplasmic membrane anchored structure in the center of the cell via GTP-dependent self-polymerization. This “Z-ring“ serves as a scaffold for recruiting and organizing other components of the divisome complex for septum assembly and guides cell division (Fig. 10). Filamenting temperature-sensitive mutant Z is a key component for most Gram-negatives and -positives as it is highly conserved and ubiquitous across most bacteria [92, 93].

Fig. 10.

a Structure of TXA709. The cleavage site to give the active agent TXA707 is indicated by a dotted line. b TXA707’s mechanism of action. Adapted from [88]. c Crystal structure of TXA 707 binding to an inter-subdomain pocket of Staphylococcus aureus FtsZ (PDB: 5XDT) [89]

The imide TXA709 (Fig. 10) is an anti-MRSA prodrug [94] of benzamide TXA707, an inhibitor of FtsZ, developed by TAXIS Pharmaceuticals [95]. The imide TXA709 is based on Prolysis’s compound PC190723 [91, 96], a potent FtsZ-inhibitor with bactericidal activity against Staphylococcus spp. (incl. MRSA), yet limited metabolic stability. In contrast, the imide prodrug TXA709 possesses enhanced oral bioavailability and superior in vivo efficacy against MRSA. The analogues also exhibited bactericidal activity against S. aureus strains (MIC ≤ 1 μg/mL) resistant to the current standard of care drugs vancomycin and linezolid [90]. TXA709 was the first FtsZ-inhibitor entering human clinical trials and serves as the lead compound for further development targeting bacteria such as E. coli and K. pneumoniae. Synergistic effects with other antibiotics such as β-lactams have been described [88, 90].

RG6436 (GDC-0829)

Bacterial type I signal peptidases (SPase I enzymes) are essential, membrane-bound proteases that cleave membrane-bound preproteins, thus releasing mature proteins into the periplasm or the outside of the cell [97]. Their inhibition leads to an accumulation of the preproteins in the membrane, which ultimately results in cell death (Fig. 11) [98]. Natural arylomycins are macrocyclic lipopeptides, that inhibit the active side of SPases on the cell surface of Gram-positive bacteria, while not being able to reach the inner membrane-bound SPases of Gram-negative bacteria [99]. The structure optimization of arylomycins resulted in G0775 (Fig. 11), a compound with improved penetration of the OM through a porin-independent mechanism, yet insufficient physicochemical properties. In vitro tests showed activity against ESKAPE-pathogens and improved potency against Gram-positive MRSA [100]. The remarkable widening of the bacterial spectrum illustrates the power of medicinal chemistry in antibiotic hit optimization, and it positions the macrocycles as a promising new class of antibiotics with novel MoA.

Fig. 11.

a Structure of G0775. b Mechanism of action of optimized arylomycin with activity against Gram-negative bacteria. CP cytoplasm, IM inner membrane, OM outer membrane, PP periplasm. Adapted from [101]

RG6436 is an arylomycin with an undisclosed structure inhibiting the SPase LepB in Gram-negative bacteria. Since it was acquired from Enterprise Therapeutics, the development is led by the Roche subsidiary Genentech [102, 103]. In vitro data showed a broad activity against Gram-negative bacteria, including Enterobacterales—most importantly E. coli, K. pneumoniae, E. cloacae—as well as A. baumannii, P. aeruginosa and Serratia marcescens (MIC₉₀ = 0.5–2 μg/mL) [98]. RG6436 is currently under development for the treatment of complicated urinary tract infections (cUTIs) and is being investigated in a Phase I clinical trial on healthy volunteers (ISRCTN18049481) [102].

Small Molecules and Peptides Acting as Membrane Disruptors

Antimicrobial peptides (AMPs), which are integral components of the innate immune system and thus also referred to as host defense peptides (HDPs), are found across a broad spectrum of species [104]. Most AMPs have an amphiphilic structure [105]. Positively charged groups preferably bind to negatively charged bacterial membrane components [104] over mostly zwitterionic eukaryotic membranes [106], while the hydrophobic side of AMPs mediates their integration into the membrane, resulting in membrane disruption and subsequent cell lysis [105]. However, the split between antibiotic activity and eukaryotic cytotoxicity seen in cellular assays often did not translate in sufficient therapeutic windows in vivo following systemic use and hemolysis has been an often-encountered safety issue [107]. Therefore, no earlier-generation AMPs have reached drug approval. On the other hand, bacterial resistance development to AMPs is very difficult due to the non-proteogenic lipid targets. We therefore present a selection of next-generation AMPs in the current development pipeline.

Voxvoganan (LTX-109)

Staphylococcus aureus infections are associated with prolonged hospital stays, high mortality rates, and medical costs [108]. Nasal decolonization protocols for S. aureus have been implemented to mitigate the risk of severe infections in surgical, dialysis, and immunocompromised patients, as well as to prevent transmission to non-carriers [109]. Due to rising resistance to the widely established decolonization regimen with the polyketide mupirocin, new agents are currently under development. Voxvoganan is a synthetic cationic tripeptide, characterized by a preferred amphipathic conformation and a C-terminal 2-phenylethylamine cap (Fig. 12) [110], which impeded proteolytic degradation [111]. Irrespective of the reduced susceptibility of S. aureus strains to β-lactams, vancomycin, daptomycin, linezolid, clindamycin, trimethoprim-sulfamethoxazole, and mupirocin, voxvoganan maintained a consistent minimum inhibitory concentration (MIC) range of 2–4 µg/mL and a rapid dose-dependent bactericidal effect within 0.5–4 h in vitro [112]. Additionally, it possessed a longer post-antibiotic effect than mupirocin [113] and exhibited a low tendency for resistance development [112]. Presumably owing to its hemolytic activity, evidenced by 50% lysis of erythrocytes at 175 µg/mL [110], voxvoganan’s clinical investigation is currently confined to topical application. In persistent nasal MRSA/MSSA carriers, notable nasal decolonization efficacy was achieved within two days using a 2% or 5% voxvoganan hydrogel applied to the anterior nares thrice daily, complemented by a standard local hygiene regimen encompassing body and hair cleansing, with low systemic bioavailability and no safety concerns over the 9-week follow-up period (NCT01158235) [109]. However, recurrence of the bacteria after five days following completion of the three-day treatment was noted in all participants except one.

Fig. 12.

Structure of voxvoganan

PL-18

PL-18 is a 15mer, all-d-amino-acid, α-helical, cationic, amphipathic peptide derived from the N-terminus of ribosomal protein L1 (RpL1) of H. pylori (Fig. 13). The peptide is further stabilized by an N-terminal acetyl residue and C-terminal primary amide [114]. With MIC values between 1–4 µM, PL-18 demonstrated a broad spectrum of activity against Gram-negative and Gram-positive bacteria, notwithstanding H. pylori's intrinsic resistance to the N-terminal region of the protein [115]. Presumably due to the demonstrated hemolytic activity of the enantiomer HPRP-A1 [116, 117], PL-18 is currently only being clinically investigated as a topical application in the form of a 1–15 mg suppository against bacterial vaginosis (NCT05340790).

Fig. 13.

Structure of PL-18

PLG0206 (WLBU2)

PLG0206 is a de novo designed, 24-amino-acid, α-helical, cationic, amphipathic peptide containing valine and tryptophan residues in the hydrophobic face and exclusively arginine residues on the hydrophilic side (Fig. 14) [118, 119]. Interaction of PLG0206 with the bacterial cell membrane led to local stiffening and changes in membrane thickness [120, 121]. Those effects caused a spacing mismatch in lipid headgroups and reduced the energy barrier for ion flux across the membrane, resulting in a bactericidal effect within minutes [122]. PLG0206 exhibited broad-spectrum activity against Gram-negative and -positive bacteria, including > 1200 multidrug-resistant (MDR) ESKAPEE clinical isolates (MIC₉₀ = 0.25–16 μg/mL) [123], while having little to no cytotoxic effects on human primary cells at bactericidal concentrations [124]. Serial passage experiments with P. aeruginosa strains have shown a development of resistance only after 25 days [119]. The low tendency for resistance development was corroborated through single-step spontaneous mutation frequency assays [123]. Of particular value is the strong PLG0206 anti-biofilm activity [122, 123, 125] against S. aureus, the most common pathogen responsible for persistent infections that develop around joint prostheses, such as hip and knee replacements. Five-year mortality for such periprosthetic joint infection (PJI) is about 25% [126]. After explanted components of total knee arthroplasties (TKA) from patients with chronic PJI were treated ex vivo with a 1 mg/mL PLG0206 solution for 15 minutes, rinsed and sonicated in 1% Tween 20, 10 of 17 prostheses became culture-negative (NCT05137314) [127, 128]. The observation that infected prostheses exposed to PLG0206 showed a mean 4-log₁₀ reduction in CFU compared to the untreated control suggests the development of PLG0206 as a local irrigation solution directly in the wound cavity for patients with PJI after total knee/hip arthroplasty. In a further Phase I study, the IV administration of PLG0206 as a single dose between 0.05–1 mg/kg appeared to be safe and well tolerated as long as the drug concentration and infusion rate remained below 0.5 mg/mL and 25 mg/h, respectively [129, 130]. Detailed reviews of the preclinical and clinical development of PLG0206 have recently been published [124, 131].

Fig. 14.

Amino acid sequence of PLG0206

OMN6

Cecropins are 29–42 amino acids long, cationic, linear AMPs found in the orders of Diptera, commonly known as flies, and Lepidoptera, commonly known as butterflies and moths [132]. Their membrane-disrupting properties are attributed to the secondary structure consisting of two amphipathic α-helices connected by a hinge. OMN6 is a synthetic 40mer, all-l-amino-acid peptide based on cecropin A, cyclized via a disulfide bridge between engineered Cys² and Cys⁴⁰ residues to increase stability and decrease proteolytic degradation (Fig. 15). OMN6 exhibited activity against Gram-negative bacteria, in particular against 401 A. baumannii strains, with a very narrow MIC range of 4–8 µg/mL, despite partial colistin resistance [133]. In vitro serial passaging studies with four strains of the ABC complex demonstrated unchanged MIC values after 20 passages (20 days), and thus no development of resistance [132]. Up to a concentration of 868 μg/mL, OMN6 had no effect on the survival rate of HEK293T cells or the hemolysis of erythrocytes. Since OMN6 showed increased in vitro activity in the presence of bovine pulmonary surfactant [133], it might be suitable for the treatment of lung infections. In a corresponding mouse model with the MDR A. baumannii strain ACC0000535, three IV injections of 21, 35, or 49 mg/kg OMN6 at 1-hour intervals starting 2 hours post-infection resulted in a reduction in bacterial load of > 4.4 log CFU/lungs compared to the vehicle-treated group after 24 hours. For a first-in-human Phase I study (CS0379-200475 Omnix), healthy volunteers received doses of 7.5–300 mg OMN6 spread across up to three 3-hour infusions, interspersed with a 5-hour wash-out period [134]. All treatments were well tolerated and adverse events were mild and transient. A half-life of 0.9 hours was determined for single infusions of 80 or 100 mg OMN6.

Fig. 15.

Structure of OMN6

Brilacidin (PMX-30063)

Researchers at the University of Pennsylvania found small, synthetic, non-peptidic HDP mimetics against a variety of multi-drug–resistant Gram-negative and -positive bacteria [135, 136]. Their spin-off PolyMedix was founded in 2002. The most promising compounds had an arylamide backbone equipped with multiple charged and hydrophobic elements, resulting in an overall amphiphilic structure with a molecular size < 1000 Da [135]. Further structure optimization for selectivity against S. aureus led to the discovery of brilacidin. The arylamide foldamer shows a planar structure with four positively charged guanadine- and pyrrolidine-groups as well as two hydrophobic trifluoromethane elements (Fig. 16) [135, 137].

Fig. 16.

Structure of brilacidin

Brilacidin was active against a broad range of both Gram-negative and -positive bacteria including MRSA with MIC₉₀ values ranging from 0.25–64 μg/mL [138]. It has been tested in two randomized Phase II trials for the treatment of ABSSSI (NCT02052388 and NCT01211470) [139, 140]. In the latter, a single dose of 0.6 mg/kg IV brilacidin, the lowest dosage tested in the trial, was well tolerated and showed an efficacy similar to 7-day treatment with daptomycin. Although Innovation Pharmaceuticals Inc., formerly known as Cellceutic, who acquired PolyMedix in 2013, announced plans in 2015 to advance to Phase III ABSSSI trials, we are not aware that such a trial has commenced to date [141].

Brilacidin also shows antifungal [142] and antiviral [136, 143, 144] properties and has been identified as a potential drug against the malaria-causing parasite Plasmodium falciparum [145]. In more recent studies, Innovation Pharmaceuticals Inc. investigated the efficacy of a brilacidin oral rinse (NCT02324335) and in COVID-19 patients (NCT04784897).

β-Lactamase Inhibitors

β-Lactamase inhibitors (BLIs) prevent the hydrolytic inactivation of β-lactam motives found in penicillins, cephalosporines, penems, and monobactams [146]. The targeted β-lactamases are predominantly responsible for the resistance of Gram-negative pathogens towards those β-lactam antibiotics. They are categorized into Ambler classes A, B, C and D based on amino acid sequence homology [147, 148], but other classification systems, such as the one of Bush-Jacoby-Medeiros, that groups by substrate specificity and response to inhibitors, also exist [149–151]. The Ambler classes A, C and D comprise serine β-lactamases (SBLs), which catalyze the ring-opening hydrolysis of β-lactam substrates via a serine residue at the active site, resulting in the formation of an acylated-enzyme intermediate (Fig. 17) [152]. Numerous inhibitors targeting SBLs are known to react with the serine residue in a reversible or irreversible fashion [153, 154]. The Ambler class B comprises metallo-β-lactamases (MBLs) that hydrolyse β-lactams through the attack of water facilitated by one or more zinc cations. Aztreonam, a monobactam antibiotic, was generally unaffected by MBLs, yet hydrolyzed by extended-spectrum β-lactamases [155]. The recently introduced cefiderocol showed reduced susceptibility in vitro [156], yet all other β-lactam antibiotics were vulnerable to MBLs [157]. The first generation of BLIs, such as clavulanic acid [158] or tazobactam (YTR 830) [159], were β-lactams themselves. In the past decade, a second chemical class named diazabicyclooctane (DBO) with an activated urea moiety, was introduced to the market with launched products such as avibactam [160], durlobactam (ETX2514) [161] or relebactam (MK-7655) [162], and several analogs in clinical development (Table 1). In this review, we would like to highlight a third class named after its unusual reactivity center, the boronates [163]. Taniborbactam, xeruborbactam, and KSP-1007 are currently in clinical trials as the first broad-spectrum BLIs, targeting both SBLs and MBLs. Given that in 2022 approximately 50% of all antibiotics prescribed in outpatient settings in the USA were β-lactams, this new class of BLIs holds particular significance [164]. The dual MoA for taniborbactam and xeruborbactam is shown in Figure 17. While the boron atom in the boronic acid is a strong electrophile that blocks the active serine in SBLs, also the active Zn²⁺ ions of MBLs could be bound by the same inhibitor. This remarkable achievement cannot be generalized for all bicyclic boronate BLIs; for example ledaborbactam lacks activity against MBLs [165, 166].

Fig. 17.

a Penicillin hydrolysis by serine β-lactamases (top) and a di-zinc B1 metallo-β-lactamase (bottom). B_A base for acylation step, B_D base for the deacylation step. Adapted from [152, 167]. b Dual mechanism of action of some bicyclic boronate β-lactamase inhibitors based on the crystal structures of taniborbactam (PDB: 6SP6 and 6SP7) and xeruborbactam (PDB: 6V1J and 6V1P) [168, 169]

Taniborbactam (VNRX-5133)

Taniborbactam is a bicyclic boronate BLI (Fig. 18) developed by Venatorx Pharmaceutical [170]. In 2020, GARDP supported the development of the drug and in early 2024, the Menarini group acquired the exclusive rights for commercialization of a cefepime/taniborbactam (FEP/TAN) combination in 96 countries [170]. According to in vitro data, taniborbactam was highly active against SBLs and most MBLs. Yet, weaker effects were found against certain MBLs, such as IMP-1 [169, 171]. In a Phase III study, the combination FEP/TAN showed non-inferiority in adults with cUTI while having a lower adverse effect frequency compared to meropenem (NCT03840148) [172]. Superiority was demonstrated in pre-specified secondary parameters, specifically microbiologic and clinical success during late follow-up, 28–35 days after therapy initiation. An additional Phase III study against HABP/VABP is planned (NCT06168734) [173]. A detailed review about FEP/TAN was published recently [174].

Fig. 18.

Structure of taniborbactam

Xeruborbactam (QPX7728)

Xeruborbactam (Fig. 19) was developed by Qpex Biopharma, which was acquired by Shionogi in 2023 [175]. Compared to taniborbactam, xeruborbactam showed a broader spectrum against both SBLs and MBLs in vitro [176–178], which is particularly remarkable given the very small size (molecular weight: 222 g/mol) of the compound. Additionally, at concentrations (MIC₉₀ = 16 to > 64 μg/mL) generally higher than those required for β-lactamase inhibition, an intrinsic antibacterial effect was observed [179]. Xeruborbactam and its orally available isobutyryloxymethyl ester prodrug QPX7831 underwent Phase I studies alone and in combination with QPX2014, a compound with an undisclosed structure (NCT04380207, NCT04578873) [180–182]. The steady-state PK of xeruborbactam (500 mg initial and 250 mg q8h or 1000 mg initial and 500 mg q8h) showed a half-life of 31 h and 24.9 h and a low volume of distribution at steady-state of 15.5 L and 17.8 L [181]. More recently, clinical trials have been initiated to evaluate PK and safety of the combination of QPX7831 (prodrug) and the orally applicable cephalosporin ceftibuten (QPX2015) in healthy volunteers (NCT06079775) [183].

Fig. 19.

Structure of xeruborbactam

KSP-1007

KSP-1007 (Fig. 20) was discovered by Sumitomo Pharma and is developed in collaboration with the Kitsato Institute in Japan [184]. In combination with meropenem, Sumitomo Pharma proposed an indication against cUTI, complicated intra-abdominal infections as well as HABP/VABP [185]. In vitro studies demonstrated that, when combined with meropenem, there was a significant antimicrobial activity against meropenem-susceptible and non-susceptible Enterobacterales. Lower in vitro activity was found against A. baumannii and P. aeruginosa. In a direct comparison with taniborbactam, the in vitro studies hint towards a better activity of KSP-1007 against MBL-producing strains, yet conclusive evidence about the superiority over taniborbactam and xeruborbactam is missing [186]. During single and multiple ascending IV dose Phase I studies, both with and without meropenem, a half-life of 2–4 hours was determined (NCT05226923). At the highest dose of 1500 mg KSP-1007 combined with 2 g of meropenem every 8 hours for 5 days, the most common adverse events were nausea, vomiting and transient increases of serum creatinine [187].

Fig. 20.

Structure of KSP-1007

Anti-virulence Therapeutics

Anti-virulence therapeutics represent a new approach for the prevention and treatment of bacterial infections. In contrast to a bactericidal (killing) or bacteriostatic (growth-limiting) antibiotic, these novel substances limit the disease-causing potential of bacteria or severity of an infection [188]. A variety of virulence mechanisms involved in the colonization, invasion and persistence in a susceptible host have been addressed by such virulence inhibitors, including bacterial adhesion to host cells, the pili- or flagella-mediated motility, biofilm formation, the assembly of secretion systems, communication through quorum sensing, immune evasion, as well as the secretion of toxins and destructive enzymes [188–190]. Although the bacterial load is not reduced directly, blocking virulence facilitates the elimination of the pathogen by the host's natural immune response. As the viability of the bacteria remains unaffected, it is believed that the reduced selection pressure will slow down the development of resistances [188]. A second major advantage is that, since virulence factors are mainly associated with pathogenic bacteria, an anti-virulence treatment preserves the integrity of the host microbiome [189]. This prevents the colonization of pathogenic bacteria in the gastrointestinal tract, thereby reducing the risk of infection and associated health complications, including antibiotic-associated diarrhea. Unlike antibiotics, anti-virulence treatment also allows for uncomplicated preventive use in high-risk patients (e.g., immunocompromised patients) [190]. Furthermore, it is anticipated that combination therapy [190] with low-dose antibiotics will result in a more effective treatment with fewer side effects. On the other hand, the clinical translation of anti-virulence approaches is challenging, because it poses special requirements on biomarker-driven patient selection and the establishment of pharmacodynamic markers for dose-finding. If virulence blockers are to be used as an adjunctive therapy on top of standard antibiotics, a clinical trial design that demonstrates superiority is required [190]. In spite of these challenges, monoclonal antibodies that neutralize toxins have been launched (against Bacillus anthracis, C. difficile) or are in clinical development (against S. aureus, [191, 192]). The first small molecules that entered clinical trials are highlighted below.

Fluorothiazinone (Ftortiazinon, CL-55)

Fluorothiazinone (Fig. 21), developed by the Gamaleya Research Institute of Epidemiology and Microbiology, is a thiadiazinone-based inhibitor of the type 3 secretion system (T3SS), one of the main pathogenicity factors of many Gram-negative bacteria [193, 194]. This multiprotein complex consists of more than 20 different proteins, spans the bacterial cell wall and has a structure reminiscent of a needle with a syringe mechanism [195]. Direct secretion of linearly unrolled effector proteins from the bacterial cell into the cytoplasm of eukaryotic cells facilitates bacterial colonization of these cells. In addition, this secretion system enables the pathogen to evade the host's immune response or even to kill host cells by altering signaling pathways. In numerous murine infection models against urogenital Chlamydia trachomatis serovar D [196], intraperitoneal (IP) injected [197] or orally administered Salmonella enterica serovar Typhimurium [198], septicemic A. baumannii [199], uropathogenic E. coli [200], as well as pulmonary K. pneumoniae [201] and P. aeruginosa clinical isolates [202, 203], it has been shown that fluorothyazinone, given as prevention or treatment, led to a decrease in the bacterial load. Subsequently, fewer pathomorphological changes in organs, decreased modulation of the local immune response, inhibition of biofilm formation as well as improved survival rates of mice, without affecting bacterial growth in vitro, were demonstrated. Neither a single IP dose of 5000 mg/kg in mice and rats, nor 50 mg/kg po for 14 days in rats and rabbits were toxic to the animals [204]. However, a 10-fold increase of the dose in the latter experiment led to reversible pathological findings in rat thymi. Furthermore, no carcinogenic or mutagenic effects (Ames test) or increased levels of chromosomal aberrations in bone marrow cells (comet assay) were observed in vitro [204]. This favorable safety profile is particularly important for a prophylactic setting.

Fig. 21.

a Structure of fluorothiazinone. b Schematic structure of a bacterial type 3 secretion system injecting effector proteins from the bacterial cytoplasm into the host cell. IM inner membrane, OM outer membrane. Adapted from [193]

Two Phase II studies assessed PK, safety, and efficacy. In NCT03638830, the treatment of hospitalized patients with cUTI caused by P. aeruginosa in combination with the fourth-generation cephalosporin cefepime was investigated. The results have not yet been published. In NCT06135350, the prophylaxis of ventilator-associated pneumonia caused by Gram-negative bacteria is being investigated with a monotherapy of up to 2400 mg/day fluorothiazinone over a period of up to 14 days. The study is expected to be completed by the end of 2024.

GSK3882347

Uropathogenic E. coli (UPEC) bacteria form reservoirs in the host gut, allowing them to repeatedly colonize the periurethral area or the vagina through fecal transmission [205]. Followed by an ascent in the urethra, they reach the urinary tract, where they cause UTIs. In this process, appendages, such as type 1 pili, facilitate adhesion to human uroplakins, proteins found in the cell membrane of the urothelium (epithelium of the urinary tract). FimH, a lectin (carbohydrate-binding protein) at the tip of the type 1 pilus of UPEC, binds to those mannosylated proteins, enabling colonization of the bladder and invasion of urothelial cells, where the pathogen replicates intracellularly [206]. GSK3882347 is an orally available [207] mannose-based (mannoside) [208] FimH antagonist [209], co-developed by Fimbrion Therapeutics and GSK with CARB-X support. It prevented E. coli from binding to the bladder wall, thus allowing the body to naturally eliminate the pathogen [207].

Mannosides like M4284 (Fig. 22) also reduce the intestinal colonization of different UPEC isolates in the feces, cecum, and colon of mice, without notably disrupting the gut microbial communities [205]. This dual MoA could significantly reduce the rate of (recurrent) UTIs. A single and multiple ascending dose Phase I study of GSK3882347 has been completed (NCT04488770). Although the exact structure of GSK3882347 has not been reported, detailed studies on O- [205, 206, 210–214] and C-mannosides [215, 216] have been published.

Fig. 22.

a Structure of M4284. b Schematic structure of the type 1 pilus of uropathogenic E. coli, displaying FimH at the tip. Adapted from [217]. c Cellular mechanism of action of FimH antagonists. Adapted from [218]

Conclusion

A previous pipeline analysis conducted 10–15 years ago detected and warned about a steady decline of antibiotic approvals over time [219, 220]. However, compared to an all-time low with 7 launches in the years 2000–2009, the following decade again saw an increase with 15 antibiotic drug launches [221]. And yet, the AMR problem has not been alleviated. First, the availability of novel antibiotics for patients has remained limited because of economic constraints that hinder a launch in low-, middle-, and even in a large portion of high-income countries [222]. Second, the licensed drugs were dominantly derivatives of established chemical classes, that hardly met the four innovation criteria established by the WHO – namely, the introduction of a new chemical class, a novel target, a new mode of action, and a lack of cross-resistance to existing antibiotics [8]. The current development pipeline is also dominated by derivatives of established chemical classes, which carry smaller development risks, but rarely overcome the existing resistance mechanisms completely. Despite these concerns, research and development activities strengthened by large, global consortia and public-private partnerships start yielding in innovative and unprecedented solutions against AMR. This includes, on the one hand, a broad range of new drug formats such as engineered phages [223], LBPs, monoclonal antibodies, RNA-targeting drugs, or new vaccination approaches [8]. On the other hand, small molecule antibiotics addressing new targets with new chemical structures have entered development. These were the main focus of this review.

Targeted therapies against specific bacterial species, like zosurabalpin for Acinetobacter spp., murepavadin for Pseudomonas spp., and afabicin for Staphylococcus ssp. mitigate unwanted selection pressure on other pathogenic but non-disease–causing bacteria and thus the development of resistance in the normal flora. The former two examples exemplify first successes in targeting outer membrane biosynthesis of Gram-negative bacteria. However, the effective use of such narrow spectrum agents necessitates the prior identification of the causative pathogen and the exclusion of a polybacterial, mixed infection. Therefore, it is essential to assure the availability of appropriate diagnostic tools, which often require a co-development alongside the selective therapeutic.

Antibody–antibiotic conjugates represent an innovative new approach, enabling the selective delivery of otherwise too toxic substances or compounds with poor pharmacokinetics to the site of infection [224]. Furthermore, as exemplified by DSTA4637S, targeted eradication of intracellular pathogens is achievable through an appropriate linker chemistry [54]. Given the successful use of antibody-drug conjugates in cancer treatment, this format allows a re-evaluation of previously unsuccessful small molecule antibiotic projects by considering their development as conjugates [225–227]. On the other hand, the costs of development but also production of AACs exceed those of standard antibiotics significantly.

The low propensity towards resistance development, coupled with the broad-spectrum activity against resistant pathogens, are attractive features of peptidic membrane disruptors that mimic a part of the innate immune responses against pathogens, even though their in vitro activity is often lower (MIC values between 1–4 µM) compared to conventional antibiotics. But their biggest challenge is to define a sufficient therapeutic window by limiting eukaryotic cell toxicity. Some development programs therefore focus on a non-systemic application; in addition, the switch from peptides to peptidomimetic structures (e.g., as in voxvoganan or brilacidin) help to fine-tune stability and toxicity properties.

The high number of β-lactam antibiotics in combination with a BLI in the development pipeline is striking. Given their broad spectrum of activity, bactericidal effect, low toxicity, good tissue penetration, inexpensive production, and extensive clinical experience spanning over 50 years, it is anticipated that these agents will continue to play a critical role in therapeutic practice globally [228]. We would like to highlight two developments: the optimization of BLIs targeting all four Ambler classes was enabled by chemical innovations, in particular through the switch to boronate as a chemical motif that binds to both serine nucleophiles as well as ionic zinc lewis acids. Second, the diazabicyclooctanes ETX0462 [229] and EBL-1463, [49] as well as other compounds [230], demonstrate that it is possible to evolve a conventional BLI to a dual-action inhibitor targeting additionally penicillin-binding proteins (PBPs). Inhibiting PBPs with non–β-lactam pharmacophores that are not affected by the widespread β-lactamases may open up a sustained exploration of this mechanism.

Anti-virulence therapeutics offer a promising new strategy to limit the damage caused by virulence factors on host cells that is orthogonal to direct-acting antibiotics. These therapeutics may render bacterial eradication by the host immune system more effective, when used synergistically with standard-of-care antibiotics, which needs to be demonstrated clinically through superiority trials. Alternatively, their prophylactic use is conceivable, in particular when antibiotics are not indicated, requiring careful patient stratification strategies. While the first successes have been achieved with toxin-neutralizing monoclonal antibodies, the fact that small molecules have also entered clinical development indicates that virulence blockers indeed represent a viable, complementary approach to fight AMR [188].

Counteracting AMR with novel antibiotics is possible and ongoing. Some resistance mechanisms could be alleviated through derivatization of established compound classes [231]. But novel chemical scaffolds – as illustrated in this review – are of particular interest for addressing AMR, due to their new modes of action and/or distinct binding sites compared to clinically used drug classes. The research and preclinical development pipeline demonstrates that antibiotic research does not suffer from a lack of ideas or innovative concepts. However, the overall scale in terms of number of projects is regarded as too small. For comparison, > 2000 oncology clinical trials started in 2023 with novel modalities [232]. With a Phase I to approval success rate for antibiotics of about 16%, attrition is high in particular for new, initially non-validated targets and new chemical scaffolds with unknown human side effects [233]. Because the clinical translation of antibiotics is both challenging and costly, in particular the unclear economic incentives are seen as major hurdles on the way to medicines against drug-resistant infections that are broadly available for patients. This calls for further action, in science and beyond.

Declarations

Conflict of interest

Alexandra Jana Kohnhäuser is employee of IPG DXTRA (Germany) GmbH, working for dna communications, but the work on this review was neither work-related, nor did she write about content connected to her work-related clients. Dominik Heimann, Daniel Kohnhäuser, Alexandra Jana Kohnhäuser and Mark Brönstrup have declared no conflicts of interest that may be relevant to the contents of this review.

Ethics approval

Not applicable.

Consent for publication

Not applicable.

Consent to participate

Not applicable.

Availability of data and materials

Not applicable.

Code availability

Not applicable.

Funding

Open Access funding enabled and organized by Projekt DEAL. Deutsches Zentrum für Infektionsforschung (TTU09.712).

Authors’ contribution

All authors: Design and concept of the entire manuscript. DH: Draft of the introduction, conclusion and chapters about DSTA4637S, zosurabalpin, murepavadin, voxvoganan, PL-18, PLG0206, OMN6 and anti-virulence therapeutics; creation of all figures and the global pipeline table. DK: Draft of chapters about DNA gyrase and topoisomerase IV inhibitors as well as β-lactamase inhibitors; creation of the global pipeline table. AJK: Draft of chapters about afabicin, TXA709, RG6436 and brilacidin. MB: Writing—review and editing, supervision.